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comparison MDSplot/mdsplot.xml @ 4:10627af23f10 draft

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planemo upload
author gandres
date Tue, 15 Dec 2015 05:18:02 -0500
parents 345f88a8f483
children ec22fcacb66c
comparison
equal deleted inserted replaced
3:345f88a8f483 4:10627af23f10
6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work --> 6 <!-- [OPTIONAL] 3rd party tools, binaries, modules... required for the tool to work -->
7 <requirements> 7 <requirements>
8 <requirement type="binary">perl</requirement> 8 <requirement type="binary">perl</requirement>
9 <requirement type="package" version="1.07">plink</requirement> 9 <requirement type="package" version="1.07">plink</requirement>
10 </requirements> 10 </requirements>
11
12 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
13 <stdio>
14 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
15 <exit_code range="1:" level="fatal" />
16 </stdio>
17
11 18
12 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> 19 <!-- [OPTIONAL] Command to be executed to get the tool's version string -->
13 <version_command> 20 <version_command>
14 <!-- 21 <!--
15 tool_binary -v 22 tool_binary -v
16 --> 23 -->
17 </version_command> 24 </version_command>
18 25
19 <!-- [REQUIRED] The command to execute --> 26 <!-- [REQUIRED] The command to execute -->
20 <command interpreter="bash"> 27 <command interpreter="bash">
21 mdsplot.sh $fileped $filemap $fileout_label $fileout_matrix $fileout_plot $fileout_log 28 mdsplot.sh $fileped $filemap $fileout_matrix $fileout_plot $fileout_log
22 </command> 29 </command>
23 30
24 <!-- [REQUIRED] Input files and tool parameters --> 31 <!-- [REQUIRED] Input files and tool parameters -->
25 <inputs> 32 <inputs>
26 <param name="fileped" type="data" format="txt" optional="false" label="PED input" /> 33 <param name="fileped" type="data" format="txt" optional="false" label="PED input" />
33 <data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" /> 40 <data name="fileout_matrix" type="data" format="tabular" label="${fileout_label}.ibs_matrix.txt" />
34 <data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" /> 41 <data name="fileout_plot" type="data" format="tabular" label="${fileout_label}.mds_plot.txt" />
35 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" /> 42 <data name="fileout_log" type="data" format="txt" label="${fileout_label}.log" />
36 </outputs> 43 </outputs>
37 44
38 <!-- [STRONGLY RECOMMANDED] Exit code rules -->
39 <stdio>
40 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
41 <exit_code range="1:" level="fatal" />
42 </stdio>
43
44 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> 45 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
45 <tests> 46 <tests>
46 <!-- [HELP] Test files have to be in the ~/test-data directory --> 47 <!-- [HELP] Test files have to be in the ~/test-data directory -->
47 48
48 <test> 49 <test>
49 <param name="fileped" value="input.ped" /> 50 <param name="fileped" value="MDSplot-input.ped" />
50 <param name="filemap" value="input.map" /> 51 <param name="filemap" value="MDSplot-input.map" />
51 <output name="fileout_matrix" file="output.ibs_matrix.txt" /> 52 <output name="fileout_matrix" file="MDSplot-output.ibs_matrix.txt" />
52 <output name="fileout_plot" file="output.mds_plot.txt" /> 53 <output name="fileout_plot" file="MDSplot-output.mds_plot.txt" />
53 <output name="fileout_log" file="output.log" />
54 </test> 54 </test>
55 55
56 <!-- [HELP] Multiple tests can be defined with different parameters --> 56 <!-- [HELP] Multiple tests can be defined with different parameters -->
57 <!-- 57 <!--
58 <test> 58 <test>