|
15
|
1 <tool id="ConvertTranscriptFile" name="convert transcript file">
|
|
6
|
2 <description>Convert a file from a format to another.</description>
|
|
|
3 <command interpreter="python"> ../Java/Python/convertTranscriptFile.py -i $inputFormatType.inputFileName
|
|
|
4 #if $inputFormatType.FormatInputFileName == 'gff3':
|
|
|
5 -f gff3
|
|
|
6 #elif $inputFormatType.FormatInputFileName == 'bed':
|
|
|
7 -f bed
|
|
|
8 #elif $inputFormatType.FormatInputFileName == 'bam':
|
|
|
9 -f blast
|
|
|
10 #elif $inputFormatType.FormatInputFileName == 'sam':
|
|
|
11 -f sam
|
|
|
12 #elif $inputFormatType.FormatInputFileName == 'gtf':
|
|
|
13 -f gtf
|
|
|
14 #end if
|
|
|
15
|
|
|
16 -g $outputFormatType.outFormat
|
|
|
17
|
|
|
18 -n $name
|
|
|
19 $strand
|
|
|
20 -o $outputFile
|
|
|
21
|
|
|
22 </command>
|
|
|
23 <inputs>
|
|
|
24 <conditional name="inputFormatType">
|
|
|
25 <param name="FormatInputFileName" type="select" label="Input File Format">
|
|
|
26 <option value="gff3">GFF3</option>
|
|
|
27 <option value="bed">BED</option>
|
|
|
28 <option value="bam">BAM</option>
|
|
|
29 <option value="sam">SAM</option>
|
|
|
30 <option value="gtf">GTF</option>
|
|
|
31 </param>
|
|
|
32 <when value="gff3">
|
|
|
33 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
|
|
|
34 </when>
|
|
|
35 <when value="bed">
|
|
|
36 <param name="inputFileName" format="bed" type="data" label="Input File"/>
|
|
|
37 </when>
|
|
|
38 <when value="bam">
|
|
|
39 <param name="inputFileName" format="bam" type="data" label="Input File"/>
|
|
|
40 </when>
|
|
|
41 <when value="sam">
|
|
|
42 <param name="inputFileName" format="sam" type="data" label="Input File"/>
|
|
|
43 </when>
|
|
|
44 <when value="gtf">
|
|
|
45 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
|
|
|
46 </when>
|
|
|
47 </conditional>
|
|
|
48
|
|
|
49
|
|
|
50 <conditional name="outputFormatType">
|
|
|
51 <param name="outFormat" type="select" label="Please choose the format that you want to convert to (corresponding to your input file format).">
|
|
|
52 <option value="gff3">GFF3</option>
|
|
|
53 <option value="bed">BED</option>
|
|
|
54 <option value="wig">WIG</option>
|
|
|
55 <option value="sam">SAM</option>
|
|
|
56 <option value="csv">CSV</option>
|
|
|
57 <option value="gtf">GTF</option>
|
|
|
58 </param>
|
|
|
59 <when value="gff3">
|
|
|
60 </when>
|
|
|
61 <when value="bed">
|
|
|
62 </when>
|
|
|
63 <when value="wig">
|
|
|
64 </when>
|
|
|
65 <when value="sam">
|
|
|
66 </when>
|
|
|
67 <when value="csv">
|
|
|
68 </when>
|
|
|
69 <when value="gtf">
|
|
|
70 </when>
|
|
|
71 </conditional>
|
|
|
72
|
|
|
73 <param name="name" type="text" value="SMART" label="name for the transcripts"/>
|
|
|
74
|
|
|
75 <param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/>
|
|
|
76
|
|
|
77 </inputs>
|
|
|
78
|
|
|
79 <outputs>
|
|
|
80 <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat">
|
|
|
81 <change_format>
|
|
|
82 <when input="outputFormatType.outFormat" value="bed" format="bed" />
|
|
15
|
83 <when input="outputFormatType.outFormat" value="gff" format="gff" />
|
|
6
|
84 <when input="outputFormatType.outFormat" value="wig" format="wig" />
|
|
|
85 <when input="outputFormatType.outFormat" value="sam" format="sam" />
|
|
|
86 <when input="outputFormatType.outFormat" value="csv" format="csv" />
|
|
|
87 <when input="outputFormatType.outFormat" value="gtf" format="gtf" />
|
|
|
88 </change_format>
|
|
|
89 </data>
|
|
|
90 </outputs>
|
|
|
91
|
|
|
92 <help>
|
|
15
|
93 Simple conversion tool.
|
|
6
|
94 </help>
|
|
|
95 </tool>
|
