Mercurial > repos > chemteam > biopdb_align_and_rmsd

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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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6352d6dd74e2 planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit b90c5ab8f15397299e8baf2e903a9911c44d7668
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1 <tool id="biopdb_align_and_rmsd" name="Align structures and compute relative RMSDs" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@">
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2 <description>using Biopython</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">1.79</token>
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5 <token name="@GALAXY_VERSION@">0</token>
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="1.79">biopython</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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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
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14 ]]></command>
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15 <inputs>
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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" />
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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"/>
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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."/>
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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."/>
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20 </inputs>
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22 <outputs>
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23 <data name="aligned_structure" format="pdb" label="PDB file of the aligned structure ${on_string}"></data>
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24 <data name="rmsd_out" format="tabular" label="RMSD of the aligned structure ${on_string}"></data>
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25 </outputs>
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27 <tests>
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28 <test>
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29 <param name="start_residue" value="1" />
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30 <param name="end_residue" value="15"/>
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31 <param name="ref_structure" value="reference_structure.pdb" />
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32 <param name="model" value="model.pdb" />
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33 <output name="aligned_structure" ftype="pdb">
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34 <assert_contents>
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35 <has_text text="ATOM 5 CA ARG 1 6.016 6.125 -0.066 1.00 0.00 C"/>
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36 <has_text text="ATOM 29 CA HIS 2 4.909 5.168 3.434 1.00 0.00 C"/>
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37 <has_text text="ATOM 46 CA TYR 3 7.956 4.326 5.551 1.00 0.00 C"/>
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38 </assert_contents>
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39 </output>
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40 <output name="rmsd_out" ftype="tabular">
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41 <assert_contents>
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42 <has_text text="5.492787964992471"/>
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43 </assert_contents>
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44 </output>
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45 </test>
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46 </tests>
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47
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48 <help><![CDATA[
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49 Tool to align protein structures and compute relative RMSDs, using the alpha carbon coordinates.
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50
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51 .. class:: infomark
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53 **Inputs**
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54
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55 PDB files for the reference structure, a model, as well as the starting and ending residues for the alignment.
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56
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57 .. class:: infomark
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58
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59 **Outputs**
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60
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61 1) Tabular file containing the RMSD.
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62 2) PDB file of the model with the aligned coordinates.
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63
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64
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65 ]]></help>
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66 <citations>
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67 <citation type="doi">https://doi.org/10.1093/bioinformatics/btp163</citation>
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68 </citations>
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69 </tool>