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comparison multiqc.xml @ 29:ef6bd40a30d2 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 4095773348da6faeb6096f58785b66898b09befa
author iuc
date Fri, 10 Oct 2025 20:11:35 +0000
parents e99aaf069191
children
comparison
equal deleted inserted replaced
28:e99aaf069191 29:ef6bd40a30d2
210 --comment '$comment' 210 --comment '$comment'
211 #end if 211 #end if
212 212
213 $flat 213 $flat
214 $export 214 $export
215 215
216 #if $configfile == "T" 216 #if $configfile == "T"
217 --config '$multiqc_config' 217 --config '$multiqc_config'
218 #end if 218 #end if
219 219
220 && 220 &&
221 mkdir -p ./plots && 221 mkdir -p ./plots &&
222 ls -l ./report_data/ && 222 ls -l ./report_data/ &&
223 ##cat ./report_data/multiqc_busco.txt && 223 ##cat ./report_data/multiqc_busco.txt &&
224 cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated 224 cp ./report_data/*plot*.txt ./plots/ | true ## don't fail if no plot files are generated
225
226 #if $png_plots == "true"
227 && mkdir -p ./png_plots
228 && cp ./report_plots/png/*.png ./png_plots/ | true ## don't fail if no png plots are generated
229 #end if
225 230
226 ]]></command> 231 ]]></command>
227 <expand macro="configfile"/> 232 <expand macro="configfile"/>
228 <inputs> 233 <inputs>
229 <repeat name="results" title="Results" min="1"> 234 <repeat name="results" title="Results" min="1">
496 </sanitizer> 501 </sanitizer>
497 <validator type="regex">[0-9a-zA-Z,: _.-]+</validator> 502 <validator type="regex">[0-9a-zA-Z,: _.-]+</validator>
498 </param> 503 </param>
499 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/> 504 <param argument="--flat" type="boolean" truevalue="--flat" falsevalue="" checked="false" label="Use only flat plots (non-interactive images)" help="To consume less disk space and resources to display. Used by default when there are 100 or more samples."/>
500 <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/> 505 <param argument="--export" type="boolean" truevalue="--export" falsevalue="" checked="false" label="Output the multiQC plots raw data?" help="This will output a file for each plot containing the raw data used to generate the plot"/>
506 <param name="png_plots" type="boolean" truevalue="true" falsevalue="false" label="Output PNG plots?" help="Choose if you want PNG plots in an output collection"/>
501 </inputs> 507 </inputs>
502 <outputs> 508 <outputs>
503 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage"/> 509 <data name="html_report" format="html" from_work_dir="report.html" label="${tool.name} on ${on_string}: Webpage"/>
504 <data name="stats" format="tabular" from_work_dir="report_data/multiqc_general_stats.txt" label="${tool.name} on ${on_string}: Stats"/> 510 <data name="stats" format="tabular" from_work_dir="report_data/multiqc_general_stats.txt" label="${tool.name} on ${on_string}: Stats"/>
505 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots"> 511 <collection name="plots" type="list" label="${tool.name} on ${on_string}: Plots">
506 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="plots"/> 512 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" directory="plots"/>
507 <filter>export</filter> 513 <filter>export</filter>
508 </collection> 514 </collection>
515 <collection name="png_plot" type="list" label="${tool.name} on ${on_string}: PNG Plots">
516 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" format="png" directory="png_plots"/>
517 <filter>png_plots</filter>
518 </collection>
509 </outputs> 519 </outputs>
510 <tests> 520 <tests>
511 <expand macro="general_tests"/> 521 <expand macro="general_tests"/>
512 <expand macro="bcftools_test"/> 522 <expand macro="bcftools_test"/>
513 <expand macro="bowtie2_test"/> 523 <expand macro="bowtie2_test"/>
514 <expand macro="fastqc_test"/> 524 <expand macro="fastqc_test"/>
515 <expand macro="trimmomatic_test"/> 525 <expand macro="trimmomatic_test"/>
516 <!-- Test 10 --> 526 <!-- Test 10 -->
517 <expand macro="flexbar_test"/> 527 <expand macro="flexbar_test"/>
518 <expand macro="fastp_test"/> 528 <expand macro="fastp_test"/>
519 <expand macro="bismark_test"/> 529 <expand macro="bismark_test"/>
520 <expand macro="rseqc_test"/> 530 <expand macro="rseqc_test"/>
521 <expand macro="star_test"/> 531 <expand macro="star_test"/>
542 <expand macro="megahit_test"/> 552 <expand macro="megahit_test"/>
543 <expand macro="nonpareil_test"/> 553 <expand macro="nonpareil_test"/>
544 <expand macro="gtdbtk_test"/> 554 <expand macro="gtdbtk_test"/>
545 <expand macro="sambamba_test"/> 555 <expand macro="sambamba_test"/>
546 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? --> 556 <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
547 557
548 </tests> 558 </tests>
549 <help><![CDATA[ 559 <help><![CDATA[
550 **What it does** 560 **What it does**
551 561
552 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report. 562 `MultiQC <http://multiqc.info/>`_ aggregates results from bioinformatics analyses across many samples into a single report.