Commit 489a7811 authored by Maxime Manno's avatar Maxime Manno 🍜
Browse files

Update archive name and fast5archive analysis visu

parent 64a64d88
......@@ -20,10 +20,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="params" value=" "|explode:$analyse.params}
{foreach from=$analyse_results key=sample item=sample_results}
{assign var="sample" value=$sample}
{/foreach}
<ul>
<li class="parameter"> {$analyse.params} : Reads that contain adapters in the middle will be removed.</li>
</ul>
{/foreach}>
{/block}
......@@ -44,79 +41,18 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
<legend>Analyse results report - Sample name : {$descriptions.sample_1}</legend>
<br>
<table id="ont_stats_datatable" class="table table-striped table-bordered dataTable analysis-result-table">
<thead>
<tr>
{assign var="nb_samples" value=$ont_sample_count}
<th class="string-sort" rowspan="2" id="th_id_1"><center>Sample {if $nb_samples > 1 }({$nb_samples}){/if}</center></th>
<th colspan="{$ont_metrics_count}"><center>Trimmed ONT files results</center></th>
</tr>
<tr>
{assign var="th_id" value=2}
{foreach from=$ont_metrics_names key=k item=head}
{if $head == 'read_trim_start'}
<th class = "numeric-sort" id="th_id_{$th_id}">Read_trim_start</th>
{elseif $head == 'read_total_start'}
<th class = "numeric-sort" id="th_id_{$th_id}">Read_total_start</th>
{elseif $head == 'bp_removed_start'}
<th class = "numeric-sort" id="th_id_{$th_id}">Bp_removed_start</th>
{elseif $head == 'read_trim_end'}
<th class = "numeric-sort" id="th_id_{$th_id}">Read_trim_end</th>
{elseif $head == 'read_total_end'}
<th class = "numeric-sort" id="th_id_{$th_id}">Read_total_end</th>
{elseif $head == 'bp_removed_end'}
<th class = "numeric-sort" id="th_id_{$th_id}">Bp_removed_end</th>
{/if}
{$th_id = $th_id +1}
{/foreach}
</tr>
</thead>
<body>
{foreach from=$analyse_results_sorted key=sample item=sample_results}
<tr>
<td id='sample_{$i}_col_1' class="sample_name">{$sample}</td>
{$col_id = 2}
{foreach from=$ont_metrics_names key=k item=head}
{if $head == 'read_trim_start'}
<th id="sample_{$i}_col_{$col_id}">{($sample_results.$head)|number_format:0:',':' '}</th>
{elseif $head == 'read_total_start'}
<th id="sample_{$i}_col_{$col_id}">{($sample_results.$head)|number_format:0:',':' '}</th>
{elseif $head == 'bp_removed_start'}
<th id="sample_{$i}_col_{$col_id}">{($sample_results.$head)|number_format:0:',':' '}</th>
{elseif $head == 'read_trim_end'}
<th id="sample_{$i}_col_{$col_id}">{($sample_results.$head)|number_format:0:',':' '}</th>
{elseif $head == 'read_total_end'}
<th id="sample_{$i}_col_{$col_id}">{($sample_results.$head)|number_format:0:',':' '}</th>
{elseif $head == 'bp_removed_end'}
<th id="sample_{$i}_col_{$col_id}">{($sample_results.$head)|number_format:0:',':' '}</th>
{/if}
{$col_id = $col_id + 1}
{/foreach}
</tr>
{$i = $i + 1}
{/foreach}
</body>
</table>
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>Help for Trimmed ONT files results :</p>
<p>Help for extract files results :</p>
<span class="meta">
<ul>
<li><strong>read_trim</strong> :
The number of reads trimmed for this sample.
<li><strong>Download archive</strong> :
Use the Downloads view tab to download the archive.
The archive was compressed by tar + gzip.
</li>
<li><strong>read_total</strong> :
The total number of reads for this sample.
<li><strong>Decompress archive</strong> :
Use tar -xzf fast5archive.tar.gz
</li>
<li><strong>bp_removed</strong> :
The number of bases removed for this sample.
</li>
<li><strong>_start</strong> :
Previous metrics from the start of the read.
</li>
<li><strong>_end</strong> :
Previous metrics to the end of the read.
</li>
</ul>
</span>
</div>
......
......@@ -54,5 +54,5 @@ class OntQualityCheck (NG6Workflow):
ontstat = self.add_component("Run_stats", [self.summary_file, self.barcoded])
trim_porechop = self.add_component("Trim_porechop", [self.get_all_reads(), self.nb_threads, self.fileformat , "discard_middle"])
if self.fast5dir != None:
fast5archive = self.add_component("Fast5archive", [self.fast5dir, "fast5archive"])
fast5archive = self.add_component("Fast5archive", [self.fast5dir, "fast5archive.tar"])
......@@ -63,7 +63,7 @@ class Fast5archive (Analysis):
This module archive the fast5 files
"""
def define_parameters(self, fast5dir, archivename="fast5_archive"):
def define_parameters(self, fast5dir, archivename="fast5_archive.tar"):
self.add_parameter("fast5dir", "Path of the fast5 directory", default=fast5dir, type='str')
self.add_parameter("archive_name", "Name of the archive", default=archivename, type='str')
list_subdir = get_last_subdirectories(self.fast5dir)
......
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