Mercurial > repos > dereeper > sniplay
comparison SNP_density/calculateSlidingWindowsSNPdensitiesFromHapMap_wrapper.xml @ 4:10627af23f10 draft
planemo upload
author | gandres |
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date | Tue, 15 Dec 2015 05:18:02 -0500 |
parents | 420b57c3c185 |
children | ec22fcacb66c |
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3:345f88a8f483 | 4:10627af23f10 |
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1 <tool id="sniplay_density" name="SNP density" version="1.2.0"> | 1 <tool id="sniplay_density" name="SNP density" version="1.3.0"> |
2 | 2 |
3 <!-- [REQUIRED] Tool description displayed after the tool name --> | 3 <!-- [REQUIRED] Tool description displayed after the tool name --> |
4 <description> Calculate SNP densities along chromosome from HapMap</description> | 4 <description> Calculate SNP densities along chromosome from HapMap</description> |
5 | 5 |
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 </requirements> | 9 </requirements> |
10 | 10 |
11 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
12 <stdio> | |
13 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
14 <exit_code range="1:" level="fatal" /> | |
15 </stdio> | |
16 | |
11 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> | 17 <!-- [OPTIONAL] Command to be executed to get the tool's version string --> |
12 <version_command> | 18 <version_command> |
13 <!-- | 19 <!-- |
14 tool_binary -v | 20 tool_binary -v |
15 --> | 21 --> |
17 | 23 |
18 <!-- [REQUIRED] The command to execute --> | 24 <!-- [REQUIRED] The command to execute --> |
19 <command interpreter="bash"> | 25 <command interpreter="bash"> |
20 calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step | 26 calculateSlidingWindowsSNPdensitiesFromHapmap.sh $filein $fileout $fileout_bysample $step |
21 </command> | 27 </command> |
22 | 28 |
23 <!-- [REQUIRED] Input files and tool parameters --> | 29 <!-- [REQUIRED] Input files and tool parameters --> |
24 <inputs> | 30 <inputs> |
25 <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" /> | 31 <param name="filein" type="data" format="txt" optional="false" label="Hapmap input" /> |
26 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> | 32 <param name="step" type="integer" value="200000" label="Step" help="Step in bp"/> |
27 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" /> | 33 <param name="fileout_label" type="text" value="densities" label="Output name" help="Output name for tabular files" /> |
30 <!-- [REQUIRED] Output files --> | 36 <!-- [REQUIRED] Output files --> |
31 <outputs> | 37 <outputs> |
32 <data name="fileout" type="data" format="tabular" label="${fileout_label}" /> | 38 <data name="fileout" type="data" format="tabular" label="${fileout_label}" /> |
33 <data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" /> | 39 <data name="fileout_bysample" type="data" format="tabular" label="${fileout_label}.by_sample" /> |
34 </outputs> | 40 </outputs> |
35 | 41 |
36 <!-- [STRONGLY RECOMMANDED] Exit code rules --> | |
37 <stdio> | |
38 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | |
39 <exit_code range="1:" level="fatal" /> | |
40 </stdio> | |
41 | |
42 <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin --> | |
43 <tests> | 42 <tests> |
44 <!-- [HELP] Test files have to be in the ~/test-data directory --> | 43 <test> |
45 <!-- | 44 <param name="filein" value="SNPden-hapmap" /> |
46 <test> | 45 <param name="step" value="200000" /> |
47 <param name="input" value="input_test.txt" /> | 46 <output name="fileout" file="SNPden-result.txt" /> |
48 <output name="output" file="output_test.txt" /> | 47 <output name="fileout_bysample" file="SNPden-result_bysample.txt" /> |
49 </test> | 48 </test> |
50 --> | |
51 <!-- [HELP] Multiple tests can be defined with different parameters --> | 49 <!-- [HELP] Multiple tests can be defined with different parameters --> |
52 <!-- | 50 <!-- |
53 <test> | 51 <test> |
54 </test> | 52 </test> |
55 --> | 53 --> |