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comparison spring_map.xml @ 0:023800b21a2a draft

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"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
author guerler
date Tue, 23 Mar 2021 13:54:20 +0000
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children 5f5cdcfaa1a9
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1 <tool id="spring_map" name="SPRING Map" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>with BLAST</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 spring_map.py
9 @pdb_source@
10 -l '$list'
11 -c '$cross'
12 -e $evalue
13 -o '$output'
14 -g '$log'
15 ]]> </command>
16 <inputs>
17 <expand macro="pdb_source" />
18 <param name="list" type="data" format="tabular" label="PDB Chain Identifiers" help="List of PDB chains `PDB_CHAIN`." />
19 <param name="cross" type="data" format="tabular" label="Cross Reference (unmapped)" help="Unmapped SPRING PDB Cross Reference as produced by SPRING Cross tool." />
20 <param name="evalue" type="float" value="0.0" min="0.0" max="1.0" label="E-value Threshold" help="Specify an e-Value threshold to filter the alignment results" />
21 <expand macro="logfile" />
22 </inputs>
23 <outputs>
24 <data format="tabular" name="output" label="SPRING Map Cross Reference" />
25 <data format="txt" name="log" label="SPRING Map Log">
26 <filter>logfile</filter>
27 </data>
28 </outputs>
29 <tests>
30 <test expect_num_outputs="1">
31 <conditional name="pdb_source">
32 <param name="pdb_source_selector" value="history" />
33 <param name="ffdata" value="cross/pdb.ffdata" />
34 <param name="ffindex" value="cross/pdb.ffindex" />
35 </conditional>
36 <param name="list" value="map/chains.tabular" ftype="tabular" />
37 <param name="cross" value="cross/reference.tabular" ftype="tabular" />
38 <output name="output" file="map/mapped.reference.tabular" />
39 </test>
40 <test expect_num_outputs="2">
41 <conditional name="pdb_source">
42 <param name="pdb_source_selector" value="indexed" />
43 <param name="pdb" value="pdb01_cross" />
44 </conditional>
45 <param name="list" value="map/chains.tabular" ftype="tabular" />
46 <param name="cross" value="cross/reference.tabular" ftype="tabular" />
47 <param name="logfile" value="true" />
48 <output name="output" file="map/mapped.reference.tabular" />
49 </test>
50 </tests>
51 <help><![CDATA[
52
53 **What it does**
54
55 Creates additional columns for the SPRING cross reference containing the chain identifier of the homologues from the template library.
56
57 ]]> </help>
58 <expand macro="citations" />
59 </tool>