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comparison SMART/galaxy/ConvertTranscriptFile.xml @ 38:2c0c0a89fad7

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author m-zytnicki
date Thu, 02 May 2013 09:56:47 -0400
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children 97aa2e42bfdf
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37:d22fadc825e3 38:2c0c0a89fad7
1 <tool id="ConvertTranscriptFile" name="convert transcript file">
2 <description>Convert a file from a format to another.</description>
3 <requirements>
4 <requirement type="set_environment">PYTHONPATH</requirement>
5 </requirements>
6 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName
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 $outputFile
24
25 </command>
26 <inputs>
27 <conditional name="inputFormatType">
28 <param name="FormatInputFileName" type="select" label="Input File Format">
29 <option value="gff3">GFF3</option>
30 <option value="bed">BED</option>
31 <option value="bam">BAM</option>
32 <option value="sam">SAM</option>
33 <option value="gtf">GTF</option>
34 </param>
35 <when value="gff3">
36 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
37 </when>
38 <when value="bed">
39 <param name="inputFileName" format="bed" type="data" label="Input File"/>
40 </when>
41 <when value="bam">
42 <param name="inputFileName" format="bam" type="data" label="Input File"/>
43 </when>
44 <when value="sam">
45 <param name="inputFileName" format="sam" type="data" label="Input File"/>
46 </when>
47 <when value="gtf">
48 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
49 </when>
50 </conditional>
51
52
53 <conditional name="outputFormatType">
54 <param name="outFormat" type="select" label="Please choose the format that you want to convert to (corresponding to your input file format).">
55 <option value="gff3">GFF3</option>
56 <option value="bed">BED</option>
57 <option value="wig">WIG</option>
58 <option value="sam">SAM</option>
59 <option value="csv">CSV</option>
60 <option value="gtf">GTF</option>
61 </param>
62 <when value="gff3">
63 </when>
64 <when value="bed">
65 </when>
66 <when value="wig">
67 </when>
68 <when value="sam">
69 </when>
70 <when value="csv">
71 </when>
72 <when value="gtf">
73 </when>
74 </conditional>
75
76 <param name="name" type="text" value="SMART" label="name for the transcripts"/>
77
78 <param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/>
79
80 </inputs>
81
82 <outputs>
83 <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat">
84 <change_format>
85 <when input="outputFormatType.outFormat" value="bed" format="bed" />
86 <when input="outputFormatType.outFormat" value="gff" format="gff" />
87 <when input="outputFormatType.outFormat" value="wig" format="wig" />
88 <when input="outputFormatType.outFormat" value="sam" format="sam" />
89 <when input="outputFormatType.outFormat" value="csv" format="csv" />
90 <when input="outputFormatType.outFormat" value="gtf" format="gtf" />
91 </change_format>
92 </data>
93 </outputs>
94
95 <help>
96 Simple conversion tool.
97 </help>
98 </tool>