Mercurial > repos > jay > pdaug_tsvtofasta

annotate PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.xml @ 5:f93187136dfb draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit edb37634e419f75dd66292e712de51278746d883"
author jay
date Wed, 30 Dec 2020 02:42:16 +0000
parents 87b77f2ddb0c
children 391e7e836fe9
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1 <tool id="pdaug_tsvtofasta" name="PDAUG TSVtoFASTA" version="0.1.0">
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3 <description>Converts tabular peptide sequence data into fasta format</description>
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5 <requirements>
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6 <requirement type="package" version="0.24.2">pandas</requirement>
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7 <requirement type="package" version="4.1.2">modlamp</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1" level="fatal" />
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11 </stdio>
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12 <command detect_errors="exit_code"><![CDATA[
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14 python '$__tool_directory__/PDAUG_TSVtoFASTA.py' -I '$InFile' -M '$Method'
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16 #if $Method == 'WithClassLabel'
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17 -P '$OutFile1'
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18 -N '$OutFile2'
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19 #end if
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21 #if $Method == 'NoClassLabel'
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22 -O '$OutFile3'
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23 #end if
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25 ]]></command>
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27 <inputs>
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28 <param name="InFile" type="data" label="Input file" format="tabular" argument= "--InFile1" help="Input tabular file"/>
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29 <param name="Method" type="select" label="Data conversion" argument="--Method" help="Split file if class labels are present" >
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30 <option value="WithClassLabel"> WithClassLabel </option>
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31 <option value="NoClassLabel" selected="true" > NoClassLabel </option>
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32 </param>
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33 </inputs>
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35 <outputs>
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36 <data name='OutFile1' format='fasta' label="${tool.name} on $on_string - first (fasta)" >
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37 <filter>Method == "WithClassLabel"</filter>
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38 </data>
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39
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40 <data name='OutFile2' format='fasta' label="${tool.name} on $on_string - second (fasta)">
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41 <filter>Method == "WithClassLabel"</filter>
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42 </data>
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43
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44 <data name='OutFile3' format='fasta' label="${tool.name} on $on_string - (fasta)" >
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45 <filter>Method == "NoClassLabel"</filter>
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46 </data>
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47 </outputs>
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48 <tests>
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49 <test>
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50 <param name="InFile" value="test1.tsv"/>
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51 <param name="Method" value="WithClassLabel"/>
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52 <output name="OutFile1" file="test1/FirstDataFile.fasta"/>
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53 <output name="OutFile2" file="test1/SecondDataFile.fasta"/>
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54 </test>
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55 <test>
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56 <param name="InFile" value="test2.tsv"/>
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57 <param name="Method" value="NoClassLabel"/>
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58 <output name="OutFile3" file="test2/Out.fasta"/>
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59 </test>
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60 </tests>
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61 <help><![CDATA[
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62 .. class:: infomark
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63
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64 **What it does**
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65
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66 This tool converts tabular files into fasta file and split fasta file on the basis of the class label.
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67
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68 -----
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69
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70 **Inputs**
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71 * **--InFile** Takes input as Tabular file with or without label.
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72
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73 -----
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74
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75 **Outputs**
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76 * Returns fasta file.]]></help>
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77 <citations>
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78 <citation type="bibtex">
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79 @misc{PDAUGGITHUB,
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80 author = {Joshi, Jayadev and Blankenberg, Daniel},
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81 year = {2020},
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82 title ={PDAUG - a Galaxy based toolset for peptide library analysis, visualization, and machine learning modeling},
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83 publisher = {GitHub},
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84 journal = {GitHub repository},
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85 url =
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86 {https://github.com/jaidevjoshi83/pdaug.git},
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87 }
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88 </citation>
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89 </citations>
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90 </tool>
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91
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92
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93