Mercurial > repos > nikhil-joshi > deseq_and_sam2counts

comparison deseq/sam2counts.xml @ 0:d7f27b43b8ff draft

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author nikhil-joshi
date Thu, 05 Jul 2012 21:02:43 -0400
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1 <tool id="sam2counts" name="SAM To Counts">
2 <description>Produce count data from SAM 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 ${first_input}
12 #for $input_file in $input_files:
13 ${input_file.additional_input}
14 #end for
15
16 -o $counts
17 -l $colnames
18 </command>
19
20 <inputs>
21 <param name="colnames" type="text" size="30" label="Short names for samples" help="A comma-separated list of short names for the samples in order">
22 <validator type="empty_field"/>
23 <validator type="regex" message="Must be a comma-separated tuple with no spaces">^(\w+,)+\w+$</validator>
24 </param>
25
26 <param format="sam" name="first_input" type="data" label="SAM file" help=""/>
27 <repeat name="input_files" title="Additional SAM Files">
28 <param format="sam" name="additional_input" type="data" label="SAM file" help=""/>
29 </repeat>
30 </inputs>
31
32 <outputs>
33 <data format="tabular" name="counts"/>
34 </outputs>
35
36 <help>
37 </help>
38
39 </tool>