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comparison multiqc.xml @ 20:9e0d04f86d87 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 230281ee52ab6fc5bf75bfca7cee0e9964057985"
author iuc
date Tue, 02 Mar 2021 21:07:32 +0000
parents 713cf94ffd77
children 6dbde6ce9d93
comparison
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19:713cf94ffd77 20:9e0d04f86d87
1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@"> 1 <tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@+galaxy1">
2 <description>aggregate results from bioinformatics analyses into a single report</description> 2 <description>aggregate results from bioinformatics analyses into a single report</description>
3 <macros> 3 <macros>
4 <token name="@WRAPPER_VERSION@">1.9</token> 4 <token name="@WRAPPER_VERSION@">1.9</token>
5 <token name="@ESCAPE_IDENTIFIER@"> 5 <token name="@ESCAPE_IDENTIFIER@">
6 <![CDATA[ 6 <![CDATA[
10 <![CDATA[ 10 <![CDATA[
11 #if $file_path in $file_paths 11 #if $file_path in $file_paths
12 #set $file_path += '_' + str($file_paths.count($file_path)) 12 #set $file_path += '_' + str($file_paths.count($file_path))
13 #end if 13 #end if
14 #set $file_paths += [$file_path] 14 #set $file_paths += [$file_path]
15 grep -q "$pattern" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" && 15 grep -q '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
16 ln -s '$file' '$file_path' && 16 ln -s '$file' '$file_path' &&
17 ]]></token> 17 ]]></token>
18 <token name="@CREATE_REPEAT_DIR_1@"> 18 <token name="@CREATE_REPEAT_DIR_1@">
19 <![CDATA[ 19 <![CDATA[
20 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j)) 20 #set repeat_dir = os.path.join($software_dir, str($repeat2.type) + '_' + str($j))
279 @LN_2_FILES@ 279 @LN_2_FILES@
280 #end if 280 #end if
281 #end for 281 #end for
282 #elif str($repeat.software_cond.software) == "prokka" 282 #elif str($repeat.software_cond.software) == "prokka"
283 #set $pattern = "contigs:" 283 #set $pattern = "contigs:"
284 @LN_FILES@
285 #elif str($repeat.software_cond.software) == "pycoqc"
286 #set $pattern = "\"pycoqc\":"
284 @LN_FILES@ 287 @LN_FILES@
285 #elif str($repeat.software_cond.software) == "qualimap" 288 #elif str($repeat.software_cond.software) == "qualimap"
286 #for $file in $repeat.software_cond.input 289 #for $file in $repeat.software_cond.input
287 #if re.search("genome_results", str($file.element_identifier)) 290 #if re.search("genome_results", str($file.element_identifier))
288 sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" && 291 sample="\$(grep 'bam file = ' $file | sed 's/bam file = //g' | sed 's: ::g')" &&
568 <!--<option value="mtnucratio">mtnucratio</option>--> 571 <!--<option value="mtnucratio">mtnucratio</option>-->
569 <!--<option value="peddy">Peddy</option>--> 572 <!--<option value="peddy">Peddy</option>-->
570 <option value="picard">Picard</option> 573 <option value="picard">Picard</option>
571 <!--<option value="preseq">Preseq</option>--> 574 <!--<option value="preseq">Preseq</option>-->
572 <option value="prokka">Prokka</option> 575 <option value="prokka">Prokka</option>
576 <option value="pycoqc">PycoQC</option>
573 <!--<option value="qorts">QoRTs</option>--> 577 <!--<option value="qorts">QoRTs</option>-->
574 <option value="qualimap">Qualimap (BamQC or RNASeq output)</option> 578 <option value="qualimap">Qualimap (BamQC or RNASeq output)</option>
575 <option value="quast">QUAST</option> 579 <option value="quast">QUAST</option>
576 <!--<option value="rna_seqc">RNA-SeQC</option>--> 580 <!--<option value="rna_seqc">RNA-SeQC</option>-->
577 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>--> 581 <!--<option value="rsem">RSEM (rsem-calculate-regex output)</option>-->
699 <param name="input" type="data" format="txt" multiple="true" label="Picard output"/> 703 <param name="input" type="data" format="txt" multiple="true" label="Picard output"/>
700 </repeat> 704 </repeat>
701 </when> 705 </when>
702 <when value="prokka"> 706 <when value="prokka">
703 <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/> 707 <param name="input" type="data" format="txt" multiple="true" label="Output of Prokka" help="It should contain 'contigs:'"/>
708 </when>
709 <when value="pycoqc">
710 <param name="input" type="data" format="txt,json" multiple="true" label="Output of PycoQC"/>
704 </when> 711 </when>
705 <when value="qualimap"> 712 <when value="qualimap">
706 <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" /> 713 <param name="input" type="data" format="txt,tabular,tsv" multiple="true" label="Output of Qualimap BamQC" help="First result input should be genome_coverage (default from tool output). Run the Flatten Collection tool to keep all output in one report" />
707 </when> 714 </when>
708 <when value="quast"> 715 <when value="quast">
1318 </output_collection> 1325 </output_collection>
1319 <output_collection name="plots" type="list" count="7"> 1326 <output_collection name="plots" type="list" count="7">
1320 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/> 1327 <element name="fastqc_per_base_sequence_quality_plot_1" file="mqc_fastqc_per_base_sequence_quality_plot_1.txt" compare="sim_size" delta="10"/>
1321 </output_collection> 1328 </output_collection>
1322 </test> 1329 </test>
1330 <test expect_num_outputs="2">
1331 <repeat name="results">
1332 <conditional name="software_cond">
1333 <param name="software" value="pycoqc" />
1334 <param name="input" value="pycoqc.json"/>
1335 </conditional>
1336 </repeat>
1337 <param name="title" value="Title of the report"/>
1338 <param name="comment" value="Commment for the report"/>
1339 <!-- <param name="flat" value="true"/> -->
1340 <output name="html_report">
1341 <assert_contents>
1342 <has_text text="Title of the report" />
1343 <has_text text="Commment for the report" />
1344 <has_text text="General Statistics" />
1345 <has_text text="pycoqc_count_plot" />
1346 <has_text text="pycoqc_read_len_plot" />
1347 <has_text text="pycoqc_read_qual_plot" />
1348 </assert_contents>
1349 </output>
1350 <output_collection name="stats" type="list" count="2"/>
1351 </test>
1323 </tests> 1352 </tests>
1324 <help><![CDATA[ 1353 <help><![CDATA[
1325 **What it does** 1354 **What it does**
1326 1355
1327 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools. 1356 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools.