Mercurial > repos > nikhil-joshi > deseq_and_sam2counts

comparison deseq/deseq/sam2counts.xml @ 2:669899d20e59 draft

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author nikhil-joshi
date Wed, 09 Jan 2013 18:27:59 -0500
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1:3348f484c49c 2:669899d20e59
1 <tool id="sam2counts" name="SAM/BAM To Counts">
2 <description>Produce count data from SAM or BAM files</description>
3
4 <requirements>
5 <requirement type="python-module">sam2counts_galaxy.py</requirement>
6 </requirements>
7
8 <command interpreter="python">
9 sam2counts_galaxy.py
10
11 #if str($filetype.ftype_select) == "sam":
12 ${first_input_sam}
13 #for $input_file_sam in $filetype.input_files_sam:
14 ${input_file_sam.additional_input_sam}
15 #end for
16 #end if
17
18 #if str($filetype.ftype_select) == "bam":
19 -b
20
21 ${first_input_bam}
22 #for $input_file_bam in $filetype.input_files_bam:
23 ${input_file_bam.additional_input_bam}
24 #end for
25 #end if
26
27 -o $counts
28 -l $colnames
29 </command>
30
31 <inputs>
32 <param name="colnames" type="text" size="30" label="Short names for samples" help="A comma-separated list of short names for the samples in order">
33 <validator type="empty_field"/>
34 <validator type="regex" message="Must be a comma-separated tuple with no spaces">^(\w+,)+\w+$</validator>
35 </param>
36
37 <conditional name="filetype">
38
39 <param name="ftype_select" type="select" label="Are the input files SAM or BAM format?">
40 <option value="sam">SAM</option>
41 <option value="bam">BAM</option>
42 </param>
43
44 <when value="sam">
45 <param format="sam" name="first_input_sam" type="data" label="SAM file" help=""/>
46 <repeat name="input_files_sam" title="Additional SAM Files">
47 <param format="sam" name="additional_input_sam" type="data" label="SAM file" help=""/>
48 </repeat>
49 </when>
50
51 <when value="bam">
52 <param format="bam" name="first_input_bam" type="data" label="BAM file" help=""/>
53 <repeat name="input_files_bam" title="Additional BAM Files">
54 <param format="bam" name="additional_input_bam" type="data" label="BAM file" help=""/>
55 </repeat>
56 </when>
57
58 </conditional>
59 </inputs>
60
61 <outputs>
62 <data format="tabular" name="counts"/>
63 </outputs>
64
65 <help>
66 </help>
67
68 </tool>