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comparison smart_toolShed/SMART/galaxy/CleanTranscriptFile.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="CleanTranscriptFile" name="Clean Transcript File">
2 <description> Clean a transcript file so that it is useable for S-MART.</description>
3 <command interpreter="python"> ../Java/Python/CleanTranscriptFile.py -i $formatType.inputFileName
4 #if $formatType.FormatInputFileName == 'gff':
5 -f gff
6 #elif $formatType.FormatInputFileName == 'gtf':
7 -f gtf
8 #elif $formatType.FormatInputFileName == 'gff3':
9 -f gff3
10 #end if
11 #if $optionType.type == 'Yes':
12 -t $optionType.value
13 #end if
14 -o $outputFile
15 </command>
16
17 <inputs>
18 <conditional name="formatType">
19 <param name="FormatInputFileName" type="select" label="Input File Format">
20 <option value="gff">gff</option>
21 <option value="gtf">gtf</option>
22 <option value="gff3">gff3</option>
23 </param>
24 <when value="gff">
25 <param name="inputFileName" format="gff" type="data" label="Input File"/>
26 </when>
27 <when value="gtf">
28 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
29 </when>
30 <when value="gff3">
31 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
32 </when>
33 </conditional>
34
35 <conditional name="optionType">
36
37 <param name="type" type="select" label="You can choose the tag that you are interested in, like tRNA,rRNA,ncRNA,CDS,exon, etc." help="Name of the types you want to keep in GFF/GTF (list separated by commas)">
38 <option value="Yes">Yes</option>
39 <option value="No" selected="true">No</option>
40 </param>
41 <when value="Yes">
42 <param name="value" type="text" value="tRNA,rRNA,ncRNA,CDS,exon"/>
43 </when>
44 <when value="No">
45 </when>
46 </conditional>
47
48 </inputs>
49
50
51 <outputs>
52 <data name="outputFile" format="gtf">
53 <change_format>
54 <when input="formatType.FormatInputFileName" value="gff" format="gff" />
55 <when input="formatType.FormatInputFileName" value="gff3" format="gff3" />
56 </change_format>
57 </data>
58
59 </outputs>
60 </tool>