annotate spring_model.xml @ 0:7ec607bad681 draft

"planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
author guerler
date Tue, 23 Mar 2021 13:55:00 +0000
parents
children 719931bce361
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
1 <tool id="spring_model" name="SPRING Model" license="MIT" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
2 <description>complex structures</description>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
3 <macros>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
4 <import>macros.xml</import>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
5 </macros>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
6 <expand macro="requirements" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
7 <command detect_errors="exit_code"><![CDATA[
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
8 spring_model.py
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
9 -a '$first_target'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
10 -b '$second_target'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
11 @pdb_source@
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
12 -c '$cross'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
13 -o '$output'
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
14 ]]> </command>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
15 <inputs>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
16 <param name="first_target" format="hhr" type="data" label="First HHR target file" help="Threading result for target sequence using HHsearch." />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
17 <param name="second_target" format="hhr" type="data" label="Second HHR target file" help="Threading result for target sequence using HHsearch." />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
18 <param name="cross" format="tabular" type="data" label="Cross Reference" help="SPRING PDB Cross Reference as produced by SPRING Cross tool." />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
19 <expand macro="pdb_source" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
20 </inputs>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
21 <outputs>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
22 <data format="pdb" name="output" label="SPRING Model Structure" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
23 </outputs>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
24 <tests>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
25 <test>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
26 <param name="first_target" value="model/ACE2_HUMAN.hhr" ftype="hhr" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
27 <param name="second_target" value="model/SPIKE_SARS2.hhr" ftype="hhr" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
28 <conditional name="pdb_source">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
29 <param name="pdb_source_selector" value="history" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
30 <param name="ffindex" value="model/pdb_structures.ffindex" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
31 <param name="ffdata" value="model/pdb_structures.ffdata" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
32 </conditional>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
33 <param name="cross" value="model/crossreference.txt" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
34 <output name="output" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
35 </test>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
36 <test>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
37 <param name="first_target" value="model/ACE2_HUMAN.hhr" ftype="hhr" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
38 <param name="second_target" value="model/SPIKE_SARS2.hhr" ftype="hhr" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
39 <conditional name="pdb_source">
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
40 <param name="pdb_source_selector" value="indexed" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
41 <param name="pdb" value="pdb01_model" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
42 </conditional>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
43 <param name="cross" value="model/crossreference.txt" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
44 <output name="output" file="model/sp|Q9BYF1|ACE2_HUMAN.sp|P0DTC2|SPIKE_SARS2.pdb" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
45 </test>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
46 </tests>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
47 <help><![CDATA[
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
48
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
49 **What it does**
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
50
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
51 Creates protein complex model from HHsearch threading results.
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
52
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
53 ]]> </help>
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
54 <expand macro="citations" />
7ec607bad681 "planemo upload commit 6158473dbced09024b0a805a7df2c93d47705d87"
guerler
parents:
diff changeset
55 </tool>