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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
author jay
date Tue, 12 Jan 2021 19:21:13 +0000
parents 0fc091fb7e8f
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1 <tool id="pdaug_peptide_core_descriptors" name="PDAUG Peptide Core Descriptors" version="0.1.0">
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2 <description>Calculates core descriptors of peptide sequences</description>
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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="4.2.1">modlamp</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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13 python '$__tool_directory__/PDAUG_Peptide_Core_Descriptors.py' -I '$input1' -N '$ngrams' -O '$output1'
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15 ]]></command>
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17 <inputs>
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18 <param name="input1" type="data" label="Input file" format="fasta" argument= "--InFile1" help="Input fasta file with peptides"/>
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19 <param name="ngrams" type="integer" label="ngram size" value="3" help="ngram size"/>
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20 </inputs>
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22 <outputs>
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23 <data name='output1' format='tabular' label="${tool.name} on $on_string - n-grams (tabular)" />
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24 </outputs>
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25 <tests>
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26 <test>
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27 <param name="input1" value="test.fasta"/>
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28 <param name="ngrams" value="3" />
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29 <output name="output1" file="Out.tsv"/>
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30 </test>
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31 </tests>
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32 <help><![CDATA[
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33 .. class:: infomark
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34
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35 **What it does**
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37 Calculates the frequency of ngrames in peptide sequences.
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39 -----
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41 **Inputs**
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42 * **--InFile** Fasta file with peptide sequences as Input File.
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43 * **--Ngrams** Integer value of Ngrams frequency to be calculated.
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45 -----
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47 **Outputs**
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48 * **--OutFile** Returns tabular data file. ]]></help>
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49 <citations>
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50 <citation type="bibtex">
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51 @misc{PDAUGGITHUB,
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52 author = {Joshi, Jayadev and Blankenberg, Daniel},
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53 year = {2020},
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54 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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55 publisher = {GitHub},
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56 journal = {GitHub repository},
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57 url =
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58 {https://github.com/jaidevjoshi83/pdaug.git},
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59 }
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60 </citation>
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61
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62 <citation type="bibtex">
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63 @article{müller_gabernet_hiss_schneider_2017,
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64 title={modlAMP: Python for antimicrobial peptides},
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65 volume={33},
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66 DOI={10.1093/bioinformatics/btx285},
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67 number={17},
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68 journal={Bioinformatics},
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69 author={Müller, Alex T and Gabernet, Gisela and Hiss, Jan A and Schneider, Gisbert},
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70 year={2017},
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71 pages={2753–2755}
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72 }
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73 </citation>
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74 </citations>
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75 </tool>
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