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Commit 760f7db5 authored by Jerome Mariette's avatar Jerome Mariette
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delete french handling for analysis

parent 6b0506dc
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ui/nG6/pi1/analyzes/AdaptorcleanerAnalyse.tpl
View file @ 760f7db5
......@@ -17,18 +17,18 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{extends file='BasicAnalyse.tpl'}
{block name=params_title} {$llang.AdaptorcleanerAnalyse_params_title} {/block}
{block name=params_title} Cleaning options {/block}
{block name=params_content}
{assign var="params" value=" "|explode:$analyse.params}
<ul>
{assign var="score_index" value=$params|@array_keys:"--score"}
<li class="parameter">{$llang.AdaptorcleanerAnalyse_minscore|replace:"###MIN_SCORE###":$params[$score_index[0]+1]}</li>
<li class="parameter">Min score used by crossmatch : {$params[$score_index[0]+1]}% of adaptor length.</li>
{assign var="match_index" value=$params|@array_keys:"--match"}
<li> class="parameter"{$llang.AdaptorcleanerAnalyse_minmatch|replace:"###MIN_MATCH###":$params[$match_index[0]+1]}</li>
<li class="parameter">Min match used by crossmatch : {$params[$match_index[0]+1]}% of adaptor length.</li>
{assign var="len_index" value=$params|@array_keys:"--minlen"}
<li class="parameter">{$llang.AdaptorcleanerAnalyse_minlen|replace:"###MIN_LEN###":$params[$len_index[0]+1]}</li>
<li class="parameter">Clean reads with a smaller lenght than $params[$len_index[0]+1]} bp.</li>
{if $analyse_results["all"]["default"]["adaptor_file"] == ""}
<li class="parameter">{$llang.AdaptorcleanerAnalyse_adaptor} <br />
<li class="parameter">Adaptor used: <br />
{$isseq=false}
{foreach $params as $param}
{if $isseq}
......@@ -43,7 +43,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</li>
{else}
{assign var="index" value=$params|@array_keys:"--adaptor"}
<li class="parameter">{$llang.AdaptorcleanerAnalyse_adaptor}
<li class="parameter">Adaptor used:
<br />
<div class="file-display">{$analyse_results["all"]["default"]["adaptor_file"]}</div>
</li>
......@@ -53,18 +53,18 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{block name=results}
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
<h3> {$llang.AdaptorcleanerAnalyse_result_title} </h3>
<h3> Cleaning results </h3>
<div class="underline"> </div>
<table class="tx-nG6-pi1-listrow">
<tr>
{if $analyse_results|@count > 1 }
<th>{$llang.Analyse_sample} ({$analyse_results|@count})</th>
<th>Samples ({$analyse_results|@count})</th>
{/if}
<th>{$llang.AdaptorcleanerAnalyse_before_cleaning}</th>
<th>{$llang.AdaptorcleanerAnalyse_after_cleaning}</th>
<th>{$llang.AdaptorcleanerAnalyse_adaptor_cleaning}</th>
<th>{$llang.AdaptorcleanerAnalyse_too_short}</th>
<th>{$llang.AdaptorcleanerAnalyse_deleted}</th>
<th>Before cleaning</th>
<th>After cleaning</th>
<th>Only adaptor found</th>
<th>Too short</th>
<th>% deleted</th>
</tr>
{foreach from=$analyse_results_sorted key=sample item=sample_results}
{if $sample != "all"}
......@@ -82,7 +82,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/foreach}
</table>
<h3> {$llang.AdaptorcleanerAnalyse_adaptor_title} </h3>
<h3> Per adaptor(s) information </h3>
<div class="underline"> </div>
{* First find out all adaptors used *}
{assign var="adaptors" value=array()}
......@@ -96,7 +96,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<table class="tx-nG6-pi1-listrow">
<tr>
{if $analyse_results|@count > 1 }
<th>{$llang.Analyse_sample} ({$analyse_results|@count})</th>
<th>Samples ({$analyse_results|@count})</th>
{/if}
{foreach $adaptors as $adaptor}
<th> {$adaptor} </th>
......
ui/nG6/pi1/analyzes/BWAContaminationSearchAnalyse.tpl
View file @ 760f7db5
......@@ -20,7 +20,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{block name=params}{/block}
{block name=results}
<h3> {$llang.BWAContaminationSearchAnalyse_result_title} </h3>
<h3> Search results </h3>
<div class="underline"> </div>
{* First find out all databse used *}
{assign var="database" value=array()}
......@@ -36,14 +36,14 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<table class="tx-nG6-pi1-listrow">
<tr>
{if $analyse_results|@count > 1 }
<th>{$llang.Analyse_sample} ({$analyse_results|@count})</th>
<th>Samples ({$analyse_results|@count})</th>
{/if}
{foreach $database as $group}
{if $group != "total"}
<th> {$group} </th>
{/if}
{/foreach}
<th> {$llang.Analyse_total} </th>
<th> Total </th>
</tr>
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
{foreach from=$analyse_results_sorted key=sample item=sample_results}
......
ui/nG6/pi1/analyzes/BasicAnalyse.tpl
View file @ 760f7db5
......@@ -18,30 +18,20 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div id="img_dialog" title=""></div>
<div id="table_dialog" title=""></div>
<input type="hidden" id="analyse_name" value="{$analyse.name}"/>
<input type="hidden" id="DataTables_length_menu" value="{$llang.DataTables_length_menu}" />
<input type="hidden" id="DataTables_zero_records" value="{$llang.DataTables_zero_records}" />
<input type="hidden" id="DataTables_info" value="{$llang.DataTables_info}" />
<input type="hidden" id="DataTables_info_empty" value="{$llang.DataTables_info_empty}" />
<input type="hidden" id="DataTables_info_filtered" value="{$llang.DataTables_info_filtered}" />
<input type="hidden" id="DataTables_search" value="{$llang.DataTables_search}" />
<input type="hidden" id="DataTables_pagination_first" value="{$llang.DataTables_pagination_first}" />
<input type="hidden" id="DataTables_pagination_last" value="{$llang.DataTables_pagination_last}" />
<input type="hidden" id="DataTables_pagination_next" value="{$llang.DataTables_pagination_next}" />
<input type="hidden" id="DataTables_pagination_previous" value="{$llang.DataTables_pagination_previous}" />
{block name=description}
<div class="analysis">
<h2>{$llang.analyse} {$analyse.name} :</h2>
<h2>Analysis {$analyse.name} :</h2>
<p><strong>{$analyse.description}</strong> <br />
<br />
{($llang.analyse_desc|replace:"###ANALYSE_SIZE###":"<strong>###ANALYSE_SIZE###</strong>")|replace:"###ANALYSE_SIZE###":$analyse_size}
All data related to this analysis use <strong> {$analyse_size} </strong> on the hard drive.
</p>
</div>
{/block}
{block name=params}
{if $analyse.params != ""}
<h3> {block name=params_title} {$llang.Analyse_params} {/block} </h3>
<h3> {block name=params_title} Parameters used {/block} </h3>
<div class="underline"> </div>
{block name=params_content}
<ul>
......@@ -54,7 +44,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{block name=results}{/block}
{block name=download}
<h3> {$llang.Analyse_archives_title} </h3>
<h3> Result file(s) </h3>
<div class="underline"> </div>
<p><ul>
{$dir=$data_folder|cat:$analyse.directory}
......@@ -68,6 +58,6 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/foreach}
</ul></p>
{if $nb_files == 0}
<p>{$llang.not_synchro}</p>
<p>Results folder not synchronized yet</p>
{/if}
{/block}
\ No newline at end of file
ui/nG6/pi1/analyzes/BlastContaminationSearchAnalyse.tpl
View file @ 760f7db5
......@@ -17,7 +17,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{extends file='BasicAnalyse.tpl'}
{block name=params_title} {$llang.BlastContaminationSearchAnalyse_params_title} {/block}
{block name=params_title} Search parameters {/block}
{block name=params_content}
{assign var="params" value=";"|explode:$analyse.params}
<ul>
......@@ -27,7 +27,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/block}
{block name=results}
<h3> {$llang.BlastContaminationSearchAnalyse_result_title} </h3>
<h3> Search results </h3>
<div class="underline"> </div>
{* First find out all databse used *}
{assign var="database" value=array()}
......@@ -43,14 +43,14 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<table class="tx-nG6-pi1-listrow">
<tr>
{if $analyse_results|@count > 1 }
<th>{$llang.Analyse_sample} ({$analyse_results|@count})</th>
<th>Samples ({$analyse_results|@count})</th>
{/if}
{foreach $database as $group}
{if $group != "total"}
<th> {$group} </th>
{/if}
{/foreach}
<th> {$llang.Analyse_total} </th>
<th> Total </th>
</tr>
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
{foreach from=$analyse_results_sorted key=sample item=sample_results}
......
ui/nG6/pi1/analyzes/CutAdaptAnalyse.tpl
View file @ 760f7db5
......@@ -17,7 +17,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{extends file='BasicAnalyse.tpl'}
{block name=params_title} {$llang.CutAdaptAnalyse_params_title} {/block}
{block name=params_title} Cleaning options {/block}
{block name=params_content}
{assign var="params" value=" "|explode:$analyse.params}
{assign var="error_index" value=$params|@array_keys:"-e"}
......@@ -25,25 +25,25 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="max_index" value=$params|@array_keys:"-M"}
{assign var="adaptor_index" value=$params|@array_keys:"-a"}
<ul>
<li class="parameter">{$llang.CutAdaptAnalyse_error_rate|replace:"###ERROR_RATE###":$params[$error_index[0]+1]}</li>
<li class="parameter">{($llang.CutAdaptAnalyse_len|replace:"###MIN_LEN###":$params[$min_index[0]+1])|replace:"###MAX_LEN###":$params[$max_index[0]+1]}</li>
<li class="parameter">{$llang.CutAdaptAnalyse_adaptors|replace:"###ADAPTOR_USED###":$params[$adaptor_index[0]+1]}</li>
<li class="parameter">Maximum allowed error rate of {$params[$error_index[0]+1]}.</li>
<li class="parameter">Discard trimmed reads with a length not in between [{$params[$min_index[0]+1]}pb; {$params[$max_index[0]+1]}pb].</li>
<li class="parameter">Sequence of an adapter that was ligated ###ADAPTOR_USED###. {$params[$adaptor_index[0]+1]}</li>
</ul>
{/block}
{block name=results}
<h3> {$llang.CutAdaptAnalyse_result_title} </h3>
<h3> Cleaning results </h3>
<div class="underline"> </div>
<table class="tx-nG6-pi1-listrow">
<tr>
{if $analyse_results|@count > 1 }
<th>{$llang.Analyse_sample} ({$analyse_results|@count})</th>
<th>Samples ({$analyse_results|@count})</th>
{/if}
<th>{$llang.CutAdaptAnalyse_before_cleaning}</th>
<th>{$llang.CutAdaptAnalyse_after_cleaning}</th>
<th>{$llang.CutAdaptAnalyse_too_short}</th>
<th>{$llang.CutAdaptAnalyse_too_long}</th>
<th>{$llang.CutAdaptAnalyse_deleted}</th>
<th>Before cleaning</th>
<th>After cleaning</th>
<th>Too short</th>
<th>Too long</th>
<th>% deleted</th>
</tr>
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
{foreach from=$analyse_results_sorted key=sample item=sample_results}
......@@ -58,7 +58,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<td>{$sample_results["default"].total_too_long|number_format:0:' ':' '}</td>
<td>{(100.00-((($sample_results["default"].processed_reads-$sample_results["default"].total_too_short-$sample_results["default"].total_too_long)*100)/$sample_results["default"].processed_reads))|number_format:2:'.':' '}</td>
{if $analyse_results|@count > 1 }
<td><a class="imglink" href="{$sample_results["default"].len}"> {$llang.CutAdaptAnalyse_len_link} </a></td>
<td><a class="imglink" href="{$sample_results["default"].len}"> len </a></td>
{/if}
</tr>
{/foreach}
......
ui/nG6/pi1/analyzes/FastqIlluminaFilterAnalyse.tpl
View file @ 760f7db5
......@@ -17,31 +17,31 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{extends file='BasicAnalyse.tpl'}
{block name=params_title} {$llang.FastqIlluminaFilterAnalyse_params_title} {/block}
{block name=params_title} Filtering options {/block}
{block name=params_content}
{assign var="params" value=" "|explode:$analyse.params}
{assign var="filter_index" value=$params|@array_keys:"--keep"}
<ul>
{if $params[$filter_index[0]+1] == "N"}
<li class="parameter">{$llang.FastqIlluminaFilterAnalyse_Nparams}</li>
<li class="parameter">Keep reads that were not filtered (Reads that have 'N' in the read-ID line).</li>
{else}
<li class="parameter">{$llang.FastqIlluminaFilterAnalyse_Yparams}</li>
<li class="parameter">Keep reads that were filtered (Reads that have 'Y' in the read-ID line).</li>
{/if}
</ul>
{/block}
{block name=results}
<h3> {$llang.FastqIlluminaFilterAnalyse_result_title} </h3>
<h3> Filtering results </h3>
<div class="underline"> </div>
<table class="tx-nG6-pi1-listrow">
<tr>
{if $analyse_results|@count > 1 }
<th>{$llang.Analyse_sample} ({$analyse_results|@count})</th>
<th>Samples ({$analyse_results|@count})</th>
{/if}
<th>{$llang.FastqIlluminaFilterAnalyse_before_cleaning}</th>
<th>{$llang.FastqIlluminaFilterAnalyse_after_cleaning}</th>
<th>{$llang.FastqIlluminaFilterAnalyse_filtered}</th>
<th>{$llang.FastqIlluminaFilterAnalyse_percent_filtered}</th>
<th>Before filtering</th>
<th>After filtering</th>
<th>Filtered</th>
<th>% deleted</th>
</tr>
{assign var="nb_reads_begining" value=0}
{assign var="nb_reads_end" value=0}
......@@ -63,14 +63,14 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{/foreach}
{if $analyse_results|@count > 1 }
<tr class="tx-nG6-pi1-listrowlast">
<td>{$llang.Analyse_total}</td>
<td>Total</td>
<td>{$nb_reads_begining|number_format:0:' ':' '}</td>
<td>{$nb_reads_end|number_format:0:' ':' '}</td>
<td>{$filtered|number_format:0:' ':' '}</td>
<td>{(100.00-((($nb_reads_end)*100)/$nb_reads_begining))|number_format:2:'.':' '}</td>
</tr>
<tr class="tx-nG6-pi1-listrowlast">
<td>{$llang.Analyse_mean}</td>
<td>Mean</td>
<td>{($nb_reads_begining/($analyse_results|@count))|number_format:0:' ':' '}</td>
<td>{($nb_reads_end/($analyse_results|@count))|number_format:0:' ':' '}</td>
<td>{($filtered/($analyse_results|@count))|number_format:0:' ':' '}</td>
......
ui/nG6/pi1/analyzes/FastqcAnalyse.tpl
View file @ 760f7db5
......@@ -20,29 +20,29 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{block name=params}{/block}
{block name=results}
<h3> {$llang.FastqcAnalyse_stat_title} </h3>
<h3> Reads and quality statistics </h3>
<div class="underline"> </div>
<table class="analyze_table" id="fastqc_resume">
<thead>
<tr>
{if $analyse_results|@count > 1 }
<th rowspan="2">{$llang.Analyse_sample} ({$analyse_results|@count})</th>
<th rowspan="2">Samples ({$analyse_results|@count})</th>
{/if}
<th colspan="4" >{$llang.FastqcAnalyse_per_position}</th>
<th colspan="7" >{$llang.FastqcAnalyse_per_sequences}</th>
<th colspan="4" >Per position statistics</th>
<th colspan="7" >Per sequence statistics</th>
</tr>
<tr>
<th>{$llang.FastqcAnalyse_quality}</th>
<th>{$llang.FastqcAnalyse_gc}</th>
<th>{$llang.FastqcAnalyse_ns}</th>
<th>{$llang.FastqcAnalyse_content}</th>
<th>{$llang.FastqcAnalyse_nb_seq}</th>
<th>{$llang.FastqcAnalyse_quality}</th>
<th>{$llang.FastqcAnalyse_gc}</th>
<th>{$llang.FastqcAnalyse_length}</th>
<th>{$llang.FastqcAnalyse_duplication}</th>
<th>{$llang.FastqcAnalyse_kmers}</th>
<th>{$llang.FastqcAnalyse_overrepresented}</th>
<th>Quality</th>
<th>GC%</th>
<th>N content</th>
<th>Per base content</th>
<th>Number of sequences</th>
<th>Quality</th>
<th>GC%</th>
<th>Length distribution</th>
<th>Duplication level</th>
<th>Kmer profiles</th>
<th>Overrepresented sequences</th>
</tr>
</thead>
......@@ -70,7 +70,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<tfoot>
<tr>
<th align="left" colspan="{if $analyse_results|@count > 1 }13{else}11{/if}">
<button id="img_extract" type="button" class="btn pill-l"><span><span>{$llang.Analyse_img_export_btn}</span></span></button>
<button id="img_extract" type="button" class="btn pill-l"><span><span>view images</span></span></button>
</th>
</tr>
</tfoot>
......@@ -78,27 +78,57 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>{$llang.FastqcAnalyse_help_position_title}</p>
<p>Help for per position statistics :</p>
<span class="meta">
<ul>
<li><strong>{$llang.FastqcAnalyse_quality}</strong> : {$llang.FastqcAnalyse_help_quality_position}</li>
<li><strong>{$llang.FastqcAnalyse_gc}</strong> : {$llang.FastqcAnalyse_help_gc_position} </li>
<li><strong>{$llang.FastqcAnalyse_ns}</strong> : {$llang.FastqcAnalyse_help_ns_position} </li>
<li><strong>{$llang.FastqcAnalyse_content}</strong> : {$llang.FastqcAnalyse_help_content_position} </li>
<li><strong>Quality</strong> :
WARN = A warning will be issued if the lower quartile for any base is less than 10, or if the median for any base is less than 25.
FAIL = This module will raise a failure if the lower quartile for any base is less than 5 or if the median for any base is less than 20.
</li>
<li><strong>GC%</strong> :
WARN = This module issues a warning it the GC content of any base strays more than 5% from the mean GC content.
FAIL = This module will fail if the GC content of any base strays more than 10% from the mean GC content.
</li>
<li><strong>N content</strong> :
This module raises a warning if any position shows an N content of >5%.
FAIL = This module will raise an error if any position shows an N content of >20%.
</li>
<li><strong>Per base content</strong> :
WARN = This module issues a warning if the difference between A and T, or G and C is greater than 10% in any position.
FAIL = This module will fail if the difference between A and T, or G and C is greater than 20% in any position.
</li>
</ul>
</span>
</div>
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>{$llang.FastqcAnalyse_help_sequence_title}</p>
<p>Help for per sequence statistics :</p>
<span class="meta">
<ul>
<li><strong>{$llang.FastqcAnalyse_quality}</strong> : {$llang.FastqcAnalyse_help_quality_sequence}</li>
<li><strong>{$llang.FastqcAnalyse_gc}</strong> : {$llang.FastqcAnalyse_help_gc_sequence}</li>
<li><strong>{$llang.FastqcAnalyse_length}</strong> : {$llang.FastqcAnalyse_help_length_sequence}</li>
<li><strong>{$llang.FastqcAnalyse_duplication}</strong> : {$llang.FastqcAnalyse_help_duplication_sequence}</li>
<li><strong>{$llang.FastqcAnalyse_kmers}</strong> : {$llang.FastqcAnalyse_help_kmers_sequence}</li>
<li><strong>{$llang.FastqcAnalyse_overrepresented}</strong> : {$llang.FastqcAnalyse_help_overrepresented_sequence}</li>
<li><strong>Quality</strong> :
WARN = A warning is raised if the most frequently observed mean quality is below 27 - this equates to a 0.2% error rate.
FAIL = An error is raised if the most frequently observed mean quality is below 20 - this equates to a 1% error rate.
</li>
<li><strong>GC%</strong> :
WARN = A warning is raised if the sum of the deviations from the normal distribution represents more than 15% of the reads.
FAIL = This module will indicate a failure if the sum of the deviations from the normal distribution represents more than 30% of the reads.
</li>
<li><strong>Length distribution</strong> :
WARN = This module will raise a warning if all sequences are not the same length.
FAIL = This module will raise an error if any of the sequences have zero length.
</li>
<li><strong>Duplication level</strong> :
WARN = This module will issue a warning if non-unique sequences make up more than 20% of the total.
FAIL = This module will issue a error if non-unique sequences make up more than 50% of the total.
</li>
<li><strong>Kmer profiles</strong> :
WARN = This module will issue a warning if any k-mer is enriched more than 3 fold overall, or more than 5 fold at any individual position.
FAIL = This module will issue a error if any k-mer is enriched more than 10 fold at any individual base position.
</li>
<li><strong>Overrepresented sequences</strong> :
WARN = This module will issue a warning if any sequence is found to represent more than 0.1% of the total.
FAIL = This module will issue an error if any sequence is found to represent more than 1% of the total.
</li>
</ul>
</span>
</div>
......
ui/nG6/pi1/analyzes/FlashAnalyse.js
View file @ 760f7db5
......@@ -36,10 +36,10 @@ $(function () {
var max_xvalues = 30;
if ($(":checked[id^=chk_sample_]").size() == 0) {
$("#user_information_dialog").dialog("option", "title", $("#information_error_title").val());
$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>" + $("#information_dialog_zero_check").val() + "</div>").dialog("open");
$("#user_information_dialog").dialog("option", "title", "Error");
$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>No raw selected, please select a raw to access this fonctionality.</div>").dialog("open");
var buttons = {};
buttons[$("#ok_btn_label").val()] = function(){ $(this).dialog("close"); }
buttons["Ok"] = function(){ $(this).dialog("close"); }
$("#user_information_dialog").dialog('option', 'buttons', buttons);
} else {
......@@ -99,13 +99,13 @@ $(function () {
defaultSeriesType: 'line'
},
title: {
text: $("#length_distribution_title").val(),
text: "Distribution of sequence lengths over all sequences.",
x: -20 //center
},
xAxis: {
categories: x_table_labels,
title: {
text: $("#length_distribution_xtitle").val()
text: "Sequence length (bp)"
},
labels: {
rotation: -45,
......@@ -114,7 +114,7 @@ $(function () {
},
yAxis: {
title: {
text: $("#length_distribution_ytitle").val()
text: "Number of sequences"
},
min: 0,
plotLines: [{
......
ui/nG6/pi1/analyzes/FlashAnalyse.tpl
View file @ 760f7db5
......@@ -17,7 +17,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{extends file='BasicAnalyse.tpl'}
{block name=params_title} {$llang.Analyse_params} {/block}
{block name=params_title} Parameters used {/block}
{block name=params_content}
{assign var="params" value=" "|explode:$analyse.params}
{foreach from=$analyse_results key=sample item=sample_results}
......@@ -26,32 +26,26 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<ul>
{if in_array("-m", $params)}
{assign var="mindex" value=$params|@array_keys:"-m"}
<li class="parameter">{$llang.FlashAnalyse_min_overlap|replace:"###MINOVERLAP###":$params[$mindex[0]+1]}</li>
<li class="parameter">An overlap of {$params[$mindex[0]+1]}bp is required between two reads to provide a confident overlap.</li>
{/if}
{if in_array("-M", $params)}
{assign var="m2index" value=$params|@array_keys:"-M"}
<li class="parameter">{$llang.FlashAnalyse_max_overlap|replace:"###MAXOVERLAP###":$params[$m2index[0]+1]}</li>
<li class="parameter">An overlap of {$params[$m2index[0]+1]}bp is the maximum overlap length expected in approximately 90% of read pairs. </li>
{/if}
{if in_array("-x", $params)}
{assign var="xindex" value=$params|@array_keys:"-x"}
<li class="parameter">{$llang.FlashAnalyse_mismatch_ratio|replace:"###MISMATCHRATIO###":$params[$xindex[0]+1]}</li>
<li class="parameter">{$params[$xindex[0]+1]} as allowed ratio of the number of mismatches and the overlap length.</li>
{/if}
{if in_array("-p", $params)}
{assign var="pindex" value=$params|@array_keys:"-p"}
<li class="parameter">{$llang.FlashAnalyse_phred_offset|replace:"###PHREDOFFSET###":$params[$pindex[0]+1]}</li>
<li class="parameter">{$params[$pindex[0]+1]} used as phred offest.</li>
{/if}
</ul>
{/block}
{block name=results}
<input type="hidden" id="ok_btn_label" value="{$llang.ok_btn_label}"/>
<input type="hidden" id="information_dialog_zero_check" value="{$llang.information_dialog_zero_check}"/>
<input type="hidden" id="information_error_title" value="{$llang.information_error_title}"/>
<input type="hidden" id="length_distribution_title" value="{$llang.length_distribution_title}"/>
<input type="hidden" id="analyse_name" value="{$analyse.name}"/>
<input type="hidden" id="length_distribution_xtitle" value="{$llang.length_distribution_xtitle}"/>
<input type="hidden" id="length_distribution_ytitle" value="{$llang.length_distribution_ytitle}"/>
<h3> {$llang.FlashAnalyse_result_title} </h3>
<h3> Assembly results: </h3>
<div class="underline"> </div>
<br />
<table class="display analysis-result-table">
......@@ -59,10 +53,10 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<tr>
<th><center><input type="checkbox" id="chk_all_sample"></center></th>
{if $analyse_results|@count > 1 }
<th>{$llang.Analyse_sample} ({$analyse_results|@count})</th>
<th>Samples ({$analyse_results|@count})</th>
{/if}
<th>{$llang.FlashAnalyse_nb_extended}</th>
<th>{$llang.FlashAnalyse_nb_notcombined1}</th>
<th>Extended fragments (R1 associated to R2)</th>
<th>Not combined fragments (R1+R2)</th>
</tr>
</thead>
<tbody>
......@@ -93,20 +87,20 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<tfoot>
<tr>
<td class="info"></td>
<td class="info">{$llang.Analyse_total}</td>
<td class="info">Total</td>
<td class="info">{$totale|number_format:0:' ':' '}</td>
<td class="info">{$total1|number_format:0:' ':' '}</td>
</tr>
<tr>
<td class="info"></td>
<td class="info">{$llang.Analyse_mean}</td>
<td class="info">Mean</td>
<td class="info">{($totale/($analyse_results|@count))|number_format:0:' ':' '}</td>
<td class="info">{($total1/($analyse_results|@count))|number_format:0:' ':' '}</td>
</tr>
<tr>
<th align="left" colspan="4">
{$llang.toolbar_title}
<button type="button" class="btn length-view-btn"><span><span>{$llang.FlashAnalyse_length_btn}</span></span></button>
With selection :
<button type="button" class="btn length-view-btn"><span><span>Length distribution</span></span></button>
</th>
</tr>
</tfoot>
......
ui/nG6/pi1/analyzes/GAASAnalyse.js
View file @ 760f7db5
......@@ -30,10 +30,10 @@ $(function () {
$(".krona-view-btn").click(function() {
if ($(":checked[id^=chk_sample_]").size() == 0) {
$("#user_information_dialog").dialog("option", "title", $("#information_error_title").val());
$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>" + $("#information_dialog_zero_check").val() + "</div>").dialog("open");
$("#user_information_dialog").dialog("option", "title", "Error");
$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>No raw selected, please select a raw to access this fonctionality.</div>").dialog("open");
var buttons = {};
buttons[$("#ok_btn_label").val()] = function(){ $(this).dialog("close"); }
buttons["Ok"] = function(){ $(this).dialog("close"); }
$("#user_information_dialog").dialog('option', 'buttons', buttons);
} else if ($(":checked[id^=chk_sample_]").size() == 1) {
$("#img_dialog").dialog("option", "title", "nG6 - " + $("#analyse_name").val());
......@@ -43,7 +43,7 @@ $(function () {
$("#img_dialog").html('<iframe width="820px" frameborder="0" height="550px" src="' + webPAth + '"></iframe>').dialog("open");
} else {
$("#user_information_dialog").dialog("option", "title", $("#information_error_title").val());
$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>" + $("#information_dialog_multiple_check").val() + "</div>").dialog("open");
$("#user_information_dialog").html("<div class='tx-nG6-pi1-error'>Only one row should be selected to access this fonctionality.</div>").dialog("open");
var buttons = {};
buttons[$("#ok_btn_label").val()] = function(){ $(this).dialog("close"); }