Mercurial > repos > iuc > featurecounts
changeset 32:f9d49f5cb597 draft default tip
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 | |
| files | featurecounts.xml test-data/subset.sorted.featurecounts_short.tab test-data/subset.sorted.featurecounts_summary.tab |
| diffstat | 3 files changed, 1418 insertions(+), 9 deletions(-) [+] |
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--- a/featurecounts.xml Thu Mar 02 12:50:54 2023 +0000 +++ b/featurecounts.xml Sat Sep 09 21:18:37 2023 +0000 @@ -2,7 +2,7 @@ <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files</description> <macros> <token name="@TOOL_VERSION@">2.0.3</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@VERSION_SUFFIX@">2</token> <macro name="conditional_gff_opions"> <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."/> @@ -137,7 +137,7 @@ <param name="alignment" type="data" multiple="false" - format="bam,sam" + format="unsorted.bam,bam,sam" label="Alignment file" 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: ?"> </param> @@ -487,7 +487,7 @@ </outputs> <tests> <test expect_num_outputs="3"> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> + <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/> <param name="anno_select" value="history"/> <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/> <param name="format" value="tabdel_medium"/> @@ -500,7 +500,7 @@ </output> </test> <test expect_num_outputs="3"> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> + <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/> <param name="anno_select" value="history"/> <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/> <param name="format" value="tabdel_full"/> @@ -516,7 +516,7 @@ </output> </test> <test expect_num_outputs="4"> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> + <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/> <param name="anno_select" value="history"/> <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" dbkey="hg38"/> <param name="format" value="tabdel_short"/> @@ -534,7 +534,7 @@ </test> <!-- Ensure featureCounts built-in annotation works --> <test expect_num_outputs="3"> - <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/> + <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/> <param name="anno_select" value="builtin"/> <param name="format" value="tabdel_short"/> <conditional name="pe_parameters"> @@ -551,7 +551,7 @@ </test> <!-- Ensure fragment counting works --> <test expect_num_outputs="3"> - <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="bam" dbkey="hg19"/> + <param name="alignment" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" ftype="unsorted.bam" dbkey="hg19"/> <param name="anno_select" value="builtin"/> <param name="format" value="tabdel_short"/> <conditional name="pe_parameters"> @@ -568,7 +568,7 @@ </test> <!-- Ensure cached GTFs work --> <test expect_num_outputs="3"> - <param name="alignment" value="featureCounts_input1.bam" ftype="bam" dbkey="hg38"/> + <param name="alignment" value="featureCounts_input1.bam" ftype="unsorted.bam" dbkey="hg38"/> <param name="anno_select" value="cached"/> <param name="format" value="tabdel_medium"/> <param name="include_feature_length_file" value="true"/> @@ -580,7 +580,7 @@ </output> </test> <!-- Ensure BAM output works --> - <test> + <test expect_num_outputs="3"> <param name="alignment" value="subset.sorted.bam" ftype="bam"/> <param name="anno_select" value="history"/> <param name="reference_gene_sets" value="small.gtf" ftype="gtf"/> @@ -588,6 +588,10 @@ <param name="R" value="true"/> </section> <output name="output_bam" value="subset.sorted.featurecounts.bam" compare="sim_size"/> + <output name="output_short" file="subset.sorted.featurecounts_short.tab"> + <metadata name="column_names" value="Geneid,subset.sorted.bam"/> + </output> + <output name="output_summary" file="subset.sorted.featurecounts_summary.tab"/> </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/subset.sorted.featurecounts_short.tab Sat Sep 09 21:18:37 2023 +0000 @@ -0,0 +1,1390 @@ +Geneid subset.sorted.bam +f10 0 +trmt10c 14 +jam2a 0 +cnppd1 0 +klf7a 0 +lancl1 0 +plk1 0 +tmem8a 0 +eif3f 0 +trpc5a 0 +camk2d2 0 +mir2185-1 0 +fat1a 0 +clockb 0 +smc2 0 +kiaa0368 0 +tma16 0 +med28 0 +zcchc7 0 +kdm4c 0 +zmynd10 0 +n4bp2 0 +qdprb2 0 +tmem154 0 +plrg1 0 +uso1 0 +timmdc1 0 +zc3h13 0 +pcca 0 +itga6b 0 +nt5c2b 0 +cd99 0 +tpt1 0 +frem3 0 +zgc:152968 0 +scpp1 0 +hmgb2a 0 +tenm3 0 +faah2a 0 +rgs12b 0 +htt 0 +smox 0 +timm10 0 +tmx2b 0 +kdm2aa 0 +si:ch211-243a20.3 0 +zgc:174719 0 +ebpl 0 +pdxkb 0 +cryzl1 0 +zgc:136614 0 +fstl1a 0 +cfap58 0 +si:dkeyp-80c12.10 0 +col17a1a 0 +lef1 0 +papss1 0 +mdh1aa 0 +dpy30 0 +meis1a 0 +abca1a 0 +cct4 0 +nup133 0 +golga7ba 0 +vps54 0 +zgc:158803 0 +c3a.2 0 +c3a.3 0 +zgc:171470 0 +parn 0 +erg 0 +ykt6 0 +ckmt2a 0 +ddx55 0 +lppr1 0 +hnrnpd 0 +nrg1 0 +gmcl1 0 +slc35e4 0 +zgc:173443 0 +antxr2b 0 +rbm18 0 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