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comparison tools/rtg/mapf.xml @ 1:8593828f91e7 default tip

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Full galaxy wrapper
author diego
date Sat, 21 Apr 2012 21:36:15 -0400
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0:d50638ebd809 1:8593828f91e7
1 <tool id="rtg_mapf" name="Mapf">
2 <description>reads with rtg mapf</description>
3 <command interpreter="bash">galaxy-rtg-map-wrapper.sh $paired.sPaired $output1 $output2 $__new_file_path__
4 mapf -t ${template.extra_files_path}
5 --repeat-freq ${repeat}
6 -i ${reads.extra_files_path}
7 #if $paired.sPaired == "paired":
8 --min-insert-size $paired.minlength --max-insert-size $paired.maxlength
9 --max-mated-score $paired.maxscore --max-unmated-score $paired.maxuscore
10 #else:
11 --max-alignment-score $paired.maxscore
12 #end if
13 --sam
14 </command>
15 <inputs>
16 <param name="template" type="data" format="rtg_sdf" label="Reference SDF"/>
17 <param name="reads" type="data" format="rtg_sdf" label="Reads SDF"/>
18 <param name="repeat" type="text" value="90%" label="Repeat frequency">
19 <sanitizer sanitize="False"/>
20 </param>
21
22 <conditional name="paired">
23 <param name="sPaired" type="select" label="Are you mapping paired-end reads?">
24 <option value="paired">Paired-end</option>
25 <option value="single">Single-end</option>
26 </param>
27 <when value="single">
28 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for reads (percentages do not work ATM)">
29 <sanitizer sanitize="False"/>
30 </param>
31 </when>
32 <when value="paired">
33 <param name="maxscore" type="text" value="10%" label="Maximum alignment score for mated reads">
34 <sanitizer sanitize="False"/>
35 </param>
36 <param name="maxuscore" type="text" value="10%" label="Maximum alignment score for umated reads">
37 <sanitizer sanitize="False"/>
38 </param>
39 <param name="minlength" type="integer" value="200" label="Minimum insert size"/>
40 <param name="maxlength" type="integer" value="400" label="Maximum insert size"/>
41 </when>
42 </conditional>
43
44 </inputs>
45 <outputs>
46 <data name="output1" format="samix" />
47 </outputs>
48
49 <help>
50 This tool filters reads for contaminant sequences by mapping them against the contaminant template using rtg mapf
51 </help>
52
53 </tool>