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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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212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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1 <tool id="pulchra" name="PULCHRA recontruction of all atom proteins" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="22.05">
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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2 <description>from reduced representations</description>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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3 <macros>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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4 <token name="@TOOL_VERSION@">3.06</token>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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5 <token name="@GALAXY_VERSION@">0</token>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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6 </macros>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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7 <requirements>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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8 <requirement type="package" version="@TOOL_VERSION@">pulchra</requirement>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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9 </requirements>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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10 <command detect_errors="exit_code"><![CDATA[
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12 ln -s '$structure_input' ./structure_input.${structure_input.ext} &&
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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13 pulchra
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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15 ##inputs
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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16 ./structure_input.${structure_input.ext}
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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17 $skip_sidechain
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19 -v
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21 ]]></command>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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22 <inputs>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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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."/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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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."/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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25 </inputs>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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26 <outputs>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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27 <data name="output1" format="pdb" from_work_dir="*.rebuilt.pdb" label="PULCHRA rebuilt pdb file on ${on_string}"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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28 </outputs>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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29 <tests>
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30 <test>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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31 <param name="structure_input" value="model.pdb"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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32 <output name="output1" ftype="pdb">
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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33 <assert_contents>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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34 <has_text text="ATOM 1 N PHE 1 16.391 50.300 23.791"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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35 <has_text text="ATOM 12 N LEU 2 14.039 47.806 25.433"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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36 <has_text text="ATOM 20 N VAL 3 10.836 47.425 24.846"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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37 </assert_contents>
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38 </output>
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39 </test>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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40 <test>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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41 <param name="structure_input" value="model.pdb"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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42 <param name="skip_sidechain" value="true" />
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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43 <output name="output1" ftype="pdb">
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44 <assert_contents>
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45 <has_text text="ATOM 1 N PHE 1 16.391 50.300 23.791"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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46 <has_text text="ATOM 12 O VAL 3 8.414 45.957 24.602"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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47 <has_text text="ATOM 20 O MET 5 1.327 47.936 26.198"/>
212ccef97a3a planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit 3c6707a93f43fa435d290faaec728d730d8289a5
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48 </assert_contents>
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49 </output>
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50 </test>
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51 </tests>
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52 <help><![CDATA[
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54 .. class:: infomark
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56 **What it does**
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58 This tool rebuilds a protein structure from reduced representations (alpha carbon trace), producing an all-heavy atom PDB file.
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59
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60 _____
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62 .. class:: infomark
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64 **Input**
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66 - Alpha carbon trace PDB file
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69 _____
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72 .. class:: infomark
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74 **Output**
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76 - Rebuilt all-heavy atom PDB file
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78 ]]></help>
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79 <citations>
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80 <citation type="doi">10.1002/jcc.20906</citation>
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81 </citations>
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82 </tool>
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83