Commit 75c49600 authored by Penom Nom's avatar Penom Nom
Browse files

No commit message

No commit message
parent a522af6f
{*
Copyright (C) 2009 INRA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*}
{extends file='AnalysisTemplate.tpl'}
{block name=params_title} Alignment options {/block}
{block name=params_content}
{assign var="params" value=";"|explode:$analyse.params}
<ul>
{foreach from=$params item=param}
<li class="parameter">{$param}</li>
{/foreach}
</ul>
{/block}
{block name=results_title} Alignment results {/block}
{block name=results}
<table class="table table-striped table-bordered dataTable analysis-result-table">
<thead>
<tr>
{if $analyse_results|@count > 1 }
<th>Samples ({$analyse_results|@count})</th>
{/if}
<th>Aligned reads</th>
<th>After cleaning the alignment</th>
<th>Aligned out of the area</th>
<th>% deleted</th>
</tr>
</thead>
<tbody>
{assign var="nb_reads_begining" value=0}
{assign var="nb_reads_end" value=0}
{assign var="uncorrect" value=0}
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
{foreach from=$analyse_results_sorted key=sample item=sample_results}
<tr>
{if $analyse_results|@count > 1 }
<td>{$sample|get_description:$descriptions}</td>
{/if}
{$nb_reads_begining=$nb_reads_begining+$sample_results["default"].nb_aligned_reads}
{$nb_reads_end=$nb_reads_end+$sample_results["default"].nb_after_screen}
{$uncorrect=$uncorrect+($sample_results["default"].nb_aligned_reads-$sample_results["default"].nb_after_screen)}
<td>{$sample_results["default"].nb_aligned_reads|number_format:0:' ':' '}</td>
<td>{$sample_results["default"].nb_after_screen|number_format:0:' ':' '}</td>
<td>{($sample_results["default"].nb_aligned_reads-$sample_results["default"].nb_after_screen)|number_format:0:' ':' '}</td>
<td>{(100.00-((($sample_results["default"].nb_after_screen)*100)/$sample_results["default"].nb_aligned_reads))|number_format:2:'.':' '}</td>
</tr>
{/foreach}
</tbody>
<tfoot>
{if $analyse_results|@count > 1 }
<tr>
<th class="info">Total</th>
<th class="info">{$nb_reads_begining|number_format:0:' ':' '}</th>
<th class="info">{$nb_reads_end|number_format:0:' ':' '}</th>
<th class="info">{$uncorrect|number_format:0:' ':' '}</th>
<th class="info">{(100.00-((($nb_reads_end)*100)/$nb_reads_begining))|number_format:2:'.':' '}</th>
</tr>
<tr>
<th class="info">Mean</td>
<th class="info">{($nb_reads_begining/($analyse_results|@count))|number_format:0:' ':' '}</th>
<th class="info">{($nb_reads_end/($analyse_results|@count))|number_format:0:' ':' '}</th>
<th class="info">{($uncorrect/($analyse_results|@count))|number_format:0:' ':' '}</th>
<th class="info">{(100.00-((($nb_reads_end)*100)/$nb_reads_begining))|number_format:2:'.':' '}</th>
</tr>
{/if}
</tfoot>
</table>
{/block}
\ No newline at end of file
{*
Copyright (C) 2009 INRA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*}
{extends file='AnalysisTemplate.tpl'}
{block name=params_title} Mothur commands and parameters used {/block}
{block name=params_content}
{assign var="params" value=";"|explode:$analyse.params}
{foreach from=$analyse_results key=sample item=sample_results}
{assign var="sample" value=$sample}
{/foreach}
<ul>
{foreach from=$params item=param}
{assign var="args_cmd" value=","|explode:$param}
<li class="parameter">{$param}</li>
{foreach from=$args_cmd item=arg_cmd}
{assign var="params_cmd" value="="|explode:$arg_cmd}
{if in_array("bdiffs", $params_cmd)}
{assign var="bdiffs_index" value=$params_cmd|@array_keys:"bdiffs"}
<ul>
<li class="parameter">The maximum number of differences allowed with the barcode is {$params_cmd[$bdiffs_index[0]+1]|replace:')':''}.</li>
</ul>
{/if}
{/foreach}
{/foreach}
</ul>
{/block}
{block name=results_title} Cleaning results {/block}
{block name=results}
<input type="hidden" id="data_folder" value="{$data_folder}"/>
<input type="hidden" id="analysis_folder" value="{$data_folder|cat:$analyse.directory}"/>
<table class="table table-striped table-bordered dataTable analysis-result-table">
<thead>
<tr>
{if $analyse_results|@count > 1 }
<th>Samples ({$analyse_results|@count})</th>
{/if}
<th>Number of sequences</th>
</tr>
</thead>
<tbody>
{assign var="nb_reads_begining" value=0}
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
{assign var="i" value=0}
{foreach from=$analyse_results_sorted key=sample item=sample_results}
<tr>
{if $analyse_results|@count > 1 }
<td id="sample_id_{$i}">{$sample|get_description:$descriptions}</td>
{/if}
{$nb_reads_begining=$nb_reads_begining+$sample_results["default"].nb_seq}
<td>{$sample_results["default"].nb_seq|number_format:0:' ':' '}</td>
</tr>
{$i = $i +1}
{/foreach}
</tbody>
<tfoot>
{if $analyse_results|@count > 1 }
<tr>
<th class="info">Total</th>
<th class="info">{$nb_reads_begining|number_format:0:' ':' '}</th>
</tr>
<tr>
<th class="info">Mean</td>
<th class="info">{($nb_reads_begining/($analyse_results|@count))|number_format:0:' ':' '}</th>
</tr>
{/if}
</tfoot>
</table>
{/block}
\ No newline at end of file
{*
Copyright (C) 2009 INRA
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
*}
{extends file='AnalysisTemplate.tpl'}
{block name=params_title} Mothur commands and parameters used {/block}
{block name=params_content}
{assign var="params" value=";"|explode:$analyse.params}
{foreach from=$analyse_results key=sample item=sample_results}
{assign var="sample" value=$sample}
{/foreach}
<ul>
{foreach from=$params item=param}
{assign var="args_cmd" value=","|explode:$param}
<li class="parameter">{$param}</li>
{foreach from=$args_cmd item=arg_cmd}
{assign var="params_cmd" value="="|explode:$arg_cmd}
<ul>
{if in_array("qaverage", $params_cmd)}
{assign var="qaverage_index" value=$params_cmd|@array_keys:"qaverage"}
<li class="parameter">Remove sequences that have an average below {$params_cmd[$qaverage_index[0]+1]}.</li>
{/if}
{if in_array("maxambig", $params_cmd)}
{assign var="maxambig_index" value=$params_cmd|@array_keys:"maxambig"}
<li class="parameter">Cull sequences with have {$params_cmd[$maxambig_index[0]+1]} ambiguous bases.</li>
{/if}
{if in_array("maxhomop", $params_cmd)}
{assign var="maxhomop_index" value=$params_cmd|@array_keys:"maxhomop"}
<li class="parameter">Clean reads with homopolymers with a size higher than {$params_cmd[$maxhomop_index[0]+1]}.</li>
{/if}
{if in_array("minlength" , $params_cmd)}
{assign var="minlength_index" value=$params_cmd|@array_keys:"minlength"}
{assign var="maxlength_index" value=$params_cmd|@array_keys:"maxlength"}
<li class="parameter">Clean reads with a length not in between [{$params_cmd[$minlength_index[0]+1]};{$params_cmd[$maxlength_index[0]+1]}].</li>
{/if}
{if in_array("pdiffs", $params_cmd)}
{assign var="pdiffs_index" value=$params_cmd|@array_keys:"pdiffs"}
<li class="parameter">The maximum number of differences allowed with the primer is {$params_cmd[$pdiffs_index[0]+1]|replace:')':''}.</li>
{/if}
</ul>
{/foreach}
{/foreach}
</ul>
{/block}
{block name=results_title} Cleaning results {/block}
{block name=results}
<input type="hidden" id="data_folder" value="{$data_folder}"/>
<input type="hidden" id="analysis_folder" value="{$data_folder|cat:$analyse.directory}"/>
<table class="table table-striped table-bordered dataTable analysis-result-table">
<thead>
<tr>
{if $analyse_results|@count > 1 }
<th>Samples ({$analyse_results|@count})</th>
{/if}
<th>Number of sequences</th>
<th>Primers</th>
<th>Too short / too long </th>
<th>Homopolymers</th>
<th>Number of sequences after cleaning</th>
<th>% deleted</th>
</tr>
</thead>
<tbody>
{assign var="nb_reads_begining" value=0}
{assign var="primers_failed" value=0}
{assign var="length_failed" value=0}
{assign var="homopolymers_failed" value=0}
{assign var="total_failed" value=0}
{assign var="nb_reads_end" value=0}
{assign var="analyse_results_sorted" value=$analyse_results|@ksort}
{assign var="i" value=0}
{foreach from=$analyse_results_sorted key=sample item=sample_results}
<tr>
{if $analyse_results|@count > 1 }
<td id="sample_id_{$i}">{$sample|get_description:$descriptions}</td>
{/if}
{$nb_reads_begining=$nb_reads_begining+$sample_results["default"].nb_seq_after_demultiplexage_after_demultiplexage}
{$primers_failed=$primers_failed+$sample_results["default"].f+$sample_results["default"].fl}
{$length_failed=$length_failed+$sample_results["default"].l}
{$homopolymers_failed=$homopolymers_failed+$sample_results["default"].h}
{$total_failed=$primers_failed+$length_failed+$homopolymers_failed}
{$nb_reads_end=$nb_reads_begining-$total_failed}
<td>{$sample_results["default"].nb_seq_after_demultiplexage|number_format:0:' ':' '}</td>
<td>{$sample_results["default"].f+$sample_results["default"].fl|number_format:0:' ':' '}</td>
<td>{$sample_results["default"].l|number_format:0:' ':' '}</td>
<td>{$sample_results["default"].h|number_format:0:' ':' '}</td>
<td>{$sample_results["default"].nb_seq_after_demultiplexage-($sample_results["default"].f+$sample_results["default"].fl+$sample_results["default"].l+$sample_results["default"].h)|number_format:0:' ':' '}</td>
<td>{(100.00-((($sample_results["default"].nb_seq_after_demultiplexage-($sample_results["default"].f+$sample_results["default"].fl+$sample_results["default"].l+$sample_results["default"].h))*100)/$sample_results["default"].nb_seq_after_demultiplexage))|number_format:2:'.':' '}</td>
</tr>
{$i = $i +1}
{/foreach}
</tbody>
<tfoot>
{if $analyse_results|@count > 1 }
<tr>
<th class="info">Total</th>
<th class="info">{$nb_reads_begining|number_format:0:' ':' '}</th>
<th class="info">{$primers_failed|number_format:0:' ':' '}</th>
<th class="info">{$length_failed|number_format:0:' ':' '}</th>
<th class="info">{$homopolymers_failed|number_format:0:' ':' '}</th>
<th class="info">{$nb_reads_end|number_format:0:' ':' '}</th>
<th class="info">{(100.00-((($nb_reads_end)*100)/$nb_reads_begining))|number_format:2:'.':' '}</th>
</tr>
<tr>
<th class="info">Mean</td>
<th class="info">{($nb_reads_begining/($analyse_results|@count))|number_format:0:' ':' '}</th>
<th class="info">{($primers_failed/($analyse_results|@count))|number_format:0:' ':' '}</th>
<th class="info">{($length_failed/($analyse_results|@count))|number_format:0:' ':' '}</th>
<th class="info">{($homopolymers_failed/($analyse_results|@count))|number_format:0:' ':' '}</th>
<th class="info">{($nb_reads_end/($analyse_results|@count))|number_format:0:' ':' '}</th>
<th class="info">{(100.00-((($nb_reads_end)*100)/$nb_reads_begining))|number_format:2:'.':' '}</th>
</tr>
{/if}
</tfoot>
</table>
{/block}
\ No newline at end of file
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment