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comparison fromgtfTobed12.xml @ 0:418e4d0fe0bd draft

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planemo upload for repository https://github.com/lldelisle/tools-lldelisle/tree/master/tools/fromgtfTobed12 commit 1aaffda5b95e0389e315179345642c0d005867c1
author lldelisle
date Fri, 04 Nov 2022 15:37:12 +0000
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children 6fd4b3b90220
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-1:000000000000 0:418e4d0fe0bd
1 <tool id="fromgtfTobed12" name="fromgtftobed12" version="0.11.1+galaxy0">
2 <description> Convert a gtf to a bed12.</description>
3 <requirements>
4 <requirement type="package" version="0.11.1">gffutils</requirement>
5 </requirements>
6 <stdio>
7 <!-- Anything other than zero is an error -->
8 <exit_code range="1:" />
9 <exit_code range=":-1" />
10 <!-- In case the return code has not been set propery check stderr too -->
11 <regex match="Error:" />
12 <regex match="Exception:" />
13 </stdio>
14 <command>
15 <![CDATA[
16 python3 $__tool_directory__/fromgtfTobed12.py
17 $useGene
18 $mergeTranscripts
19 $ucscformat
20 --output $output
21 $input
22 ]]>
23 </command>
24 <inputs>
25 <param name="input" multiple="false" type="data" format="gtf" label="Select the gtf to convert."/>
26 <param argument="--useGene" type="boolean" checked="False" truevalue="--useGene" falsevalue="" label="Uses the gene name instead of the transcript name."/>
27 <param name="mergeTranscripts" type="select" label="Do you want to merge all transcripts of a gene in a single line?">
28 <option value="" selected="true">No</option>
29 <option value="--mergeTranscripts">Yes</option>
30 <option value="--mergeTranscriptsAndOverlappingExons">Yes and merge overlapping exons</option>
31 </param>
32 <param argument="--ucscformat" type="boolean" checked="True" truevalue="--ucscformat" falsevalue="" label="If you want that all chromosome names begin with 'chr'."/>
33 </inputs>
34
35 <outputs>
36 <data format="bed" name="output" label="$input.name as bed12"/>
37 </outputs>
38
39 <tests>
40 <test>
41 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
42 <param name="ucscformat" value="--ucscformat"/>
43 <output name="output" file="test.bed"/>
44 </test>
45 <test>
46 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
47 <param name="ucscformat" value="--ucscformat"/>
48 <param name="useGene" value="--useGene"/>
49 <output name="output" file="testWithGenes.bed"/>
50 </test>
51 <test>
52 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
53 <param name="mergeTranscripts" value="--mergeTranscripts"/>
54 <param name="useGene" value="--useGene"/>
55 <param name="ucscformat" value=""/>
56 <output name="output" file="testMergeNotUCSC.bed"/>
57 </test>
58 <test>
59 <param name="input" value="Homo_sapiens.GRCh38.95_491firstLines.gtf.gz"/>
60 <param name="mergeTranscripts" value="--mergeTranscriptsAndOverlappingExons"/>
61 <param name="useGene" value="--useGene"/>
62 <param name="ucscformat" value=""/>
63 <output name="output" file="testMergeExons.bed"/>
64 </test>
65 </tests>
66 <help><![CDATA[
67 This tool uses gffutils to convert gtf to bed12. One line per transcript.
68 It will use as names transcript_name or gene_name when available.
69 ]]> </help>
70 <citations>
71 <citation type="bibtex">@online{gffutils,
72 url = {https://pythonhosted.org/gffutils/contents.html}
73 }
74 </citation>
75 </citations>
76 </tool>