Mercurial > repos > iuc > ncbi_eutils_ecitmatch

comparison ecitmatch.xml @ 1:eb431e2636df draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_entrez_eutils commit 2d92a2be8d8725e76a32600e332dfb67cc0db10b
author iuc
date Mon, 02 Nov 2015 12:58:37 -0500
parents f1590b9068bd
children 434f140a86a6
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0:f1590b9068bd 1:eb431e2636df
3 <description>search NCBI for citations in PubMed</description> 3 <description>search NCBI for citations in PubMed</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
8 <expand macro="stdio"/>
9 <version_command>python ecitmatch.py --version</version_command> 8 <version_command>python ecitmatch.py --version</version_command>
10 <command interpreter="python"><![CDATA[ecitmatch.py 9 <command detect_errors="aggressive" interpreter="python"><![CDATA[ecitmatch.py
11 10
12 #if str($input.method) == "file": 11 #if str($input.method) == "file":
13 --file $input.citation_file 12 --file $input.citation_file
14 #else 13 #else
15 #set keys = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] ) 14 #set keys = '" "'.join( [ str( $citation.key ) for $citation in $input.citations ] )
35 <option value="file">Load citations from a formatted table</option> 34 <option value="file">Load citations from a formatted table</option>
36 <option value="direct">Direct Input</option> 35 <option value="direct">Direct Input</option>
37 </param> 36 </param>
38 <when value="file"> 37 <when value="file">
39 <param label="Citation table" name="citation_file" type="data" 38 <param label="Citation table" name="citation_file" type="data"
40 format="tabular" optional="True" help="Columns must be in a specific order, see help documentation"/> 39 format="tabular" help="Columns must be in a specific order, see help documentation"/>
41 </when> 40 </when>
42 <when value="direct"> 41 <when value="direct">
43 <repeat name="citations" title="Citations"> 42 <repeat name="citations" title="Citations">
44 <param name="journal_title" type="text" label="Journal Title" 43 <param name="journal_title" type="text" label="Journal Title"
45 help="E.g. proc natl acad sci u s a" /> 44 help="E.g. proc natl acad sci u s a" />