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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
author chemteam
date Thu, 06 Jun 2024 07:08:34 +0000
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1 <tool id="pulchra" name="PULCHRA recontruction of all atom proteins" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="22.05">
2 <description>from reduced representations</description>
3 <macros>
4 <token name="@TOOL_VERSION@">3.06</token>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">pulchra</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11
12 ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
13 pulchra
14
15 ##inputs
16 ./structure_input.${structure_input.ext}
17 $skip_sidechain
18
19 -v
20
21 ]]></command>
22 <inputs>
23 <param name="structure_input" type="data" format="pdb" label="Structure file" help="In PDB format. This input is usually an 'alpha trace' or other incomplete structure file."/>
24 <param argument="-s" name="skip_sidechain" type="boolean" truevalue="-s" falsevalue="" label="Skip sidechain reconstruction?" help="By default, both sidechains and backbone will be reconstructed otherwise."/>
25 </inputs>
26 <outputs>
27 <data name="output1" format="pdb" from_work_dir="*.rebuilt.pdb" label="PULCHRA rebuilt pdb file on ${on_string}"/>
28 </outputs>
29 <tests>
30 <test>
31 <param name="structure_input" value="model.pdb"/>
32 <output name="output1" ftype="pdb">
33 <assert_contents>
34 <has_text text="ATOM 1 N PHE 1 16.391 50.300 23.791"/>
35 <has_text text="ATOM 12 N LEU 2 14.039 47.806 25.433"/>
36 <has_text text="ATOM 20 N VAL 3 10.836 47.425 24.846"/>
37 </assert_contents>
38 </output>
39 </test>
40 <test>
41 <param name="structure_input" value="model.pdb"/>
42 <param name="skip_sidechain" value="true" />
43 <output name="output1" ftype="pdb">
44 <assert_contents>
45 <has_text text="ATOM 1 N PHE 1 16.391 50.300 23.791"/>
46 <has_text text="ATOM 12 O VAL 3 8.414 45.957 24.602"/>
47 <has_text text="ATOM 20 O MET 5 1.327 47.936 26.198"/>
48 </assert_contents>
49 </output>
50 </test>
51 </tests>
52 <help><![CDATA[
53
54 .. class:: infomark
55
56 **What it does**
57
58 This tool rebuilds a protein structure from reduced representations (alpha carbon trace), producing an all-heavy atom PDB file.
59
60 _____
61
62 .. class:: infomark
63
64 **Input**
65
66 - Alpha carbon trace PDB file
67
68
69 _____
70
71
72 .. class:: infomark
73
74 **Output**
75
76 - Rebuilt all-heavy atom PDB file
77
78 ]]></help>
79 <citations>
80 <citation type="doi">10.1002/jcc.20906</citation>
81 </citations>
82 </tool>
83