Mercurial > repos > jay > pdaug_peptide_ngrams

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit edb37634e419f75dd66292e712de51278746d883"
author jay
date Wed, 30 Dec 2020 03:06:50 +0000
parents 7557b48b2872
children
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1 <tool id="pdaug_peptide_ngrams" name="PDAUG Peptide Ngrams" version="0.1.0" python_template_version="2.7">
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2 <description>Counts n-grams in the entire sequence set and fitting their distribution with the power-law distribution (Zipf’s law)</description>
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4 <requirements>
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5 <requirement type="package" version="2.7.18">python</requirement>
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6 <requirement type="package" version="1.4.6">powerlaw</requirement>
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7 <requirement type="package" version="0.2.4">quantiprot</requirement>
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8 </requirements>
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10 <command detect_errors="exit_code"><![CDATA[
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12 python2 '$__tool_directory__/PDAUG_Peptide_Ngrams.py' -f1 '$fasta1' -f2 '$fasta2' --OutFile 'out.png'
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14 ]]></command>
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16 <inputs>
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17 <param name="fasta1" type="data" format="fasta" label="First fasta file" argument= "--fasta1" help="First fasta file"/>
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18 <param name="fasta2" type="data" format="fasta" label="Second fasta file" argument= "--fasta2" help="First fasta file"/>
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19 </inputs>
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21 <outputs>
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22 <data name='output2' format='png' label="${tool.name} on $on_string - (PNG)" from_work_dir="out.png"/>
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23 </outputs>
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25 <tests>
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26 <test>
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27 <param name="fasta1" value="test1.fasta"/>
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28 <param name="fasta2" value="test2.fasta"/>
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29 <output name="output2" file="out.png"/>
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30 </test>
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31 </tests>
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33 <help><![CDATA[
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34 .. class:: infomark
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36 **What it does**
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38 This tool counts n-grams in the entire peptide sequence set and fitting their distribution with the power-law distribution (Zipf’s law) and plot the results.
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40 -----
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42 **Inputs**
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43 * **--InFile** Takes fasta file as input with peptide sequences.
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45 -----
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47 **Outputs**
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48 * Returns html report 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 <citation type="bibtex">
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62 @article{konopka_marciniak_dyrka_2017,
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63 title={Quantiprot - a Python package for quantitative analysis of protein sequences},
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64 volume={18},
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65 DOI={10.1186/s12859-017-1751-4},
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66 number={1},
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67 journal={BMC Bioinformatics},
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68 author={Konopka, Bogumił M. and Marciniak, Marta and Dyrka, Witold},
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69 year={2017}
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70 }
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71 </citation>
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72 </citations>
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73 </tool>
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