Mercurial > repos > jay > pdaug_peptide_structure_builder
annotate PDAUG_Peptide_Structure_Builder/PDAUG_Peptide_Structure_Builder.xml @ 0:0118cc553f3b draft
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
author | jay |
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date | Wed, 28 Oct 2020 02:04:41 +0000 |
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0118cc553f3b
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit a9bd83f6a1afa6338cb6e4358b63ebff5bed155e"
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1 <tool id="pdaug_peptide_structure_builder" name="PDAUG Peptide Structure Builder" version="0.1.0"> |
0118cc553f3b
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2 <description>Builds 3D structures of peptide sequences up to 3 amino acid </description> |
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3 |
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4 <requirements> |
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5 <requirement type="package" version="0.24.2">pandas</requirement> |
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6 <requirement type="package" version="1.0.1">fragbuilder</requirement> |
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7 </requirements> |
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8 <stdio> |
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9 <exit_code range="1" level="fatal" /> |
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10 </stdio> |
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11 <command detect_errors="exit_code"><![CDATA[ |
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12 python '$__tool_directory__/PDAUG_Peptide_Structure_Builder.py' -p '$input1' |
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13 |
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14 ]]></command> |
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15 |
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16 <inputs> |
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17 <param name="input1" type="data" format="fasta" argument= "--pep" label="Input file" help="Input fasta file with peptides"/> |
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18 </inputs> |
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19 |
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20 <outputs> |
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21 <collection name="output" type="list" label="${tool.name} on $on_string - (PDB)"> |
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22 <discover_datasets pattern="__name_and_ext__" format='pdb' directory="DataFile" /> |
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23 </collection> |
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24 </outputs> |
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25 |
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26 <tests> |
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27 <test> |
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28 <param name="input1" value="test.fasta"/> |
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29 <output_collection name="output" type="list" > |
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30 <element name="GLF" file="DataFile/GLF.pdb" lines_diff="102" /> |
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31 </output_collection> |
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32 </test> |
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33 </tests> |
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34 <help><![CDATA[ |
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35 .. class:: infomark |
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36 |
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37 **What it does** |
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38 |
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39 This tool generates 3D structures of peptide sequences up to three amino acids that can be utilizedĀ for peptide docking with macromolecules with tools such as Autodock Vina. |
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40 |
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41 ----- |
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42 |
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43 **Inputs** |
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44 * **--InFile** A fasta file witth the peptide sequences. |
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45 |
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46 ----- |
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47 |
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48 **Outputs** |
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49 * Return collection of peptides with 3D structure.]]></help> |
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50 <citations> |
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51 <citation type="bibtex"> |
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52 @misc{PDAUGGITHUB, |
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53 author = {Joshi, Jayadev and Blankenberg, Daniel}, |
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54 year = {2020}, |
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55 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling}, |
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56 publisher = {GitHub}, |
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57 journal = {GitHub repository}, |
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58 url = |
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59 {https://github.com/jaidevjoshi83/pdaug.git}, |
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60 } |
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61 </citation> |
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62 |
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63 <citation type="bibtex"> |
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64 @article{christensen_hamelryck_jensen_2013, |
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65 title={FragBuilder: An efficient Python library to setup quantum chemistry calculations on peptides models}, DOI={10.7287/peerj.preprints.169v2}, |
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66 author={Christensen, Anders Steen and Hamelryck, Thomas and Jensen, Jan H}, |
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67 year={2013}} |
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68 } |
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69 </citation> |
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70 </citations> |
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71 </tool> |