Mercurial > repos > jay > pdaug_tsvtofasta

comparison PDAUG_TSVtoFASTA/PDAUG_TSVtoFASTA.xml @ 8:95c09c06f655 draft

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"planemo upload for repository https://github.com/jaidevjoshi83/pdaug commit ac4353ca5c0ac9ce60df9f4bf160ed08b99fbee3"
author jay
date Thu, 28 Jan 2021 02:47:00 +0000
parents e9fa3b6346e3
children
comparison
equal deleted inserted replaced
7:e9fa3b6346e3 8:95c09c06f655
36 36
37 ]]></command> 37 ]]></command>
38 38
39 <inputs> 39 <inputs>
40 <param name="infile" type="data" label="Peptide data" 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"/>
41 <param name="peps" type="text" label="Peptide Column" format="tabular" argument= "--InFile1" help="Input tabular file"/> 41 <param name="peps" type="text" label="Peptide Column" argument= "--PeptideColumn" help="Peptide Column Name"/>
42 42
43 <conditional name='selmethod' > 43 <conditional name='selmethod' >
44 <param name="method" type="select" label="Method to convert data" argument="--Method" help="Split file if class labels are present" > 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> 45 <option value="withoutlabel"> Convert Without Split </option>
46 <option value="withlabel" selected="true" >Split Data By Class Label</option> 46 <option value="withlabel" selected="true" >Split Data By Class Label</option>
56 </param> 56 </param>
57 57
58 <when value="advancefeature"> 58 <when value="advancefeature">
59 <param name="clmname" type="text" label="Column name with peptide IDs" argument= "--ClmPepID" help="Select Peptide ID Column"/> 59 <param name="clmname" type="text" label="Column name with peptide IDs" argument= "--ClmPepID" help="Select Peptide ID Column"/>
60 </when> 60 </when>
61 <when value="normalfeature"/>
61 </conditional> 62 </conditional>
62 </when> 63 </when>
63 64
64 <when value="withoutlabel"> 65 <when value="withoutlabel">
65 <conditional name='advancefeature' > 66 <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 <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="advancefeature" > Add Peptide ID Column Name </option>
68 <option value="normalfeature" selected="true"> No Peptide ID Column </option> 69 <option value="normalfeature" selected="true"> No Peptide ID Column </option>
69 </param> 70 </param>
70 71
71 <when value="advancefeature"> 72 <when value="advancefeature">
72 <param name="clmname" type="text" label="Select Peptide ID Column" argument= "--ClmPepID" help="Select Peptide ID Column"/> 73 <param name="clmname" type="text" label="Select Peptide ID Column" argument= "--ClmPepID" help="Select Peptide ID Column"/>
73 </when> 74 </when>
75 <when value="normalfeature"/>
74 76
75 </conditional> 77 </conditional>
76 </when> 78 </when>
77 </conditional> 79 </conditional>
78 </inputs> 80 </inputs>
93 95
94 <tests> 96 <tests>
95 97
96 <test> 98 <test>
97 <param name="infile" value="test.tsv"/> 99 <param name="infile" value="test.tsv"/>
98 <param name="method" value="withoutlabel" /> 100 <param name="method" value="withoutlabel" />
99 <param name="peps" value="Peptides" /> 101 <param name="peps" value="Peptides" />
100 <param name="output2" file="out.fasta" /> 102 <output name="output1" file="out.fasta" />
101 </test> 103 </test>
102 104
103 <test> 105 <test>
104 <param name="infile" value="test.tsv"/> 106 <param name="infile" value="test.tsv"/>
107 <param name="method" value="withlabel" />
105 <param name="peps" value="Peptides" /> 108 <param name="peps" value="Peptides" />
106 <param name="output2" file="1.fasta" /> 109 <param name="withlabel" value="Class_label" />
107 <param name="output3" file="2.fasta" /> 110 <output name="output2" file="1.fasta" />
111 <output name="output3" file="2.fasta" />
108 </test> 112 </test>
109 113
110 </tests> 114 </tests>
111 <help><![CDATA[ 115 <help><![CDATA[
112 .. class:: infomark 116 .. class:: infomark