Mercurial > repos > galaxyp > uniprotxml_downloader

comparison uniprotxml_downloader.xml @ 1:fc8c4bd28681 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/uniprotxml_downloader commit b4871f9659a924a68430aed3a93f4f9bad733fd6
author galaxyp
date Wed, 07 Dec 2016 16:44:14 -0500
parents 0bd2688166a5
children e1abc9a35c64
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0:0bd2688166a5 1:fc8c4bd28681
1 <tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.0"> 1 <tool id="uniprotxml_downloader" name="UniProtXML Download" version="1.0.1">
2 <description>proteome</description> 2 <description>proteome</description>
3 <requirements> 3 <requirements>
4 <requirement type="binary">wget</requirement> 4 <requirement type="package" version="2.7.12">python</requirement>
5 </requirements> 5 </requirements>
6 <stdio> 6 <stdio>
7 <exit_code range="1:" level="fatal" description="Error downloading proteome." /> 7 <exit_code range="1:" level="fatal" description="Error downloading proteome." />
8 </stdio> 8 </stdio>
9 <command interpreter="python"> 9 <command>
10 <![CDATA[ 10 <![CDATA[
11 uniprotxml_downloader.py -v 11 python '$__tool_directory__/uniprotxml_downloader.py'
12 #if $taxid.choice == 'common': 12 -v
13 --taxon $taxid.organism 13 #if $taxid.choice == 'common':
14 #if $taxid.reviewed: 14 --taxon '$taxid.organism'
15 --reviewed=$taxid.reviewed 15 #if $taxid.reviewed:
16 #end if 16 --reviewed=$taxid.reviewed
17 #else: 17 #end if
18 #for id in $taxid.taxons.split(','): 18 #else:
19 -t $id 19 #for id in $taxid.taxons.split(','):
20 #end for 20 -t $id
21 #end if 21 #end for
22 --output="${proteome}" 22 #end if
23 --output="${proteome}"
23 ]]> 24 ]]>
24 </command> 25 </command>
25 <inputs> 26 <inputs>
26 <conditional name="taxid"> 27 <conditional name="taxid">
27 <param name="choice" type="select" label="Select"> 28 <param name="choice" type="select" label="Select">
59 <outputs> 60 <outputs>
60 <data format="uniprotxml" name="proteome" label="UniProtXML" /> 61 <data format="uniprotxml" name="proteome" label="UniProtXML" />
61 </outputs> 62 </outputs>
62 <tests> 63 <tests>
63 <test> 64 <test>
65 <param name="choice" value="taxids"/>
64 <param name="taxons" value="1566990"/> 66 <param name="taxons" value="1566990"/>
65 <output name="uniprotxml"> 67 <output name="uniprotxml">
66 <assert_contents> 68 <assert_contents>
67 <has_text text="&lt;/uniprot&gt;" /> 69 <has_text text="&lt;/uniprot&gt;" />
68 </assert_contents> 70 </assert_contents>