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comparison multiqc.xml @ 23:abfd8a6544d7 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author iuc
date Sat, 10 Dec 2022 11:22:18 +0000
parents 9a913cdee30e
children
comparison
equal deleted inserted replaced
22:9a913cdee30e 23:abfd8a6544d7
411 </when> 411 </when>
412 <when value="rseqc"> 412 <when value="rseqc">
413 <repeat name="output" title="RSeQC output" min="1"> 413 <repeat name="output" title="RSeQC output" min="1">
414 <conditional name="type"> 414 <conditional name="type">
415 <param name="type" type="select" label="Type of RSeQC output?"> 415 <param name="type" type="select" label="Type of RSeQC output?">
416 <option value="bam_stat">bam_stat</option> 416 <option value="bam_stat">BAM/SAM mapping stats</option>
417 <option value="gene_body_coverage">gene_body_coverage</option> 417 <option value="gene_body_coverage">Gene body coverage</option>
418 <option value="infer_experiment">infer_experiment</option> 418 <option value="infer_experiment">Infer experiment</option>
419 <option value="inner_distance">inner_distance</option> 419 <option value="inner_distance">Inner distance</option>
420 <option value="junction_annotation">junction_annotation</option> 420 <option value="junction_annotation">Junction annotation</option>
421 <option value="junction_saturation">junction_saturation</option> 421 <option value="junction_saturation">Junction saturation</option>
422 <option value="read_distribution">read_distribution</option> 422 <option value="read_distribution">Read distribution</option>
423 <option value="read_duplication_pos">read_duplication_pos</option> 423 <option value="read_duplication_pos">Read duplication</option>
424 <option value="read_gc">read_gc</option> 424 <option value="read_gc">Read GC</option>
425 </param> 425 </param>
426 <when value="bam_stat"> 426 <when value="bam_stat">
427 <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC bam_stat output" help="It should contain 'Proper-paired reads map to different chrom:'"/> 427 <param name="input" type="data" format="txt,tabular" multiple="true" label="RSeQC BAM stat: output file" help="It should contain 'Proper-paired reads map to different chrom:'"/>
428 </when> 428 </when>
429 <when value="gene_body_coverage"> 429 <when value="gene_body_coverage">
430 <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene_body_coverage output"/> 430 <param name="input" type="data" format="txt" multiple="true" label="RSeQC gene body coverage: stats file"/>
431 </when> 431 </when>
432 <when value="infer_experiment"> 432 <when value="infer_experiment">
433 <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer_experiment output" help="It should contain 'Fraction of reads explained by'"/> 433 <param name="input" type="data" format="txt" multiple="true" label="RSeQC infer experiment: configuration output" help="It should contain 'Fraction of reads explained by'"/>
434 </when> 434 </when>
435 <when value="inner_distance"> 435 <when value="inner_distance">
436 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC inner_distance output"/> 436 <param name="input" type="data" format="txt" multiple="true" label="RSeQC inner distance: frequency file"/>
437 </when> 437 </when>
438 <when value="junction_annotation"> 438 <when value="junction_annotation">
439 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC junction_annotation output" help="It should contain 'Partial Novel Splicing Junctions:'"/> 439 <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction annotation: stats file" help="It should contain 'Partial Novel Splicing Junctions:'"/>
440 </when> 440 </when>
441 <when value="junction_saturation"> 441 <when value="junction_saturation">
442 <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction_saturation output"/> 442 <param name="input" type="data" format="txt" multiple="true" label="RSeQC junction saturation: junction saturation plot Rscript file"/>
443 </when> 443 </when>
444 <when value="read_distribution"> 444 <when value="read_distribution">
445 <param name="input" type="data" format="txt,xls,tabular" multiple="true" label="RSeQC read_distribution output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/> 445 <param name="input" type="data" format="txt" multiple="true" label="RSeQC read distribution: stats output" help="It should contain 'Group Total_bases Tag_count Tags/Kb'"/>
446 </when> 446 </when>
447 <when value="read_duplication_pos"> 447 <when value="read_duplication_pos">
448 <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_duplication_pos output"/> 448 <param name="input" type="data" format="xls" multiple="true" label="RSeQC read duplication: positions XLS file"/>
449 </when> 449 </when>
450 <when value="read_gc"> 450 <when value="read_gc">
451 <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read_gc output"/> 451 <param name="input" type="data" format="csv,xls,tabular" multiple="true" label="RSeQC read GC output"/>
452 </when> 452 </when>
453 </conditional> 453 </conditional>
454 </repeat> 454 </repeat>
455 </when> 455 </when>
456 <when value="samblaster"> 456 <when value="samblaster">
1074 <has_text text="pycoqc_read_qual_plot" /> 1074 <has_text text="pycoqc_read_qual_plot" />
1075 </assert_contents> 1075 </assert_contents>
1076 </output> 1076 </output>
1077 <output_collection name="stats" type="list" count="2"/> 1077 <output_collection name="stats" type="list" count="2"/>
1078 </test> 1078 </test>
1079 <!--Test 07-->
1080 <test expect_num_outputs="2">
1081 <repeat name="results">
1082 <conditional name="software_cond">
1083 <param name="software" value="rseqc" />
1084 <repeat name="output">
1085 <conditional name="type">
1086 <param name="type" value="junction_annotation"/>
1087 <param name="input" value="junction_annotation.txt"/>
1088 </conditional>
1089 </repeat>
1090 <repeat name="output">
1091 <conditional name="type">
1092 <param name="type" value="junction_saturation"/>
1093 <param name="input" value="junction_saturation.txt"/>
1094 </conditional>
1095 </repeat>
1096 </conditional>
1097 </repeat>
1098 <param name="title" value="RSEQC report"/>
1099 <!-- <param name="flat" value="true"/> -->
1100 <output name="html_report">
1101 <assert_contents>
1102 <has_text text="RSEQC report" />
1103 <has_text text="Junction Annotation" />
1104 <has_text text="Junction Saturation" />
1105 </assert_contents>
1106 </output>
1107 <output_collection name="stats" type="list" count="2"/>
1108 </test>
1079 </tests> 1109 </tests>
1080 <help><![CDATA[ 1110 <help><![CDATA[
1081 **What it does** 1111 **What it does**
1082 1112
1083 `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. 1113 `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.