Mercurial > repos > iuc > multiqc

comparison macros.xml @ 25:a7e081ceb76a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 1805997f0c29291dd6fc96add4481422e28e6265
author iuc
date Sat, 25 Jan 2025 17:24:12 +0000
parents f7e2f1eb3a16
children
comparison
equal deleted inserted replaced
24:f7e2f1eb3a16 25:a7e081ceb76a
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">1.24.1</token> 2 <token name="@TOOL_VERSION@">1.27</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="bio_tools"> 4 <xml name="bio_tools">
5 <xrefs> 5 <xrefs>
6 <xref type="bio.tools">multiqc</xref> 6 <xref type="bio.tools">multiqc</xref>
7 </xrefs> 7 </xrefs>
178 <has_text text="R1_fq"/> 178 <has_text text="R1_fq"/>
179 <has_text text="poulet5_1"/> 179 <has_text text="poulet5_1"/>
180 <has_text text="result_right"/> 180 <has_text text="result_right"/>
181 <has_text text="bwa-mem-fastq1_fq"/> 181 <has_text text="bwa-mem-fastq1_fq"/>
182 <has_text text="25839_merged"/> 182 <has_text text="25839_merged"/>
183 <has_text text="Slamdunk_mqc_generalstats_slamdunk_retained"/> 183 <has_text text="slamdunk-retained"/>
184 <has_text text="C2"/> 184 <has_text text="C2"/>
185 <has_n_lines n="11"/> 185 <has_n_lines n="11"/>
186 <has_n_columns n="22"/> 186 <has_n_columns n="22"/>
187 </assert_contents> 187 </assert_contents>
188 </output> 188 </output>
273 <has_text text="treat2"/> 273 <has_text text="treat2"/>
274 <has_text text="hicexplorer_3_hicexplorer2_log_small_test_rf"/> 274 <has_text text="hicexplorer_3_hicexplorer2_log_small_test_rf"/>
275 <has_text text="hisat2_2_txt"/> 275 <has_text text="hisat2_2_txt"/>
276 <has_text text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1"/> 276 <has_text text="HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1"/>
277 <has_text text="treat2"/> 277 <has_text text="treat2"/>
278 <has_text text="Cutadapt"/> 278 <has_text text="cutadapt-percent_trimmed"/>
279 <has_text text="star_log_txt"/> 279 <has_text text="star_log_txt"/>
280 <has_text text="tophat_txtalign"/> 280 <has_text text="tophat_txtalign"/>
281 <has_n_lines n="17"/> 281 <has_n_lines n="17"/>
282 <has_n_columns n="23"/> 282 <has_n_columns n="23"/>
283 </assert_contents> 283 </assert_contents>
486 </output> 486 </output>
487 <output name="stats"> 487 <output name="stats">
488 <assert_contents> 488 <assert_contents>
489 <has_text text="bamtools_txt"/> 489 <has_text text="bamtools_txt"/>
490 <has_text text="Test1"/> 490 <has_text text="Test1"/>
491 <has_text text="Prokka_mqc_generalstats_prokka_contigs"/> 491 <has_text text="prokka-contigs"/>
492 <has_text text="5: TopHat on data 1, data 14, and data 13"/> 492 <has_text text="5: TopHat on data 1, data 14, and data 13"/>
493 <has_text text="gatk_varianteval_txt"/> 493 <has_text text="gatk_varianteval_txt"/>
494 <has_text text="x_bam"/> 494 <has_text text="x_bam"/>
495 <has_text text="htseq_txt"/> 495 <has_text text="htseq_txt"/>
496 <has_text text="picard_CollectRnaSeqMetrics_bam"/> 496 <has_text text="picard_CollectRnaSeqMetrics_bam"/>
498 <has_text text="Helicobacter pylori"/> 498 <has_text text="Helicobacter pylori"/>
499 <has_text text="Sample2"/> 499 <has_text text="Sample2"/>
500 <has_text text="14892_1#15"/> 500 <has_text text="14892_1#15"/>
501 <has_text text="samtools_flagstat_txt"/> 501 <has_text text="samtools_flagstat_txt"/>
502 <has_text text="mapped_passed"/> 502 <has_text text="mapped_passed"/>
503 <has_text text="stats_mqc_generalstats_samtools_stats_error_rate"/> 503 <has_text text="samtools_stats-error_rate"/>
504 <has_text text="samtools_stats_txt"/> 504 <has_text text="samtools_stats_txt"/>
505 <has_text text="snpeff_csv"/> 505 <has_text text="snpeff_csv"/>
506 <has_text text="Bamtools"/> 506 <has_text text="bamtools-mapped_reads_pct"/>
507 <has_text text="bamtools-duplicates_pct"/>
507 <has_n_lines n="22"/> 508 <has_n_lines n="22"/>
508 <has_n_columns n="46"/> 509 <has_n_columns n="50"/>
509 </assert_contents> 510 </assert_contents>
510 </output> 511 </output>
511 </test> 512 </test>
512 <!--Test 04--> 513 <!--Test 04-->
513 <test expect_num_outputs="2"> 514 <test expect_num_outputs="2">
523 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab"/> 524 <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab"/>
524 </conditional> 525 </conditional>
525 </repeat> 526 </repeat>
526 <output name="html_report" ftype="html"> 527 <output name="html_report" ftype="html">
527 <assert_contents> 528 <assert_contents>
528 <has_size value="4594258" delta="500"/> 529 <has_size value="4766687" delta="500"/>
529 </assert_contents> 530 </assert_contents>
530 </output> 531 </output>
531 <!--output name="stats" ftype="tabular"> 532 <!--output name="stats" ftype="tabular">
532 Not created anymore. Proper test needed. 533 Not created anymore. Proper test needed.
533 <assert_contents> 534 <assert_contents>
558 </assert_contents> 559 </assert_contents>
559 </output> 560 </output>
560 <output name="stats" ftype="tabular"> 561 <output name="stats" ftype="tabular">
561 <assert_contents> 562 <assert_contents>
562 <has_text text="poulet5_2"/> 563 <has_text text="poulet5_2"/>
563 <has_text text="FastQC"/> 564 <has_text text="fastqc-percent_gc"/>
564 <has_n_lines n="3"/> 565 <has_n_lines n="3"/>
565 <has_n_columns n="7"/> 566 <has_n_columns n="7"/>
566 </assert_contents> 567 </assert_contents>
567 </output> 568 </output>
568 <output_collection name="plots" type="list" count="7"> 569 <output_collection name="plots" type="list" count="7">
594 <has_text text="pycoqc_read_qual_plot"/> 595 <has_text text="pycoqc_read_qual_plot"/>
595 </assert_contents> 596 </assert_contents>
596 </output> 597 </output>
597 <output name="stats" ftype="tabular"> 598 <output name="stats" ftype="tabular">
598 <assert_contents> 599 <assert_contents>
599 <has_text text="pycoQC_mqc_generalstats_pycoqc_passed_median_read_length"/> 600 <has_text text="pycoqc-passed_median_read_length"/>
600 <has_text text="pycoqc_json"/> 601 <has_text text="pycoqc_json"/>
601 </assert_contents> 602 </assert_contents>
602 </output> 603 </output>
603 </test> 604 </test>
604 </xml> 605 </xml>