Mercurial > repos > yufei-luo > s_mart

comparison SMART/galaxy/CollapseReads.xml @ 56:97aa2e42bfdf

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Uploaded
author m-zytnicki
date Wed, 05 Feb 2014 11:51:11 -0500
parents 2c0c0a89fad7
children 1473ab954708
comparison
equal deleted inserted replaced
55:2ac71607aa60 56:97aa2e42bfdf
13 -f gff2 13 -f gff2
14 #elif $formatType.FormatInputFileName == 'gff3': 14 #elif $formatType.FormatInputFileName == 'gff3':
15 -f gff3 15 -f gff3
16 #elif $formatType.FormatInputFileName == 'sam': 16 #elif $formatType.FormatInputFileName == 'sam':
17 -f sam 17 -f sam
18 #elif $formatType.FormatInputFileName == 'bam':
19 -f bam
18 #elif $formatType.FormatInputFileName == 'gtf': 20 #elif $formatType.FormatInputFileName == 'gtf':
19 -f gtf 21 -f gtf
20 #end if 22 #end if
21 -$strand 23 -$strand
22 -o $outputFileGff 24 -o $outputFileGff
28 <option value="bed">bed</option> 30 <option value="bed">bed</option>
29 <option value="gff">gff</option> 31 <option value="gff">gff</option>
30 <option value="gff2">gff2</option> 32 <option value="gff2">gff2</option>
31 <option value="gff3">gff3</option> 33 <option value="gff3">gff3</option>
32 <option value="sam">sam</option> 34 <option value="sam">sam</option>
35 <option value="bam">bam</option>
33 <option value="gtf">gtf</option> 36 <option value="gtf">gtf</option>
34 </param> 37 </param>
35 <when value="bed"> 38 <when value="bed">
36 <param name="inputFileName" format="bed" type="data" label="Input File"/> 39 <param name="inputFileName" format="bed" type="data" label="Input File"/>
37 </when> 40 </when>
44 <when value="gff3"> 47 <when value="gff3">
45 <param name="inputFileName" format="gff3" type="data" label="Input File"/> 48 <param name="inputFileName" format="gff3" type="data" label="Input File"/>
46 </when> 49 </when>
47 <when value="sam"> 50 <when value="sam">
48 <param name="inputFileName" format="sam" type="data" label="Input File"/> 51 <param name="inputFileName" format="sam" type="data" label="Input File"/>
52 </when>
53 <when value="bam">
54 <param name="inputFileName" format="bam" type="data" label="Input File"/>
49 </when> 55 </when>
50 <when value="gtf"> 56 <when value="gtf">
51 <param name="inputFileName" format="gtf" type="data" label="Input File"/> 57 <param name="inputFileName" format="gtf" type="data" label="Input File"/>
52 </when> 58 </when>
53 </conditional> 59 </conditional>