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comparison spring_model_all.xml @ 0:64cb5fab9c60 draft

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"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
author guerler
date Tue, 23 Mar 2021 13:57:37 +0000
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children e56e0f4c84fb
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1 <tool id="spring_model_all" name="SPRING Model-All" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>complex structures</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 spring_model_all.py
9 -p '$pairs'
10 @hhr_source@
11 @pdb_source@
12 -c '$crossreference'
13 -o 'models'
14 -g '$log'
15 ]]> </command>
16 <inputs>
17 <param name="pairs" type="data" format="tabular" label="Interacting Pairs" help="Tabular 2-column file containing putative protein interaction pairs." />
18 <param name="crossreference" type="data" format="tabular" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool." />
19 <expand macro="hhr_source" />
20 <expand macro="pdb_source" />
21 <expand macro="logfile" />
22 </inputs>
23 <outputs>
24 <collection name="models" type="list" label="SPRING Model Structures">
25 <discover_datasets pattern="__name_and_ext__" directory="models" />
26 </collection>
27 <data format="tabular" name="log" label="SPRING Model Log">
28 <filter>logfile</filter>
29 </data>
30 </outputs>
31 <tests>
32 <test>
33 <param name="pairs" value="model/pairs.txt" ftype="tabular" />
34 <conditional name="hhr_source">
35 <param name="hhr_source_selector" value="history" />
36 <param name="ffindex" value="model/hhr.ffindex" />
37 <param name="ffdata" value="model/hhr.ffdata" />
38 </conditional>
39 <conditional name="pdb_source">
40 <param name="pdb_source_selector" value="history" />
41 <param name="ffindex" value="model/pdb_structures.ffindex" />
42 <param name="ffdata" value="model/pdb_structures.ffdata" />
43 </conditional>
44 <param name="crossreference" value="model/crossreference.txt" />
45 <param name="logfile" value="true" />
46 <output name="log" file="model/log.txt" />
47 <output_collection name="models" type="list" count="1">
48 <element name="sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
49 </output_collection>
50 </test>
51 <test>
52 <param name="pairs" value="model/pairs.txt" ftype="tabular" />
53 <conditional name="hhr_source">
54 <param name="hhr_source_selector" value="indexed" />
55 <param name="hhr" value="hhr_model" />
56 </conditional>
57 <conditional name="pdb_source">
58 <param name="pdb_source_selector" value="indexed" />
59 <param name="pdb" value="pdb01_model" />
60 </conditional>
61 <param name="crossreference" value="model/crossreference.txt" />
62 <param name="logfile" value="true" />
63 <output name="log" file="model/log.txt" />
64 <output_collection name="models" type="list" count="1">
65 <element name="sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
66 </output_collection>
67 </test>
68 </tests>
69 <help><![CDATA[
70
71 **What it does**
72
73 Creates protein complex model from HHsearch threading results.
74
75 ]]> </help>
76 <expand macro="citations" />
77 </tool>