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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit fc2a03ae0ef4d1d0d5f2f05a6ecc0fc4812931e1
author iuc
date Sat, 09 Sep 2023 21:18:37 +0000
parents 6f66ae7c5f7a
children
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31:6f66ae7c5f7a 32:f9d49f5cb597
1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09"> 1 <tool id="featurecounts" name="featureCounts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.09">
2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> 2 <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.0.3</token> 4 <token name="@TOOL_VERSION@">2.0.3</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">2</token>
6 6
7 <macro name="conditional_gff_opions"> 7 <macro name="conditional_gff_opions">
8 <param name="gff_feature_type" type="text" value="exon" argument="-t" label="GFF feature type filter" help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default."/> 8 <param name="gff_feature_type" type="text" value="exon" argument="-t" label="GFF feature type filter" help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default."/>
9 <param name="gff_feature_attribute" type="text" value="gene_id" argument="-g" label="GFF gene identifier" help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization. Ex: if the 9th column is 'gene_id &quot;ENSG00000223972&quot;; gene_name &quot;DDX11L1&quot; gene_source &quot;havana&quot;' (GTF) or 'gene_id=ENSG00000223972; gene_name=DDX11L1; gene_source=havana' (GFF), the available attributes for this feature are 'gene_id', 'gene_name' and 'gene_source'."/> 9 <param name="gff_feature_attribute" type="text" value="gene_id" argument="-g" label="GFF gene identifier" help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization. Ex: if the 9th column is 'gene_id &quot;ENSG00000223972&quot;; gene_name &quot;DDX11L1&quot; gene_source &quot;havana&quot;' (GTF) or 'gene_id=ENSG00000223972; gene_name=DDX11L1; gene_source=havana' (GFF), the available attributes for this feature are 'gene_id', 'gene_name' and 'gene_source'."/>
10 <param name="summarization_level" type="boolean" truevalue=" -f" falsevalue="" argument="-f" label="On feature level" help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level."/> 10 <param name="summarization_level" type="boolean" truevalue=" -f" falsevalue="" argument="-f" label="On feature level" help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level."/>
135 ]]></command> 135 ]]></command>
136 <inputs> 136 <inputs>
137 <param name="alignment" 137 <param name="alignment"
138 type="data" 138 type="data"
139 multiple="false" 139 multiple="false"
140 format="bam,sam" 140 format="unsorted.bam,bam,sam"
141 label="Alignment file" 141 label="Alignment file"
142 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?"> 142 help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files must be in the same format. Unless you are using a Gene annotation file from the History, these files must have the database/genome attribute already specified e.g. hg38, not the default: ?">
143 </param> 143 </param>
144 144
145 <param name="strand_specificity" 145 <param name="strand_specificity"
485 </actions> 485 </actions>
486 </data> 486 </data>
487 </outputs> 487 </outputs>
488 <tests> 488 <tests>
489 <test expect_num_outputs="3"> 489 <test expect_num_outputs="3">
490 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> 490 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
491 <param name="anno_select" value="history"/> 491 <param name="anno_select" value="history"/>
492 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/> 492 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
493 <param name="format" value="tabdel_medium"/> 493 <param name="format" value="tabdel_medium"/>
494 <param name="include_feature_length_file" value="true"/> 494 <param name="include_feature_length_file" value="true"/>
495 <output name="output_medium" file="output_1_medium.tab"> 495 <output name="output_medium" file="output_1_medium.tab">
498 <output name="output_summary" file="output_1_summary.tab"> 498 <output name="output_summary" file="output_1_summary.tab">
499 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> 499 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
500 </output> 500 </output>
501 </test> 501 </test>
502 <test expect_num_outputs="3"> 502 <test expect_num_outputs="3">
503 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> 503 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
504 <param name="anno_select" value="history"/> 504 <param name="anno_select" value="history"/>
505 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/> 505 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
506 <param name="format" value="tabdel_full"/> 506 <param name="format" value="tabdel_full"/>
507 <param name="include_feature_length_file" value="true"/> 507 <param name="include_feature_length_file" value="true"/>
508 <output name="output_full" file="output_1_full.tab"> 508 <output name="output_full" file="output_1_full.tab">
514 <output name="output_feature_lengths" file="output_feature_lengths.tab"> 514 <output name="output_feature_lengths" file="output_feature_lengths.tab">
515 <metadata name="column_names" value="Feature,Length"/> 515 <metadata name="column_names" value="Feature,Length"/>
516 </output> 516 </output>
517 </test> 517 </test>
518 <test expect_num_outputs="4"> 518 <test expect_num_outputs="4">
519 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> 519 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
520 <param name="anno_select" value="history"/> 520 <param name="anno_select" value="history"/>
521 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/> 521 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/>
522 <param name="format" value="tabdel_short"/> 522 <param name="format" value="tabdel_short"/>
523 <param name="include_feature_length_file" value="true"/> 523 <param name="include_feature_length_file" value="true"/>
524 <param name="count_exon_exon_junction_reads" value="-J"/> 524 <param name="count_exon_exon_junction_reads" value="-J"/>
532 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/> 532 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
533 </output> 533 </output>
534 </test> 534 </test>
535 <!-- Ensure featureCounts built-in annotation works --> 535 <!-- Ensure featureCounts built-in annotation works -->
536 <test expect_num_outputs="3"> 536 <test expect_num_outputs="3">
537 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/> 537 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/>
538 <param name="anno_select" value="builtin"/> 538 <param name="anno_select" value="builtin"/>
539 <param name="format" value="tabdel_short"/> 539 <param name="format" value="tabdel_short"/>
540 <conditional name="pe_parameters"> 540 <conditional name="pe_parameters">
541 <param name="paired_end_status" value="PE_individual"/> 541 <param name="paired_end_status" value="PE_individual"/>
542 </conditional> 542 </conditional>
549 <output name="output_summary" file="output_summary_builtin_hg19.tab"/> 549 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
550 <output name="output_bam" file="output.bam" ftype="bam"/> 550 <output name="output_bam" file="output.bam" ftype="bam"/>
551 </test> 551 </test>
552 <!-- Ensure fragment counting works --> 552 <!-- Ensure fragment counting works -->
553 <test expect_num_outputs="3"> 553 <test expect_num_outputs="3">
554 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/> 554 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/>
555 <param name="anno_select" value="builtin"/> 555 <param name="anno_select" value="builtin"/>
556 <param name="format" value="tabdel_short"/> 556 <param name="format" value="tabdel_short"/>
557 <conditional name="pe_parameters"> 557 <conditional name="pe_parameters">
558 <param name="paired_end_status" value="PE_fragments"/> 558 <param name="paired_end_status" value="PE_fragments"/>
559 </conditional> 559 </conditional>
566 <output name="output_summary" file="output_summary_builtin_hg19_fragments.tab"/> 566 <output name="output_summary" file="output_summary_builtin_hg19_fragments.tab"/>
567 <output name="output_bam" file="output_fragments.bam" ftype="bam"/> 567 <output name="output_bam" file="output_fragments.bam" ftype="bam"/>
568 </test> 568 </test>
569 <!-- Ensure cached GTFs work --> 569 <!-- Ensure cached GTFs work -->
570 <test expect_num_outputs="3"> 570 <test expect_num_outputs="3">
571 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> 571 <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/>
572 <param name="anno_select" value="cached"/> 572 <param name="anno_select" value="cached"/>
573 <param name="format" value="tabdel_medium"/> 573 <param name="format" value="tabdel_medium"/>
574 <param name="include_feature_length_file" value="true"/> 574 <param name="include_feature_length_file" value="true"/>
575 <output name="output_medium" file="output_1_medium.tab"> 575 <output name="output_medium" file="output_1_medium.tab">
576 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/> 576 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
578 <output name="output_summary" file="output_1_summary.tab"> 578 <output name="output_summary" file="output_1_summary.tab">
579 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> 579 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
580 </output> 580 </output>
581 </test> 581 </test>
582 <!-- Ensure BAM output works --> 582 <!-- Ensure BAM output works -->
583 <test> 583 <test expect_num_outputs="3">
584 <param name="alignment" value="subset.sorted.bam" ftype="bam"/> 584 <param name="alignment" value="subset.sorted.bam" ftype="bam"/>
585 <param name="anno_select" value="history"/> 585 <param name="anno_select" value="history"/>
586 <param name="reference_gene_sets" value="small.gtf" ftype="gtf"/> 586 <param name="reference_gene_sets" value="small.gtf" ftype="gtf"/>
587 <section name="extended_parameters"> 587 <section name="extended_parameters">
588 <param name="R" value="true"/> 588 <param name="R" value="true"/>
589 </section> 589 </section>
590 <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/> 590 <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/>
591 <output name="output_short" file="subset.sorted.featurecounts_short.tab">
592 <metadata name="column_names" value="Geneid,subset.sorted.bam"/>
593 </output>
594 <output name="output_summary" file="subset.sorted.featurecounts_summary.tab"/>
591 </test> 595 </test>
592 </tests> 596 </tests>
593 597
594 <help><![CDATA[ 598 <help><![CDATA[
595 featureCounts 599 featureCounts