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comparison purge_gtf_from_multichrom_genes.xml @ 6:45a30e216fec draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6
author artbio
date Sun, 03 Jun 2018 19:50:57 -0400
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5:835a2f3372b5 6:45a30e216fec
1 <tool id="purgegtffrommultichromgenes" name="Purge GTF" version="@WRAPPER_VERSION@">
2 <description>from multi-chromosomes genes</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 </requirements>
8 <stdio>
9 <exit_code range="1:" level="warning" description="Tool exception" />
10 </stdio>
11 <command detect_errors="exit_code"><![CDATA[
12 python '$__tool_directory__'/purge_gtf_from_multichrom_genes.py
13 --input '$input'
14 --output '$output'
15 --log '$log'
16
17 ]]></command>
18 <inputs>
19 <param name="input" type="data" format="gtf" label="GTF input file to be purged of multichromosome genes" />
20 </inputs>
21
22 <outputs>
23 <data format="tabular" name="log" label="gtf purge LOG" />
24 <data format="gtf" name="output" label="purged_${input.name}" />
25 </outputs>
26
27 <tests>
28 <test>
29 <param name="input" value="GTF_to_purge.gtf"/>
30 <output name="output" value="purged.gtf" ftype="gtf" />
31 <output name="log" value="purged.gtf.log" ftype="tabular" />
32 </test>
33 </tests>
34
35 <help>
36 .. class:: infomark
37
38 This script removes genes with multichromosome locations from gtf file. This avoid rsem error
39 due to ambiguous feature coordinates on multiple chromosomes.
40
41
42 </help>
43 <citations>
44 <citation type="doi">10.1186/1471-2105-12-323</citation>
45 </citations>
46
47 </tool>