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update wrapper + tests
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@lldelisle
lldelisle committed Nov 3, 2023
1 parent cb87884 commit 6e3d237
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18 changes: 12 additions & 6 deletions tools/fromgtfTobed12/fromgtfTobed12.xml
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
<tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy0">
<tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy1">
<description> Convert a gtf to a bed12.</description>
<requirements>
<requirement type="package" version="0.11.1">gffutils</requirement>
Expand All @@ -14,7 +14,9 @@
<command>
<![CDATA[
python3 $__tool_directory__/fromgtfTobed12.py
$useGene
#if str($preferedName) != "":
--preferedName $preferedName
#end if
$mergeTranscripts
$ucscformat
--output $output
Expand All @@ -23,12 +25,12 @@
</command>
<inputs>
<param name="input" multiple="false" type="data" format="gtf" label="Select the gtf to convert."/>
<param argument="--useGene" type="boolean" checked="False" truevalue="--useGene" falsevalue="" label="Uses the gene name instead of the transcript name."/>
<param name="mergeTranscripts" type="select" label="Do you want to merge all transcripts of a gene in a single line?">
<option value="" selected="true">No</option>
<option value="--mergeTranscripts">Yes</option>
<option value="--mergeTranscriptsAndOverlappingExons">Yes and merge overlapping exons</option>
</param>
<param argument="--preferedName" type="text" value="" label="Use a specific name for the 4th column" help="By default the 4th column will be transcript_name or gene_name if you merge transcripts. If you prefer 'gene_id', for example, then set this option." />
<param argument="--ucscformat" type="boolean" checked="True" truevalue="--ucscformat" falsevalue="" label="If you want that all chromosome names begin with 'chr'."/>
</inputs>

Expand All @@ -45,20 +47,24 @@
<test>
<param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
<param name="ucscformat" value="--ucscformat"/>
<param name="useGene" value="--useGene"/>
<param name="preferedName" value="gene_name"/>
<output name="output" file="testWithGenes.bed"/>
</test>
<test>
<param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
<param name="ucscformat" value="--ucscformat"/>
<param name="preferedName" value="gene_id"/>
<output name="output" file="testWithGeneIds.bed"/>
</test>
<test>
<param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
<param name="mergeTranscripts" value="--mergeTranscripts"/>
<param name="useGene" value="--useGene"/>
<param name="ucscformat" value=""/>
<output name="output" file="testMergeNotUCSC.bed"/>
</test>
<test>
<param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
<param name="mergeTranscripts" value="--mergeTranscriptsAndOverlappingExons"/>
<param name="useGene" value="--useGene"/>
<param name="ucscformat" value=""/>
<output name="output" file="testMergeExons.bed"/>
</test>
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105 changes: 105 additions & 0 deletions tools/fromgtfTobed12/test-data/testWithGeneIds.bed
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Original file line number Diff line number Diff line change
@@ -0,0 +1,105 @@
chr1 11868 14409 ENSG00000223972 0 + 11868 11868 0 3 359,109,1189 0,744,1352
chr1 12009 13670 ENSG00000223972 0 + 12009 12009 0 6 48,49,85,78,154,218 0,169,603,965,1211,1443
chr1 14403 29570 ENSG00000227232 0 - 14403 14403 0 11 98,34,152,159,198,136,137,147,99,154,37 0,601,1392,2203,2454,2829,3202,3511,3864,10334,15130
chr1 17368 17436 ENSG00000278267 0 - 17368 17368 0 1 68 0
chr1 29553 31097 ENSG00000243485 0 + 29553 29553 0 3 486,104,122 0,1010,1422
chr1 30266 31109 ENSG00000243485 0 + 30266 30266 0 2 401,134 0,709
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chr1 35244 36073 ENSG00000237613 0 - 35244 35244 0 2 237,353 0,476
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chr1 594197 631204 ENSG00000230021 0 - 594197 594197 0 6 559,180,102,124,88,74 0,7200,13757,18543,34721,36933
chr1 594307 598551 ENSG00000230021 0 - 594307 594307 0 2 449,1253 0,2991
chr1 594307 827769 ENSG00000230021 0 - 594307 594307 0 4 449,180,212,100 0,7090,117403,233362
chr1 594307 827796 ENSG00000230021 0 - 594307 594307 0 5 449,180,102,33,127 0,7090,13647,104619,233362
chr1 594457 733064 ENSG00000230021 0 - 594457 594457 0 8 299,180,102,33,158,169,191,84 0,6940,13497,104469,117307,125574,137559,138523
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