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comparison spring_map.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
2 <description>with BLAST</description> 2 <description>with BLAST</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.10.1">blast</requirement> 4 <requirement type="package" version="2.10.1">blast</requirement>
5 </requirements> 5 </requirements>
6 <command detect_errors="exit_code"><![CDATA[ 6 <command detect_errors="exit_code"><![CDATA[
7 python3 '$__tool_directory__/spring_map.py' -l '$list' -i '$index' -d '$database' -c '$cross' -o '$output' -g '$log' -t temp 7 python3 '$__tool_directory__/spring_map.py' -l '$list' -i '$index' -d '$database' -c '$cross' -e $evalue -o '$output' -g '$log'
8 ]]></command> 8 ]]></command>
9 <inputs> 9 <inputs>
10 <param format="tabular" name="list" type="data" label="PDB Chain Identifiers" help="List of PDB chains `PDB_CHAIN`."/> 10 <param format="tabular" name="list" type="data" label="PDB Chain Identifiers" help="List of PDB chains `PDB_CHAIN`."/>
11 <param format="ffindex" name="index" type="data" label="PDB Database Index" help="Database Index file."/> 11 <param format="ffindex" name="index" type="data" label="PDB Database Index" help="Database Index file."/>
12 <param format="ffdata" name="database" type="data" label="PDB Database" help="Database Data file."/> 12 <param format="ffdata" name="database" type="data" label="PDB Database" help="Database Data file."/>
13 <param format="tabular" name="cross" type="data" label="Cross Reference (unmapped)" help="Unmapped SPRING PDB Cross Reference as produced by SPRING Cross tool."/> 13 <param format="tabular" name="cross" type="data" label="Cross Reference (unmapped)" help="Unmapped SPRING PDB Cross Reference as produced by SPRING Cross tool."/>
14 <param name="evalue" type="float" label="E-value Threshold" help="Specify an e-Value threshold to filter the alignment results" value="0.0" />
14 </inputs> 15 </inputs>
15 <outputs> 16 <outputs>
16 <data format="tabular" name="output" label="SPRING Map Cross Reference"/> 17 <data format="tabular" name="output" label="SPRING Map Cross Reference"/>
17 <data format="txt" name="log" label="SPRING Map Log"/> 18 <data format="txt" name="log" label="SPRING Map Log"/>
18 </outputs> 19 </outputs>
19 <help><![CDATA[ 20 <help><![CDATA[
20 Creates a 3rd column for the SPRING cross reference containing the chain identifier of the binding partners homologue. 21 Creates additional columns for the SPRING cross reference containing the chain identifier of the homologues from the template library.
21 ]]></help> 22 ]]></help>
22 <tests> 23 <tests>
23 <test> 24 <test>
24 <param name="list" value="cross/chains.tabular" /> 25 <param name="list" value="map/chains.tabular" />
25 <param name="index" value="cross/pdb.ffindex" /> 26 <param name="index" value="cross/pdb.ffindex" />
26 <param name="database" value="cross/pdb.ffdata" /> 27 <param name="database" value="cross/pdb.ffdata" />
27 <param name="cross" value="cross/reference.tabular" /> 28 <param name="cross" value="cross/reference.tabular" />
28 <output name="output" file="map/mapped.reference.tabular"/> 29 <output name="output" file="map/mapped.reference.tabular"/>
29 </test> 30 </test>