Mercurial > repos > jay > pdaug_peptide_core_descriptors
annotate PDAUG_Peptide_Core_Descriptors/PDAUG_Peptide_Core_Descriptors.xml @ 8:c8d90efc885d draft default tip
"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit d396d7ff89705cc0dd626ed32c45a9f4029b1b05"
author | jay |
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date | Wed, 12 Jan 2022 20:09:08 +0000 |
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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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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="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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12 |
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13 python '$__tool_directory__/PDAUG_Peptide_Core_Descriptors.py' -I '$input1' -N '$ngrams' -O '$output1' |
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14 |
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15 ]]></command> |
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16 |
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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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21 |
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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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36 |
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37 Calculates the frequency of ngrames in peptide sequences. |
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38 |
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39 ----- |
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40 |
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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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44 |
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45 ----- |
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46 |
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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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76 |
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77 |
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78 |