Mercurial > repos > iuc > featurecounts

comparison featurecounts.xml @ 17:5c20eb47f759 draft

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/featurecounts commit 6c859db1a131f3f17aecdf44af80ad93b0e9c018
author iuc
date Wed, 20 Jun 2018 05:32:38 -0400
parents bb94bde2d492
children 34b78acbad1d
comparison
equal deleted inserted replaced
16:dc925817920b 17:5c20eb47f759
1 <tool id="featurecounts" name="featureCounts" version="1.6.0.6" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.0.7" profile="16.04">
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 <requirements> 3 <requirements>
4 <requirement type="package" version="1.6.0">subread</requirement> 4 <requirement type="package" version="1.6.0">subread</requirement>
5 <requirement type="package" version="1.7">samtools</requirement>
5 </requirements> 6 </requirements>
6 7
7 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command> 8 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
9 10
56 --fracOverlap $extended_parameters.frac_overlap 57 --fracOverlap $extended_parameters.frac_overlap
57 --fracOverlapFeature $extended_parameters.frac_overlap_feature 58 --fracOverlapFeature $extended_parameters.frac_overlap_feature
58 $extended_parameters.read_reduction 59 $extended_parameters.read_reduction
59 $extended_parameters.primary 60 $extended_parameters.primary
60 $extended_parameters.ignore_dup 61 $extended_parameters.ignore_dup
61 62 #if $extended_parameters.R:
63 $extended_parameters.R
64 #end if
62 #if str($extended_parameters.read_extension_5p) != "0": 65 #if str($extended_parameters.read_extension_5p) != "0":
63 --readExtension5 $extended_parameters.read_extension_5p 66 --readExtension5 $extended_parameters.read_extension_5p
64 #end if 67 #end if
65 68
66 #if str($extended_parameters.read_extension_3p) != "0": 69 #if str($extended_parameters.read_extension_3p) != "0":
106 109
107 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J": 110 #if str($extended_parameters.exon_exon_junction_read_counting_enabled.count_exon_exon_junction_reads) == "-J":
108 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}' 111 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.jcounts' > '${output_jcounts}'
109 #end if 112 #end if
110 113
114 #if $extended_parameters.R:
115 && samtools sort -o '$output_bam' -@ \${GALAXY_SLOTS:-2} *.featureCounts.bam
116 #end if
111 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}' 117 && sed -e 's|${alignment}|${alignment.element_identifier}|g' 'output.summary' > '${output_summary}'
112 ]]></command> 118 ]]></command>
113 <inputs> 119 <inputs>
114 <param name="alignment" 120 <param name="alignment"
115 type="data" 121 type="data"
387 falsevalue="" 393 falsevalue=""
388 argument="--ignoreDup" 394 argument="--ignoreDup"
389 label="Ignore reads marked as duplicate" 395 label="Ignore reads marked as duplicate"
390 help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." /> 396 help="If specified, reads that were marked as duplicates will be ignored. Bit Ox400 in the FLAG field of a SAM/BAM file is used for identifying duplicate reads. In paired end data, the entire read pair will be ignored if at least one end is found to be a duplicate read." />
391 397
398 <param type="boolean"
399 truevalue="-R BAM"
400 falsevalue=""
401 argument="-R"
402 label="Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s)."
403 help="" />
404
392 <param name="count_split_alignments_only" 405 <param name="count_split_alignments_only"
393 type="boolean" 406 type="boolean"
394 truevalue=" --countSplitAlignmentsOnly" 407 truevalue=" --countSplitAlignmentsOnly"
395 falsevalue="" 408 falsevalue=""
396 argument="--countSplitAlignmentsOnly" 409 argument="--countSplitAlignmentsOnly"
406 <actions> 419 <actions>
407 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" /> 420 <action name="column_names" type="metadata" default="Geneid,${alignment.element_identifier},Length" />
408 </actions> 421 </actions>
409 </data> 422 </data>
410 423
424 <data format="bam"
425 name="output_bam"
426 label="${tool.name} on ${on_string}: Alignment file">
427 <filter>extended_parameters['R']</filter>
428 </data>
429
411 <data format="tabular" 430 <data format="tabular"
412 name="output_short" 431 name="output_short"
413 label="${tool.name} on ${on_string}"> 432 label="${tool.name} on ${on_string}">
414 <filter>format == "tabdel_short"</filter> 433 <filter>format == "tabdel_short"</filter>
415 <actions> 434 <actions>
498 <output name="output_jcounts" file="output_1_jcounts.tab"> 517 <output name="output_jcounts" file="output_1_jcounts.tab">
499 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/> 518 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
500 </output> 519 </output>
501 </test> 520 </test>
502 <!-- Ensure featureCounts built-in annotation works --> 521 <!-- Ensure featureCounts built-in annotation works -->
503 <test expect_num_outputs="2"> 522 <test expect_num_outputs="3">
504 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" /> 523 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" />
505 <param name="anno_select" value="builtin"/> 524 <param name="anno_select" value="builtin"/>
506 <param name="format" value="tabdel_short" /> 525 <param name="format" value="tabdel_short" />
526 <section name="extended_parameters">
527 <param name="R" value="true" />
528 </section>
507 <output name="output_short" file="output_builtin_hg19.tab"> 529 <output name="output_short" file="output_builtin_hg19.tab">
508 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 530 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
509 </output> 531 </output>
510 <output name="output_summary" file="output_summary_builtin_hg19.tab"/> 532 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
533 <output name="output_bam" file="output.bam" ftype="bam"/>
511 </test> 534 </test>
512 <!-- Ensure cached GTFs work --> 535 <!-- Ensure cached GTFs work -->
513 <test expect_num_outputs="3"> 536 <test expect_num_outputs="3">
514 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" /> 537 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
515 <param name="anno_select" value="cached"/> 538 <param name="anno_select" value="cached"/>