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comparison featurecounts.xml @ 11:e803ca6407c0 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/featurecounts commit 4c095ddb0f2c369d2bf3fc5ca386f6981a2fa0eb
author iuc
date Fri, 16 Mar 2018 14:05:55 -0400
parents 46cccc52be5f
children b714f4620411
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10:46cccc52be5f 11:e803ca6407c0
1 <tool id="featurecounts" name="featureCounts" version="1.6.0.2" profile="16.04"> 1 <tool id="featurecounts" name="featureCounts" version="1.6.0.3" 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 </requirements> 5 </requirements>
6 6
7 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command> 7 <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
8 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
9
9 ## Export fc path for its built-in annotation 10 ## Export fc path for its built-in annotation
11
10 export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') && 12 export FC_PATH=\$(command -v featureCounts | sed 's@/bin/featureCounts$@@') &&
11 13
12 ## Check whether all alignments are from the same type (bam || sam) 14 ## Check whether all alignments are from the same type (bam || sam)
13 featureCounts 15 featureCounts
14 16
15 #if $anno.anno_select=="gtf": 17 #if $anno.anno_select=="history":
16 #if $anno.gtf_source.ref_source=="history": 18 -a '$anno.reference_gene_sets'
17 -a '$anno.gtf_source.reference_gene_sets' 19 -F "GTF"
18 #else: 20 #elif $anno.anno_select=="cached":
19 -a '$anno.gtf_source.reference_gene_sets_builtin.fields.path' 21 -a '$anno.reference_gene_sets_builtin.fields.path'
20 #end if
21 -F "GTF" 22 -F "GTF"
22 #elif $anno.anno_select=="builtin": 23 #elif $anno.anno_select=="builtin":
23 -a \${FC_PATH}/annotation/${anno.genome}_RefSeq_exon.txt 24 -a \${FC_PATH}/annotation/${anno.bgenome}_RefSeq_exon.txt
24 -F "SAF" 25 -F "SAF"
25 #end if 26 #end if
26 27
27 -o "output" 28 -o "output"
28 -T \${GALAXY_SLOTS:-2} 29 -T \${GALAXY_SLOTS:-2}
129 <param name="alignment" 130 <param name="alignment"
130 type="data" 131 type="data"
131 multiple="false" 132 multiple="false"
132 format="bam,sam" 133 format="bam,sam"
133 label="Alignment file" 134 label="Alignment file"
134 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" /> 135 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. These files must have the database/genome attribute already specified e.g. hg38, not the default: ?" >
136 <validator type="unspecified_build"/>
137 </param>
138
135 <conditional name="anno"> 139 <conditional name="anno">
136 <param name="anno_select" type="select" label="Gene annotation file"> 140 <param name="anno_select" type="select" label="Gene annotation file">
137 <option value="builtin">featureCounts built-in</option> 141 <option value="builtin">featureCounts built-in</option>
138 <option value="gtf">GTF file</option> 142 <option value="cached" selected="True">locally cached</option>
143 <option value="history">in your history</option>
139 </param> 144 </param>
140 <when value="builtin"> 145 <when value="builtin">
141 <param name="genome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts"> 146 <param name="bgenome" type="select" label="Select built-in genome" help="Built-in gene annotations for genomes hg38, hg19, mm10 and mm9 are included in featureCounts">
142 <option value="hg38">hg38</option> 147 <options from_data_table="featurecounts_anno">
143 <option value="hg19">hg19</option> 148 <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
144 <option value="mm10">mm10</option> 149 </options>
145 <option value="mm9">mm9</option>
146 </param> 150 </param>
147 </when> 151 </when>
148 <when value="gtf"> 152 <when value="cached">
149 <conditional name="gtf_source"> 153 <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator">
150 <param name="ref_source" type="select" label="Gene annotation file"> 154 <options from_data_table="gene_sets">
151 <option value="cached">locally cached</option> 155 <filter type="data_meta" key="dbkey" ref="alignment" column="0"/>
152 <option value="history">in your history</option> 156 </options>
153 </param> 157 <validator type="no_options" message="An annotation file is not available for the build associated with the selected input file"/>
154 <when value="cached"> 158 </param>
155 <param name="reference_gene_sets_builtin" type="select" label="Using locally cached annotation" help="If the annotation file you require is not listed here, please contact the Galaxy administrator"> 159 </when>
156 <options from_data_table="gene_sets"> 160 <when value="history">
157 <filter type="sort_by" column="1" /> 161 <param name="reference_gene_sets"
158 <validator type="no_options" message="No annotations are available." /> 162 format="gff,gtf,gff3"
159 </options> 163 type="data"
160 </param> 164 label="Gene annotation file"
161 </when> 165 help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment">
162 <when value="history"> 166 <options>
163 <param name="reference_gene_sets" 167 <filter type="data_meta" key="dbkey" ref="alignment"/>
164 format="gff,gtf,gff3" 168 </options>
165 type="data" 169 <validator type="no_options" message="The current history does not include a dataset with the build associated with the selected input file"/>
166 label="Gene annotation file" 170 </param>
167 help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment" />
168 </when>
169 </conditional>
170 </when> 171 </when>
171 </conditional> 172 </conditional>
172 173
173 <param name="format" 174 <param name="format"
174 type="select" 175 type="select"
268 falsevalue="" 269 falsevalue=""
269 argument="-f" 270 argument="-f"
270 label="On feature level" 271 label="On feature level"
271 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." /> 272 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." />
272 273
273 <param name ="contribute_to_multiple_features" 274 <param name="contribute_to_multiple_features"
274 type="boolean" 275 type="boolean"
275 truevalue=" -O" 276 truevalue=" -O"
276 falsevalue="" 277 falsevalue=""
277 argument="-O" 278 argument="-O"
278 label="Allow read to contribute to multiple features" 279 label="Allow read to contribute to multiple features"
473 </actions> 474 </actions>
474 </data> 475 </data>
475 </outputs> 476 </outputs>
476 <tests> 477 <tests>
477 <test expect_num_outputs="4"> 478 <test expect_num_outputs="4">
478 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 479 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
479 <param name="anno_select" value="gtf"/> 480 <param name="anno_select" value="history"/>
480 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 481 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
481 <param name="format" value="tabdel_short_noheader" /> 482 <param name="format" value="tabdel_short_noheader" />
482 <param name="include_feature_length_file" value="true"/> 483 <param name="include_feature_length_file" value="true"/>
483 <param name="ref_source" value="history" />
484 <param name="count_exon_exon_junction_reads" value="-J"/> 484 <param name="count_exon_exon_junction_reads" value="-J"/>
485 <output name="output_short" file="output_1_short.tab"> 485 <output name="output_short" file="output_1_short.tab">
486 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/> 486 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
487 </output> 487 </output>
488 <output name="output_summary" file="output_1_summary.tab"> 488 <output name="output_summary" file="output_1_summary.tab">
491 <output name="output_jcounts" file="output_1_jcounts.tab"> 491 <output name="output_jcounts" file="output_1_jcounts.tab">
492 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/> 492 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
493 </output> 493 </output>
494 </test> 494 </test>
495 <test expect_num_outputs="3"> 495 <test expect_num_outputs="3">
496 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 496 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
497 <param name="anno_select" value="gtf"/> 497 <param name="anno_select" value="history"/>
498 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 498 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
499 <param name="format" value="tabdel_medium" /> 499 <param name="format" value="tabdel_medium" />
500 <param name="include_feature_length_file" value="true"/> 500 <param name="include_feature_length_file" value="true"/>
501 <param name="ref_source" value="history" />
502 <output name="output_medium" file="output_1_medium.tab"> 501 <output name="output_medium" file="output_1_medium.tab">
503 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/> 502 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
504 </output> 503 </output>
505 <output name="output_summary" file="output_1_summary.tab"> 504 <output name="output_summary" file="output_1_summary.tab">
506 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> 505 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
507 </output> 506 </output>
508 </test> 507 </test>
509 <test expect_num_outputs="3"> 508 <test expect_num_outputs="3">
510 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 509 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
511 <param name="anno_select" value="gtf"/> 510 <param name="anno_select" value="history"/>
512 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 511 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
513 <param name="format" value="tabdel_full" /> 512 <param name="format" value="tabdel_full" />
514 <param name="include_feature_length_file" value="true"/> 513 <param name="include_feature_length_file" value="true"/>
515 <param name="ref_source" value="history" />
516 <output name="output_full" file="output_1_full.tab"> 514 <output name="output_full" file="output_1_full.tab">
517 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/> 515 <metadata name="column_names" value="Geneid,Chr,Start,End,Strand,Length,featureCounts_input1.bam"/>
518 </output> 516 </output>
519 <output name="output_summary" file="output_1_summary.tab"> 517 <output name="output_summary" file="output_1_summary.tab">
520 <metadata name="column_names" value="Status,featureCounts_input1.bam"/> 518 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
522 <output name="output_feature_lengths" file="output_feature_lengths.tab"> 520 <output name="output_feature_lengths" file="output_feature_lengths.tab">
523 <metadata name="column_names" value="Feature,Length"/> 521 <metadata name="column_names" value="Feature,Length"/>
524 </output> 522 </output>
525 </test> 523 </test>
526 <test expect_num_outputs="4"> 524 <test expect_num_outputs="4">
527 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" /> 525 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
528 <param name="anno_select" value="gtf"/> 526 <param name="anno_select" value="history"/>
529 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" /> 527 <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38" />
530 <param name="format" value="tabdel_short" /> 528 <param name="format" value="tabdel_short" />
531 <param name="include_feature_length_file" value="true"/> 529 <param name="include_feature_length_file" value="true"/>
532 <param name="ref_source" value="history" />
533 <param name="count_exon_exon_junction_reads" value="-J"/> 530 <param name="count_exon_exon_junction_reads" value="-J"/>
534 <output name="output_short" file="output_1_short_with_header.tab"> 531 <output name="output_short" file="output_1_short_with_header.tab">
535 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/> 532 <metadata name="column_names" value="Geneid,featureCounts_input1.bam"/>
536 </output> 533 </output>
537 <output name="output_summary" file="output_1_summary_with_header.tab"> 534 <output name="output_summary" file="output_1_summary_with_header.tab">
539 </output> 536 </output>
540 <output name="output_jcounts" file="output_1_jcounts_with_header.tab"> 537 <output name="output_jcounts" file="output_1_jcounts_with_header.tab">
541 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/> 538 <metadata name="column_names" value="PrimaryGene,SecondaryGene,Site1_chr,Site1_location,Site1_strand,Site2_chr,Site2_location,Site2_strand,featureCounts_input1.bam"/>
542 </output> 539 </output>
543 </test> 540 </test>
544 <!-- Ensure built-in annotation works --> 541 <!-- Ensure featureCounts built-in annotation works -->
545 <test expect_num_outputs="2"> 542 <test expect_num_outputs="2">
546 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" /> 543 <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19" />
547 <param name="anno_select" value="builtin"/> 544 <param name="anno_select" value="builtin"/>
548 <param name="format" value="tabdel_short" /> 545 <param name="format" value="tabdel_short" />
549 <param name="genome" value="hg19" />
550 <output name="output_short" file="output_builtin_hg19.tab"> 546 <output name="output_short" file="output_builtin_hg19.tab">
551 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/> 547 <metadata name="column_names" value="Geneid,pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
552 </output> 548 </output>
553 <output name="output_summary" file="output_summary_builtin_hg19.tab"/> 549 <output name="output_summary" file="output_summary_builtin_hg19.tab"/>
550 </test>
551 <!-- Ensure cached GTFs work -->
552 <test expect_num_outputs="3">
553 <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38" />
554 <param name="anno_select" value="cached"/>
555 <param name="format" value="tabdel_medium" />
556 <param name="include_feature_length_file" value="true"/>
557 <output name="output_medium" file="output_1_medium.tab">
558 <metadata name="column_names" value="Geneid,featureCounts_input1.bam,Length"/>
559 </output>
560 <output name="output_summary" file="output_1_summary.tab">
561 <metadata name="column_names" value="Status,featureCounts_input1.bam"/>
562 </output>
554 </test> 563 </test>
555 </tests> 564 </tests>
556 565
557 <help><![CDATA[ 566 <help><![CDATA[
558 featureCounts 567 featureCounts