Mercurial > repos > jay > pdaug_tsvtofasta

comparison PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.xml @ 6:391e7e836fe9 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit 45ebf32dcaa1eed91670d3a2491f9cf3dfb535ef"
author jay
date Tue, 12 Jan 2021 18:40:09 +0000
parents 87b77f2ddb0c
children e9fa3b6346e3
comparison
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5:f93187136dfb 6:391e7e836fe9
1 <tool id="pdaug_tsvtofasta" name="PDAUG TSVtoFASTA" version="0.1.0"> 1 <tool id="pdaug_tsvtofasta" name="PDAUG TSVtoFASTA" version="0.1.0">
2 2
3 <description>Converts tabular peptide sequence data into fasta format</description> 3 <description>Converts tabular peptide sequence data into fasta format</description>
4 4
5 <requirements> 5 <requirements>
6 <requirement type="package" version="0.24.2">pandas</requirement> 6 <requirement type="package" version="1.2.0">pandas</requirement>
7 <requirement type="package" version="4.1.2">modlamp</requirement>
8 </requirements> 7 </requirements>
9 <stdio> 8 <stdio>
10 <exit_code range="1" level="fatal" /> 9 <exit_code range="1" level="fatal" />
11 </stdio> 10 </stdio>
12 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
13 12
14 python '$__tool_directory__/PDAUG_TSVtoFASTA.py' -I '$InFile' -M '$Method' 13 python '$__tool_directory__/PDAUG_TSVtoFASTA.py' -I '$infile' -P '$peps'
15 14
16 #if $Method == 'WithClassLabel' 15 #if $selmethod.method == 'withlabel'
17 -P '$OutFile1' 16 #if $selmethod.advancefeature.columnselect == 'advancefeature'
18 -N '$OutFile2' 17 --ClmPepID $selmethod.advancefeature.clmname
19 #end if 18 #end if
19 --SlcClassLabel '$selmethod.classlabel'
20 -M '$selmethod.method'
21 -F '$output2'
22 -S '$output3'
23 #end if
20 24
21 #if $Method == 'NoClassLabel' 25 #if $selmethod.method == 'withoutlabel'
22 -O '$OutFile3' 26 #if $selmethod.advancefeature.columnselect == 'advancefeature'
23 #end if 27 --ClmPepID $selmethod.advancefeature.clmname
24 28 #end if
29 -M '$selmethod.method'
30 -O '$output1'
31 #end if
32
33 &&
34
35 ls
36
25 ]]></command> 37 ]]></command>
26 38
27 <inputs> 39 <inputs>
28 <param name="InFile" type="data" label="Input file" format="tabular" argument= "--InFile1" help="Input tabular file"/> 40 <param name="infile" type="data" label="Peptide data" format="tabular" argument= "--InFile1" help="Input tabular file"/>
29 <param name="Method" type="select" label="Data conversion" argument="--Method" help="Split file if class labels are present" > 41 <param name="peps" type="text" label="Peptide Column" format="tabular" argument= "--InFile1" help="Input tabular file"/>
30 <option value="WithClassLabel"> WithClassLabel </option> 42
31 <option value="NoClassLabel" selected="true" > NoClassLabel </option> 43 <conditional name='selmethod' >
32 </param> 44 <param name="method" type="select" label="Method to convert data" argument="--Method" help="Split file if class labels are present" >
45 <option value="withoutlabel"> Convert Without Split </option>
46 <option value="withlabel" selected="true" >Split Data By Class Label</option>
47 </param>
48
49 <when value="withlabel">
50 <param name="classlabel" type="text" label="Column with the class label" value="Class_label" argument= "--SlcClassLabel" help="Select Class Label"/>
51
52 <conditional name='advancefeature' >
53 <param name="columnselect" type="select" label="Peptide ID Column" argument="--Method" help="Split file if class labels are present" >
54 <option value="advancefeature" > Add Peptide ID Column Name </option>
55 <option value="normalfeature" selected="true"> No Peptide ID Column </option>
56 </param>
57
58 <when value="advancefeature">
59 <param name="clmname" type="text" label="Column name with peptide IDs" argument= "--ClmPepID" help="Select Peptide ID Column"/>
60 </when>
61 </conditional>
62 </when>
63
64 <when value="withoutlabel">
65 <conditional name='advancefeature' >
66 <param name="columnselect" type="select" label="Column name with peptide IDs" argument="--Method" help="Split file if class labels are present" >
67 <option value="advancefeature" > Add Peptide ID Column Name </option>
68 <option value="normalfeature" selected="true"> No Peptide ID Column </option>
69 </param>
70
71 <when value="advancefeature">
72 <param name="clmname" type="text" label="Select Peptide ID Column" argument= "--ClmPepID" help="Select Peptide ID Column"/>
73 </when>
74
75 </conditional>
76 </when>
77 </conditional>
33 </inputs> 78 </inputs>
34 79
35 <outputs> 80 <outputs>
36 <data name='OutFile1' format='fasta' label="${tool.name} on $on_string - first (fasta)" > 81 <data name='output1' format='fasta' label="${tool.name} on $on_string - first (fasta)" >
37 <filter>Method == "WithClassLabel"</filter> 82 <filter>selmethod['method'] == "withoutlabel"</filter>
38 </data> 83 </data>
39 84
40 <data name='OutFile2' format='fasta' label="${tool.name} on $on_string - second (fasta)"> 85 <data name='output2' format='fasta' label="${tool.name} on $on_string - second (fasta)">
41 <filter>Method == "WithClassLabel"</filter> 86 <filter>selmethod['method'] == "withlabel"</filter>
42 </data> 87 </data>
43 88
44 <data name='OutFile3' format='fasta' label="${tool.name} on $on_string - (fasta)" > 89 <data name='output3' format='fasta' label="${tool.name} on $on_string - (fasta)" >
45 <filter>Method == "NoClassLabel"</filter> 90 <filter>selmethod['method'] == "withlabel"</filter>
46 </data> 91 </data>
47 </outputs> 92 </outputs>
93
48 <tests> 94 <tests>
95
49 <test> 96 <test>
50 <param name="InFile" value="test1.tsv"/> 97 <param name="infile" value="test.tsv"/>
51 <param name="Method" value="WithClassLabel"/> 98 <param name="method" value="withoutlabel" />
52 <output name="OutFile1" file="test1/FirstDataFile.fasta"/> 99 <param name="peps" value="Peptides" />
53 <output name="OutFile2" file="test1/SecondDataFile.fasta"/> 100 <param name="output2" file="out.fasta" />
54 </test> 101 </test>
102
55 <test> 103 <test>
56 <param name="InFile" value="test2.tsv"/> 104 <param name="infile" value="test.tsv"/>
57 <param name="Method" value="NoClassLabel"/> 105 <param name="peps" value="Peptides" />
58 <output name="OutFile3" file="test2/Out.fasta"/> 106 <param name="output2" file="1.fasta" />
107 <param name="output3" file="2.fasta" />
59 </test> 108 </test>
109
60 </tests> 110 </tests>
61 <help><![CDATA[ 111 <help><![CDATA[
62 .. class:: infomark 112 .. class:: infomark
63 113
64 **What it does** 114 **What it does**
66 This tool converts tabular files into fasta file and split fasta file on the basis of the class label. 116 This tool converts tabular files into fasta file and split fasta file on the basis of the class label.
67 117
68 ----- 118 -----
69 119
70 **Inputs** 120 **Inputs**
71 * **--InFile** Takes input as Tabular file with or without label. 121 * **Method to convert data** Converts tabular data into fasta with or without splitting based on the availability of class labels.
122
123 * **Column with the class label** Enter the column name with the class labels.
124
125 * **Peptide data** Enter the column name with peptides.
126
127 * **Peptide ID Column** Enter the column name with peptide IDs.
72 128
73 ----- 129 -----
74 130
75 **Outputs** 131 **Outputs**
76 * Returns fasta file.]]></help> 132 * Returns fasta file.]]></help>