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comparison pep_pointer.xml @ 1:dc1b0f54f626 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pep_pointer commit e70efe967398bc8d01f4847a5d22ae9f3575f4ef
author galaxyp
date Wed, 03 Jan 2018 13:55:01 -0500
parents 149ed6a9680f
children 073a2965e3b2
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0:149ed6a9680f 1:dc1b0f54f626
1 <tool id="pep_pointer" name="PepPointer" version="0.1.1"> 1 <tool id="pep_pointer" name="PepPointer" version="0.1.2">
2 <description>classify genomic location of peptides</description> 2 <description>classify genomic location of peptides</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7.9">python</requirement> 4 <requirement type="package" version="2.7.9">python</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="aggressive"><![CDATA[ 6 <command detect_errors="aggressive"><![CDATA[
7 python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified' 7 #if $gtf_input.gtf_source == "cached":
8 python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf.fields.path' '$bed' '$classified'
9 #else
10 python '$__tool_directory__/pep_pointer.py' '$gtf_input.gtf' '$bed' '$classified'
11 #end if
8 ]]></command> 12 ]]></command>
9 <inputs> 13 <inputs>
10 <conditional name="gtf_input"> 14 <conditional name="gtf_input">
11 <param type="select" name="gtf_source" label="Choose the source of the GTF file"> 15 <param type="select" name="gtf_source" label="Choose the source of the GTF file">
12 <option value="cached" selected="true">Built-in</option> 16 <option value="cached" selected="true">Locally installed</option>
13 <option value="history">From history</option> 17 <option value="history">From history</option>
14 </param> 18 </param>
15 <when value="cached"> 19 <when value="cached">
16 <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest"> 20 <param name="gtf" type="select" format="gtf" label="GTF file with the genome of interest">
17 <options from_data_table="pep_pointer"/> 21 <options from_data_table="gff_gene_annotations"/>
18 </param> 22 </param>
19 </when> 23 </when>
20 <when value="history"> 24 <when value="history">
21 <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/> 25 <param type="data" name="gtf" format="gtf" label="GTF file with the genome of interest"/>
22 </when> 26 </when>