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planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit b90c5ab8f15397299e8baf2e903a9911c44d7668
author chemteam
date Thu, 06 Jun 2024 07:09:14 +0000
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1 <tool id="biopdb_align_and_rmsd" name="Align structures and compute relative RMSDs" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
2 <description>using Biopython</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.79</token>
5 <token name="@GALAXY_VERSION@">0</token>
6 </macros>
7 <requirements>
8 <requirement type="package" version="1.79">biopython</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11
12 python3 '$__tool_directory__/BioPDB_align_and_rmsd.py' --start_residue '$start_residue' --end_residue '$end_residue' --ref_structure '$ref_structure' --model '$model' --aligned_structure '$aligned_structure' --rmsd '$rmsd_out' >> verbose.txt 2>&1
13
14 ]]></command>
15 <inputs>
16 <param name="start_residue" type="integer" label="Starting residue to align" help="This should be the same starting residue for the model and reference structure." value="0" />
17 <param name="end_residue" type="integer" label="Ending residue to align" help="This should be the same ending residue for the model and reference structure." value="0"/>
18 <param name="ref_structure" type="data" format="pdb" label="Reference structure" help="This can be an experimental structure or another model you wish to compare against."/>
19 <param name="model" type="data" format="pdb" label="Sample structure" help="This is the structure you wish to align and compute a relative RMSD for. This can also be an experimental structure or another model."/>
20 </inputs>
21
22 <outputs>
23 <data name="aligned_structure" format="pdb" label="PDB file of the aligned structure ${on_string}"></data>
24 <data name="rmsd_out" format="tabular" label="RMSD of the aligned structure ${on_string}"></data>
25 </outputs>
26
27 <tests>
28 <test>
29 <param name="start_residue" value="1" />
30 <param name="end_residue" value="15"/>
31 <param name="ref_structure" value="reference_structure.pdb" />
32 <param name="model" value="model.pdb" />
33 <output name="aligned_structure" ftype="pdb">
34 <assert_contents>
35 <has_text text="ATOM 5 CA ARG 1 6.016 6.125 -0.066 1.00 0.00 C"/>
36 <has_text text="ATOM 29 CA HIS 2 4.909 5.168 3.434 1.00 0.00 C"/>
37 <has_text text="ATOM 46 CA TYR 3 7.956 4.326 5.551 1.00 0.00 C"/>
38 </assert_contents>
39 </output>
40 <output name="rmsd_out" ftype="tabular">
41 <assert_contents>
42 <has_text text="5.492787964992471"/>
43 </assert_contents>
44 </output>
45 </test>
46 </tests>
47
48 <help><![CDATA[
49 Tool to align protein structures and compute relative RMSDs, using the alpha carbon coordinates.
50
51 .. class:: infomark
52
53 **Inputs**
54
55 PDB files for the reference structure, a model, as well as the starting and ending residues for the alignment.
56
57 .. class:: infomark
58
59 **Outputs**
60
61 1) Tabular file containing the RMSD.
62 2) PDB file of the model with the aligned coordinates.
63
64
65 ]]></help>
66 <citations>
67 <citation type="doi">https://doi.org/10.1093/bioinformatics/btp163</citation>
68 </citations>
69 </tool>