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comparison smart_toolShed/SMART/galaxy/ConvertTranscriptFile.xml @ 0:e0f8dcca02ed

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Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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-1:000000000000 0:e0f8dcca02ed
1 <tool id="ConvertTranscriptFile" name="Convert transcript file">
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 == 'gff2':
9 -f gff2
10 #elif $inputFormatType.FormatInputFileName == 'bam':
11 -f blast
12 #elif $inputFormatType.FormatInputFileName == 'sam':
13 -f sam
14 #elif $inputFormatType.FormatInputFileName == 'gtf':
15 -f gtf
16 #end if
17
18 -g $outputFormatType.outFormat
19 #if $optionSequence.choose == 'Yes':
20 -s $optionSequence.value
21 #end if
22
23
24 -n $name
25 $strand
26 -o $outputFile
27
28 </command>
29 <inputs>
30 <conditional name="inputFormatType">
31 <param name="FormatInputFileName" type="select" label="Input File Format">
32 <option value="gff3">GFF3</option>
33 <option value="bed">BED</option>
34 <option value="gff2">GFF2</option>
35 <option value="bam">BAM</option>
36 <option value="sam">SAM</option>
37 <option value="gtf">GTF</option>
38 </param>
39 <when value="gff3">
40 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
41 </when>
42 <when value="bed">
43 <param name="inputFileName" format="bed" type="data" label="Input File"/>
44 </when>
45 <when value="gff2">
46 <param name="inputFileName" format="gff2" type="data" label="Input File"/>
47 </when>
48 <when value="bam">
49 <param name="inputFileName" format="bam" type="data" label="Input File"/>
50 </when>
51 <when value="sam">
52 <param name="inputFileName" format="sam" type="data" label="Input File"/>
53 </when>
54 <when value="gtf">
55 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
56 </when>
57 </conditional>
58
59
60 <conditional name="outputFormatType">
61 <param name="outFormat" type="select" label="Please choose the format that you want to convert to (corresponding to your input file format).">
62 <option value="gff3">GFF3</option>
63 <option value="bed">BED</option>
64 <option value="gff2">GFF2</option>
65 <option value="wig">WIG</option>
66 <option value="sam">SAM</option>
67 <option value="csv">CSV</option>
68 <option value="gtf">GTF</option>
69 </param>
70 <when value="gff3">
71 </when>
72 <when value="bed">
73 </when>
74 <when value="gff2">
75 </when>
76 <when value="wig">
77 </when>
78 <when value="sam">
79 </when>
80 <when value="csv">
81 </when>
82 <when value="gtf">
83 </when>
84 </conditional>
85
86 <param name="name" type="text" value="SMART" label="name for the transcripts"/>
87
88 <conditional name="optionSequence">
89 <param name="choose" type="select" label="give the corresponding Multi-Fasta file (useful for EMBL format)">
90 <option value="Yes">Yes</option>
91 <option value="No" selected="true">No</option>
92 </param>
93 <when value="Yes">
94 <param name="value" type="data" format="mfa" />
95 </when>
96 <when value="No">
97 </when>
98 </conditional>
99
100 <param name="strand" type="boolean" truevalue="-t" falsevalue="" checked="false" label="consider the 2 strands as different (only useful for writing WIG files)"/>
101
102 </inputs>
103
104 <outputs>
105 <data name="outputFile" format="gff3" label="$inputFormatType.FormatInputFileName to $outputFormatType.outFormat">
106 <change_format>
107 <when input="outputFormatType.outFormat" value="bed" format="bed" />
108 <when input="outputFormatType.outFormat" value="gff2" format="gff2" />
109 <when input="outputFormatType.outFormat" value="wig" format="wig" />
110 <when input="outputFormatType.outFormat" value="sam" format="sam" />
111 <when input="outputFormatType.outFormat" value="csv" format="csv" />
112 <when input="outputFormatType.outFormat" value="gtf" format="gtf" />
113 </change_format>
114 </data>
115 </outputs>
116
117 <help>
118 </help>
119 </tool>