Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/ConvertTranscriptFile.xml @ 56:97aa2e42bfdf

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Uploaded
author m-zytnicki
date Wed, 05 Feb 2014 11:51:11 -0500
parents 2c0c0a89fad7
children
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55:2ac71607aa60 56:97aa2e42bfdf
1 <tool id="ConvertTranscriptFile" name="convert transcript file"> 1 <tool id="ConvertTranscriptFile" name="convert transcript file">
2 <description>Convert a file from a format to another.</description> 2 <description>Convert a file from a format to another.</description>
3 <requirements> 3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement> 4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName 6 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName -f $inputFormatType.FormatInputFileName -g $outputFormatType.outFormat -n $name $strand -o $outputFile </command>
7 #if $inputFormatType.FormatInputFileName == 'gff3':
8 -f gff3
9 #elif $inputFormatType.FormatInputFileName == 'bed':
10 -f bed
11 #elif $inputFormatType.FormatInputFileName == 'bam':
12 -f blast
13 #elif $inputFormatType.FormatInputFileName == 'sam':
14 -f sam
15 #elif $inputFormatType.FormatInputFileName == 'gtf':
16 -f gtf
17 #end if
18
19 -g $outputFormatType.outFormat
20
21 -n $name
22 $strand
23 -o $outputFile
24
25 </command>
26 <inputs> 7 <inputs>
27 <conditional name="inputFormatType"> 8 <conditional name="inputFormatType">
28 <param name="FormatInputFileName" type="select" label="Input File Format"> 9 <param name="FormatInputFileName" type="select" label="Input File Format">
29 <option value="gff3">GFF3</option> 10 <option value="gff3">GFF3</option>
30 <option value="bed">BED</option> 11 <option value="bed">BED</option>
12 <option value="sam">SAM</option>
31 <option value="bam">BAM</option> 13 <option value="bam">BAM</option>
32 <option value="sam">SAM</option>
33 <option value="gtf">GTF</option> 14 <option value="gtf">GTF</option>
34 </param> 15 </param>
35 <when value="gff3"> 16 <when value="gff3">
36 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 17 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
37 </when> 18 </when>
38 <when value="bed"> 19 <when value="bed">
39 <param name="inputFileName" format="bed" type="data" label="Input File"/> 20 <param name="inputFileName" format="bed" type="data" label="Input File"/>
40 </when> 21 </when>
22 <when value="sam">
23 <param name="inputFileName" format="sam" type="data" label="Input File"/>
24 </when>
41 <when value="bam"> 25 <when value="bam">
42 <param name="inputFileName" format="bam" type="data" label="Input File"/> 26 <param name="inputFileName" format="bam" type="data" label="Input File"/>
43 </when>
44 <when value="sam">
45 <param name="inputFileName" format="sam" type="data" label="Input File"/>
46 </when> 27 </when>
47 <when value="gtf"> 28 <when value="gtf">
48 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 29 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
49 </when> 30 </when>
50 </conditional> 31 </conditional>