Commit a95f4210 authored by Claire Kuchly's avatar Claire Kuchly
Browse files

modification de linterface - information non pertinente + aide

parent 1069cfaa
{*
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
......@@ -29,120 +30,12 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var='loading_headers' value=','|explode:$metrics['loading'].headers|@ksort}
{assign var='loading_stats_count' value=$loading_headers|@count}
{assign var='adapter_headers' value=','|explode:$metrics['adapter_stats'].headers|@ksort}
{assign var='adapter_stats_count' value=$adapter_headers|@count}
{assign var='prefilter_headers' value=','|explode:$metrics['prefilter_stats'].headers|@ksort}
{assign var='prefilter_stats_count' value=$prefilter_headers|@count}
{assign var='postfilter_headers' value=','|explode:$metrics['postfilter_stats'].headers|@ksort}
{assign var='postfilter_stats_count' value=$postfilter_headers|@count}
{assign var='subreads_headers' value=','|explode:$metrics['subreads_stats'].headers|@ksort}
{assign var='subreads_stats_count' value=$subreads_headers|@count}
<div>
<legend>Select the metrics that will be displayed</legend>
<div class="checkbox">
<label>
<input id="view_all_metrics" type="checkbox"/> View all metrics
</label>
</div>
{assign var='data_col' value=2}
<div class="row">
{if $metrics['loading']}
<div class="col-md-2 col-lg-2">
<h4>Loading report</h4>
<ul class="list-unstyled">
{foreach from=$loading_headers key=k item=head}
<li>
<div class="checkbox">
<label>
<input type="checkbox" data-column="{$data_col}" class="toogle-vis" checked/> {$head}
</label>
</div>
</li>
{$data_col = $data_col + 1}
{/foreach}
</ul>
</div>
{/if}
{if $metrics['adapter_stats']}
<div class="col-md-2 col-lg-2">
<h4>Adapter stats</h4>
<ul class="list-unstyled">
{foreach from=$adapter_headers key=k item=head}
<li>
<div class="checkbox">
<label>
<input type="checkbox" data-column="{$data_col}" class="toogle-vis"/> {$head}
</label>
</div>
</li>
{$data_col = $data_col + 1}
{/foreach}
</ul>
</div>
{/if}
{if $metrics['prefilter_stats']}
<div class="col-md-3 col-lg-3">
<h4>Polymerase reads prefilter Stats</h4>
<ul class="list-unstyled">
{foreach from=$prefilter_headers key=k item=head}
<li>
<div class="checkbox">
<label>
<input type="checkbox" data-column="{$data_col}" class="toogle-vis"/> {$head}
</label>
</div>
</li>
{$data_col = $data_col + 1}
{/foreach}
</ul>
</div>
{/if}
{if $metrics['postfilter_stats']}
<div class="col-md-3 col-lg-3">
<h4>Polymerase reads postfilter Stats</h4>
<ul class="list-unstyled">
{foreach from=$postfilter_headers key=k item=head}
<li>
<div class="checkbox">
<label>
<input type="checkbox" data-column="{$data_col}" class="toogle-vis"/> {$head}
</label>
</div>
</li>
{$data_col = $data_col + 1}
{/foreach}
</ul>
</div>
{/if}
{if $metrics['subreads_stats']}
<div class="col-md-2 col-lg-2">
<h4>Subreads Filter Stats</h4>
<ul class="list-unstyled">
{foreach from=$subreads_headers key=k item=head}
<li>
<div class="checkbox">
<label>
<input type="checkbox" data-column="{$data_col}" class="toogle-vis" checked/> {$head}
</label>
</div>
</li>
{$data_col = $data_col + 1}
{/foreach}
</ul>
</div>
{/if}
</div>
</div>
<div>
<table id="rs_subreads_datatable" class="table table-striped table-bordered dataTable analysis-result-table">
<thead>
......@@ -154,20 +47,11 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{if $metrics['loading']}
<th colspan="{$loading_stats_count}"><center>Loading report</center></th>
{/if}
{if $metrics['adapter_stats']}
<th colspan="{$adapter_stats_count}"><center>Adapter Stats</center></th>
{/if}
{if $metrics['prefilter_stats']}
<th colspan="{$prefilter_stats_count}"><center>Polymerase reads prefilter Stats</center></th>
{/if}
{if $metrics['postfilter_stats']}
<th colspan="{$postfilter_stats_count}"><center>Polymerase reads postfilter Stats</center></th>
{if $metrics['postfilter_stats']}
<th colspan="{$postfilter_stats_count}"><center>Polymerase reads Stats</center></th>
{/if}
{if $metrics['subreads_stats']}
<th colspan="{$subreads_stats_count}"><center>Subreads Filter Stats</center></th>
{/if}
......@@ -178,31 +62,20 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="th_id" value=2}
{if $metrics['loading']}
{foreach from=$loading_headers key=k item=head}
<th id="th_id_{$th_id}">{$head}</th>
{if $head == 'Productivity 0'}
<th id="th_id_{$th_id}">Empty (P0)</th>
{elseif $head == 'Productivity 1' }
<th id="th_id_{$th_id}">Productivity (P1)</th>
{elseif $head == 'Productivity 2' }
<th id="th_id_{$th_id}">Other (P2)</th>
{else}
<th id="th_id_{$th_id}">{$head}</th>
{/if}
{$th_id = $th_id +1}
{/foreach}
{/if}
{if $metrics['adapter_stats']}
{foreach from=$adapter_headers key=k item=head}
<th id="th_id_{$th_id}">{$head}</th>
{$th_id = $th_id +1}
{/foreach}
{/if}
{if $metrics['prefilter_stats']}
{foreach from=$prefilter_headers key=k item=head}
{if $head == 'readlen'}
<th id="th_id_{$th_id}">Prefilter readlength histogram</th>
{elseif $head == 'readscore'}
<th id="th_id_{$th_id}">Prefilter readscore histogram</th>
{else}
<th id="th_id_{$th_id}">{$head}</th>
{/if}
{$th_id = $th_id +1}
{/foreach}
{/if}
{if $metrics['postfilter_stats']}
{foreach from=$postfilter_headers key=k item=head}
{if $head == 'readlen'}
......@@ -241,59 +114,114 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{assign var="col_id" value=2}
{if $metrics['loading']}
{foreach from=$loading_headers key=k item=head}
<td id="sample_{$i}_col_{$col_id}">{$sample_results['loading'].$head}</td>
{if ($head == 'Productivity 0') }
<td id="sample_{$i}_col_{$col_id}">{($sample_results['loading'].$head*100)|number_format:2:',':' '}%</td>
{elseif ($head == 'Productivity 1') }
<td id="sample_{$i}_col_{$col_id}">{($sample_results['loading'].$head*100)|number_format:2:',':' '}%</td>
{elseif ($head == 'Productivity 2') }
<td id="sample_{$i}_col_{$col_id}">{($sample_results['loading'].$head*100)|number_format:2:',':' '}%</td>
{else}
<td id="sample_{$i}_col_{$col_id}">{($sample_results['loading'].$head*100)|number_format:0:' ':' '}</td>
{/if}
{$col_id = $col_id + 1}
{/foreach}
{/if}
{if $metrics['adapter_stats']}
{foreach from=$adapter_headers key=k item=head}
{if $head == 'insert'}
<td id="sample_{$i}_col_{$col_id}"><a class="imglink" href="{$sample_results['adapter_stats'].$head}" >pic</a></td>
{else}
<td id="sample_{$i}_col_{$col_id}">{$sample_results['adapter_stats'].$head}</td>
{/if}
{$col_id = $col_id + 1}
{/foreach}
{/if}
{if $metrics['prefilter_stats']}
{foreach from=$prefilter_headers key=k item=head}
{if ($head == 'readlen' || $head == 'readscore')}
<td id="sample_{$i}_col_{$col_id}"><a class="imglink" href="{$sample_results['prefilter_stats'].$head}" >pic</a></td>
{if $metrics['subreads_stats']}
{foreach from=$subreads_headers key=k item=head}
{if $head == 'report' }
<td id="sample_{$i}_col_{$col_id}"><a class="imglink" href="{$sample_results['subreads_stats'].$head}" >pic</a></td>
{else}
<td id="sample_{$i}_col_{$col_id}">{$sample_results['prefilter_stats'].$head}</td>
<td id="sample_{$i}_col_{$col_id}">{($sample_results['subreads_stats'].$head)|number_format:0:' ':' '}</td>
{/if}
{$col_id = $col_id + 1}
{/foreach}
{/if}
{if $metrics['postfilter_stats']}
{foreach from=$postfilter_headers key=k item=head}
{if ($head == 'readlen' || $head == 'readscore')}
<td id="sample_{$i}_col_{$col_id}"><a class="imglink" href="{$sample_results['postfilter_stats'].$head}" >pic</a></td>
{else}
<td id="sample_{$i}_col_{$col_id}">{$sample_results['postfilter_stats'].$head}</td>
<td id="sample_{$i}_col_{$col_id}">{($sample_results['postfilter_stats'].$head)|number_format:0:' ':' '}</td>
{/if}
{$col_id = $col_id + 1}
{/foreach}
{/if}
{if $metrics['subreads_stats']}
{foreach from=$subreads_headers key=k item=head}
{if $head == 'report' }
<td id="sample_{$i}_col_{$col_id}"><a class="imglink" href="{$sample_results['subreads_stats'].$head}" >pic</a></td>
{else}
<td id="sample_{$i}_col_{$col_id}">{$sample_results['subreads_stats'].$head}</td>
{/if}
{$col_id = $col_id + 1}
{/foreach}
{/if}
</tr>
{$i = $i + 1}
{/if}
{/foreach}
<div>
<legend>Select the metrics that will be displayed</legend>
<div class="checkbox">
<label>
<input id="view_all_metrics" type="checkbox"/> View all metrics
</label>
</div>
{assign var='data_col' value=2}
<div class="row">
{if $metrics['loading']}
<div class="col-md-2 col-lg-2">
<h4>Loading report</h4>
<ul class="list-unstyled">
{foreach from=$loading_headers key=k item=head}
<li>
<div class="checkbox">
<label>
<input type="checkbox" data-column="{$data_col}" class="toogle-vis" checked/> {$head}
</label>
</div>
</li>
{$data_col = $data_col + 1}
{/foreach}
</ul>
</div>
{/if}
{if $metrics['postfilter_stats']}
<div class="col-md-3 col-lg-3">
<h4>Polymerase reads Stats</h4>
<ul class="list-unstyled">
{foreach from=$postfilter_headers key=k item=head}
<li>
<div class="checkbox">
<label>
<input type="checkbox" data-column="{$data_col}" class="toogle-vis"/> {$head}
</label>
</div>
</li>
{$data_col = $data_col + 1}
{/foreach}
</ul>
</div>
{/if}
{if $metrics['subreads_stats']}
<div class="col-md-2 col-lg-2">
<h4>Subreads Filter Stats</h4>
<ul class="list-unstyled">
{foreach from=$subreads_headers key=k item=head}
<li>
<div class="checkbox">
<label>
<input type="checkbox" data-column="{$data_col}" class="toogle-vis" checked/> {$head}
</label>
</div>
</li>
{$data_col = $data_col + 1}
{/foreach}
</ul>
</div>
{/if}
</div>
</div>
</tbody>
<tfoot>
......@@ -308,21 +236,7 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
{$th_id = $th_id +1}
{/foreach}
{/if}
{if $metrics['adapter_stats']}
{foreach from=$adapter_headers key=k item=head}
<th><center><input type="checkbox" id="chk_col_{$th_id}"></center></th>
{$th_id = $th_id +1}
{/foreach}
{/if}
{if $metrics['prefilter_stats']}
{foreach from=$prefilter_headers key=k item=head}
<th><center><input type="checkbox" id="chk_col_{$th_id}"></center></th>
{$th_id = $th_id +1}
{/foreach}
{/if}
{if $metrics['postfilter_stats']}
{foreach from=$postfilter_headers key=k item=head}
<th><center><input type="checkbox" id="chk_col_{$th_id}"></center></th>
......@@ -346,6 +260,67 @@ along with this program. If not, see <http://www.gnu.org/licenses/>.
</tfoot>
</table>
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>Help for loading report :</p>
<span class="meta">
<ul>
<li><strong>Productive ZMWs</strong> :
The number of ZMWs for this SMRT Cell that produced results.
</li>
<li><strong>P0</strong> :
The percentage of ZMWs that are empty, with no polymerase.
</li>
<li><strong>P1</strong> :
The percentage of ZMWs that are productive and sequencing.
</li>
<li><strong>P2</strong> :
The percentage of ZMWs that are not P0 (empty) or P1 (productive). This may occur for a variety of reasons - the sequence data is not usable.
</li>
</ul>
</span>
</div>
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>Help for Subreads report :</p>
<span class="meta">
<ul>
<li><strong>Mean Subread length</strong> :
The mean length of the subreads that passed filtering.
</li>
<li><strong>Total Number of Bases</strong> :
The total number of bases in the subreads that passed filtering.
</li>
<li><strong>N50</strong> :
50% of all bases come from subreads longer than this value.
</li>
<li><strong>Number of Reads</strong> :
The total number of reads that passed filtering.
</li>
</ul>
</span>
</div>
<div class="tx-nG6-pi1-help">
<img src="" alt="" class="img" />
<p>Help for Polymerase reads report :</p>
<span class="meta">
<ul>
<li><strong>Polymerase Read Bases</strong> :
The number of bases in the polymerase reads after filtering, including adaptors.
</li>
<li><strong>Polymerase Reads</strong> :
The number of polymerases generating trimmed reads after filtering. Polymerase reads include bases from adaptors and multiple passes around a circular template.
</li>
<li><strong>Polymerase Read Length</strong> :
The mean trimmed read length of all polymerase reads after filtering. The value includes bases from adaptors as well as multiple passes around a circular template.
</li>
<li><strong>Polymerase Read Quality</strong> :
The mean single-pass read quality of all polymerase reads after filtering.
</li>
</ul>
</span>
</div>
</div>
{/block}
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