Mercurial > repos > guerler > spring_model

comparison spring_model.xml @ 0:7ec607bad681 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
author guerler
date Tue, 23 Mar 2021 13:55:00 +0000
parents
children 719931bce361
comparison
equal deleted inserted replaced
-1:000000000000 0:7ec607bad681
1 <tool id="spring_model" name="SPRING Model" 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.py
9 -a '$first_target'
10 -b '$second_target'
11 @pdb_source@
12 -c '$cross'
13 -o '$output'
14 ]]> </command>
15 <inputs>
16 <param name="first_target" format="hhr" type="data" label="First HHR target file" help="Threading result for target sequence using HHsearch." />
17 <param name="second_target" format="hhr" type="data" label="Second HHR target file" help="Threading result for target sequence using HHsearch." />
18 <param name="cross" format="tabular" type="data" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool." />
19 <expand macro="pdb_source" />
20 </inputs>
21 <outputs>
22 <data format="pdb" name="output" label="SPRING Model Structure" />
23 </outputs>
24 <tests>
25 <test>
26 <param name="first_target" value="model/ACE2_HUMAN.hhr" ftype="hhr" />
27 <param name="second_target" value="model/SPIKE_SARS2.hhr" ftype="hhr" />
28 <conditional name="pdb_source">
29 <param name="pdb_source_selector" value="history" />
30 <param name="ffindex" value="model/pdb_structures.ffindex" />
31 <param name="ffdata" value="model/pdb_structures.ffdata" />
32 </conditional>
33 <param name="cross" value="model/crossreference.txt" />
34 <output name="output" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
35 </test>
36 <test>
37 <param name="first_target" value="model/ACE2_HUMAN.hhr" ftype="hhr" />
38 <param name="second_target" value="model/SPIKE_SARS2.hhr" ftype="hhr" />
39 <conditional name="pdb_source">
40 <param name="pdb_source_selector" value="indexed" />
41 <param name="pdb" value="pdb01_model" />
42 </conditional>
43 <param name="cross" value="model/crossreference.txt" />
44 <output name="output" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
45 </test>
46 </tests>
47 <help><![CDATA[
48
49 **What it does**
50
51 Creates protein complex model from HHsearch threading results.
52
53 ]]> </help>
54 <expand macro="citations" />
55 </tool>