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comparison spring_cross.xml @ 39:172398348efd draft

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"planemo upload commit 26b4018c88041ee0ca7c2976e0a012015173d7b6-dirty"
author guerler
date Fri, 22 Jan 2021 15:50:27 +0000
parents 80a4b98121b6
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38:80a4b98121b6 39:172398348efd
1 <tool id="spring_cross" name="SPRING Cross" version="0.1.0" python_template_version="3.5" license="MIT"> 1 <tool id="spring_cross" name="SPRING Cross" version="0.1.0" python_template_version="3.5" license="MIT">
2 <description>reference builder</description> 2 <description>reference builder</description>
3 <command detect_errors="exit_code"><![CDATA[ 3 <command detect_errors="exit_code"><![CDATA[
4 python3 '$__tool_directory__/spring_cross.py' -l '$list' -i '$index' -d '$database' -o '$output' -g '$log' -t temp 4 python3 '$__tool_directory__/spring_cross.py' -i '$index' -d '$database' -o '$output' -g '$log'
5 ]]></command> 5 ]]></command>
6 <inputs> 6 <inputs>
7 <param format="tabular" name="list" type="data" label="PDB Chain Identifiers" help="List of PDB chains `PDB_CHAIN`."/>
8 <param format="ffindex" name="index" type="data" label="PDB Database Index" help="Database Index file."/> 7 <param format="ffindex" name="index" type="data" label="PDB Database Index" help="Database Index file."/>
9 <param format="ffdata" name="database" type="data" label="PDB Database" help="Database Data file."/> 8 <param format="ffdata" name="database" type="data" label="PDB Database" help="Database Data file."/>
10 </inputs> 9 </inputs>
11 <outputs> 10 <outputs>
12 <data format="tabular" name="output" label="SPRING Cross Reference"/> 11 <data format="tabular" name="output" label="SPRING Cross Reference"/>
16 Creates a 2-column cross reference between a list of input chains and all interacting chains found in the provided PDB database. This reference is required as 15 Creates a 2-column cross reference between a list of input chains and all interacting chains found in the provided PDB database. This reference is required as
17 input for the SPRING min-Z calculator. 16 input for the SPRING min-Z calculator.
18 ]]></help> 17 ]]></help>
19 <tests> 18 <tests>
20 <test> 19 <test>
21 <param name="list" value="cross/chains.tabular" />
22 <param name="index" value="cross/pdb.ffindex" /> 20 <param name="index" value="cross/pdb.ffindex" />
23 <param name="database" value="cross/pdb.ffdata" /> 21 <param name="database" value="cross/pdb.ffdata" />
24 <output name="output" file="cross/reference.tabular"/> 22 <output name="output" file="cross/reference.tabular"/>
25 </test> 23 </test>
26 </tests> 24 </tests>