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comparison ped2bed/ped2bed.xml @ 4:10627af23f10 draft

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planemo upload
author gandres
date Tue, 15 Dec 2015 05:18:02 -0500
parents 420b57c3c185
children
comparison
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3:345f88a8f483 4:10627af23f10
1 <tool id="ped2bed" name="plink: ped2bed" version="1.24"> 1 <tool id="ped2bed" name="plink: ped2bed" version="1.24">
2 <description>Convert ped to bed</description> 2 <description>Convert ped to bed</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.07">plink</requirement> 4 <requirement type="package" version="1.07">plink</requirement>
5 </requirements> 5 </requirements>
6 <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs 6 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
7 <stdio>
8 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
9 <exit_code range="1:" level="fatal" />
10 </stdio>
11 <command interpreter="bash">./ped2bed.sh $ped $map $bed $fam $bim $logs
7 </command> 12 </command>
8 <inputs> 13 <inputs>
9 <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/> 14 <param format="txt" name="ped" type="data" label="Allelic file in PED format" help="Allelic file in PED format"/>
10 <param format="txt" name="map" type="data" label="Map file" help="Map file"/> 15 <param format="txt" name="map" type="data" label="Map file" help="Map file"/>
11 </inputs> 16 </inputs>
13 <data format="txt" name="bed" label="Bed file"/> 18 <data format="txt" name="bed" label="Bed file"/>
14 <data format="txt" name="fam" label="Fam file"/> 19 <data format="txt" name="fam" label="Fam file"/>
15 <data format="txt" name="bim" label="Bim file"/> 20 <data format="txt" name="bim" label="Bim file"/>
16 <data format="txt" name="logs" label="All Logs"/> 21 <data format="txt" name="logs" label="All Logs"/>
17 </outputs> 22 </outputs>
18 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
19 <stdio>
20 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
21 <exit_code range="1:" level="fatal" />
22 </stdio>
23 23
24 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 24 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
25 <tests> 25 <tests>
26 <!-- [HELP] Test files have to be in the ~/test-data directory --> 26 <!-- [HELP] Test files have to be in the ~/test-data directory -->
27 <!-- [HELP] Multiple tests can be defined with different parameters --> 27 <!-- [HELP] Multiple tests can be defined with different parameters -->
28 <!--
29 <test> 28 <test>
29 <param name="ped" value="ped2bed-input.ped" />
30 <param name="map" value="ped2bed-input.map" />
31 <output name="bed" file="ped2bed-result.bed" />
32 <output name="fam" file="ped2bed-result.fam" />
33 <output name="bim" file="ped2bed-result.bim" />
30 </test> 34 </test>
31 -->
32 </tests> 35 </tests>
33 <help> 36 <help>
34 37
35 38
36 .. class:: infomark 39 .. class:: infomark