Mercurial > repos > iuc > multiqc
comparison multiqc.xml @ 23:abfd8a6544d7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 8a91236cee4d408ae2b53a3e9b6daebc332d631a
author | iuc |
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date | Sat, 10 Dec 2022 11:22:18 +0000 |
parents | 9a913cdee30e |
children | f7e2f1eb3a16 |
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22:9a913cdee30e | 23:abfd8a6544d7 |
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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. |