Mercurial > repos > bgruening > uniprot_rest_interface

comparison uniprot.xml @ 2:fe94765e8814 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/uniprot_rest_interface commit 074fed99c6df6bad17341bbfa57645f222907ad4
author bgruening
date Mon, 10 Apr 2017 13:19:36 -0400
parents cd2a41c65447
children 054483e27a35
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1:cd2a41c65447 2:fe94765e8814
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
7 <requirement type="package" version="2.7">requests</requirement> 7 <requirement type="package" version="2.7">requests</requirement>
8 </requirements> 8 </requirements>
9 <stdio>
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 <regex match="Error:" />
13 <regex match="Exception:" />
14 </stdio>
15 <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command> 9 <version_command>echo "UniProt ID mapping for Galaxy in version 0.1"</version_command>
16 <command><![CDATA[ 10 <command detect_errors="aggressive"><![CDATA[
17 11
18 cut -f ${id_column} $infile > id_file.tabular && 12 cut -f ${id_column} $infile > id_file.tabular &&
19 13
20 $__tool_directory__/uniprot.py 14 $__tool_directory__/uniprot.py
21 15
235 <test> 229 <test>
236 <param name="infile" value="id_uniprot.tab" ftype="tabular"/> 230 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
237 <param name="id_column" value="c1"/> 231 <param name="id_column" value="c1"/>
238 <param name="format" value="fasta"/> 232 <param name="format" value="fasta"/>
239 <param name="tool_choice" value="retrieve"/> 233 <param name="tool_choice" value="retrieve"/>
240 <output name="outfile_retrieve" file="test1_retrieve.fasta" ftype="fasta"/> 234 <output name="outfile_retrieve_fasta" file="test1_retrieve.fasta" ftype="fasta" compare="sim_size" />
241 </test> 235 </test>
242 <test> 236 <test>
243 <param name="infile" value="id_uniprot.tab" ftype="tabular"/> 237 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
244 <param name="id_column" value="c1"/> 238 <param name="id_column" value="c1"/>
245 <param name="format" value="gff"/> 239 <param name="format" value="gff"/>
246 <param name="tool_choice" value="retrieve"/> 240 <param name="tool_choice" value="retrieve"/>
247 <output name="outfile_retrieve" file="test2_retrieve.gff" ftype="gff"/> 241 <output name="outfile_retrieve_gff" file="test2_retrieve.gff" ftype="gff" compare="sim_size" />
248 </test> 242 </test>
249 <test> 243 <test>
250 <param name="infile" value="id_uniprot.tab" ftype="tabular"/> 244 <param name="infile" value="id_uniprot.tab" ftype="tabular"/>
251 <param name="id_column" value="c1"/> 245 <param name="id_column" value="c1"/>
252 <param name="tool_choice" value="map"/> 246 <param name="tool_choice" value="map"/>