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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 3c91f421d26c8f42cf2671e47db735d2cf69dde8"
author jay
date Tue, 29 Dec 2020 04:08:13 +0000
parents 070fc1da6df7
children
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1 <tool id="pdaug_uversky_plot" name="PDAUG Uversky Plot" version="0.1.0" python_template_version="3.6">
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2 <description>Uversky plot to analyze ordered and disordered proteins</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 python '$__tool_directory__/PDAUG_Uversky_Plot.py' --Fasta1 '$input1' --Fasta2 '$input2' --OutFile 'out.png'
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14 ]]></command>
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16 <inputs>
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17 <param name="input1" type="data" format="fasta" label="First fasta file" argument= "--Fasta1" help="First fasta file with Peptides"/>
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18 <param name="input2" type="data" format="fasta" label="Second fasta file" argument="--Fasta2" help="Second fasta file with Peptides"/>
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19 </inputs>
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21 <outputs>
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22 <data name='output2' format='png' label="${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="input1" value="test1.fasta"/>
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28 <param name="input2" 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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32
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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 plot divides analyze peptide sequences on globular and IDP subsets based on their mean net charge versus mean hydropathy. The line represents the permeable boundary between both subsets.
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40 -----
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42 **Inputs**
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43 * **--Fasta1** The first fasta file.
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44 * **--Fasta2** The second fasta file.
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46 -----
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48 **Outputs**
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49 * Return html file.]]></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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63 <citation type="bibtex">
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64 @article{konopka_marciniak_dyrka_2017,
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65 title={Quantiprot - a Python package for quantitative analysis of protein sequences},
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66 volume={18},
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67 DOI={10.1186/s12859-017-1751-4},
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68 number={1},
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69 journal={BMC Bioinformatics},
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70 author={Konopka, Bogumił M. and Marciniak, Marta and Dyrka, Witold},
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71 year={2017}
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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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