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comparison pep_pointer.xml @ 1:2b9fa951a6b5 draft

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planemo upload
author pravs
date Thu, 28 Dec 2017 17:25:37 -0500
parents 032f1ee171ed
children 0c67b75c7943
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0:032f1ee171ed 1:2b9fa951a6b5
1 <tool id="pep_pointer" name="PepPointer: classify genomic location of peptides" version="0.1.0"> 1 <tool id="pep_pointer" name="PepPointer" version="0.1.0">
2 <description>classify genomic location of peptides</description>
2 <requirements> 3 <requirements>
3 <requirement type="package" version="2.7.9">python</requirement> 4 <requirement type="package" version="2.7.9">python</requirement>
4 </requirements> 5 </requirements>
5 <command detect_errors="aggressive"><![CDATA[ 6 <command detect_errors="aggressive"><![CDATA[
6 python '$__tool_directory__/pep_pointer.py' '$gtf' '$bed' '$classified' 7 python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
7 ]]></command> 8 ]]></command>
8 <inputs> 9 <inputs>
9 <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/> 10 <conditional name="gtf_input">
11 <param type="select" name="gtf_source" label="Choose the source of the GTF file">
12 <option value="cached" selected="true">Built-in</option>
13 <option value="history">From history</option>
14 </param>
15 <when value="cached">
16 <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
17 <options from_data_table="pep_pointer"/>
18 </param>
19 </when>
20 <when value="history">
21 <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
22 </when>
23 </conditional>
10 <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/> 24 <param type="data" name="bed" format="bed" label="BED file with chromosomal coordinates of peptide"/>
11 </inputs> 25 </inputs>
12 <outputs> 26 <outputs>
13 <data format="tabular" name="classified"/> 27 <data format="tabular" name="classified" label="${tool.name} on ${on_string}">
28 <actions>
29 <action name="column_names" type="metadata" default="chrom,chromStart,chromStop,name,score,strand,annotation"/>
30 </actions>
31 </data>
14 </outputs> 32 </outputs>
15 <tests> 33 <tests>
16 <test> 34 <test>
35 <param name="gtf_source" value="history"/>
17 <param name="gtf" value="mus17.gtf"/> 36 <param name="gtf" value="mus17.gtf"/>
18 <param name="bed" value="novel_peptides_17.bed"/> 37 <param name="bed" value="novel_peptides_17.bed"/>
19 <output name="classified" file="classified_novel_peptides.txt"/> 38 <output name="classified" file="classified_novel_peptides.txt"/>
20 </test> 39 </test>
21 </tests> 40 </tests>