Mercurial > repos > yufei-luo > s_mart
comparison SMART/galaxy/ConvertTranscriptFile.xml @ 56:97aa2e42bfdf
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author | m-zytnicki |
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date | Wed, 05 Feb 2014 11:51:11 -0500 |
parents | 2c0c0a89fad7 |
children |
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55:2ac71607aa60 | 56:97aa2e42bfdf |
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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> |