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comparison tassel.xml @ 11:75948ef196f9 draft

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author dereeper
date Wed, 03 Jan 2024 10:22:35 +0000
parents 8dca3a43f177
children 4ca9252178df
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10:8dca3a43f177 11:75948ef196f9
1 <tool id="Tassel" name="Tassel" version="2.0.0"> 1 <tool id="Tassel" name="Tassel" version="2.0.0">
2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description> 2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="5.2.89">tassel</requirement> 4 <requirement type="package" version="5.2.89">tassel</requirement>
5 <requirement type="package" version="1.8.0.242.b08">openjdk</requirement> 5 <requirement type="package" version="1.8.0.242.b08">java-1.8.0-openjdk-devel-cos7-s390x</requirement>
6 </requirements> 6 </requirements>
7 ​ 7 ​
8 <stdio> 8 <stdio>
9 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> 9 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
10 <exit_code range="1:" level="fatal" /> 10 <exit_code range="1:" level="fatal" />
11 </stdio> 11 </stdio>
12 ​ 12 ​
13 <command detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ 13 <command>tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
14 #if $analysis_opts.fonction_selector == "mlm": 14 #if $analysis_opts.fonction_selector == "mlm":
15 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq 15 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
16 -fork2 -r $analysis_opts.trait 16 -fork2 -r $analysis_opts.trait
17 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": 17 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
18 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait 18 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait
47 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1 47 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
48 #else if $analysis_opts.fonction_selector == "ck": 48 #else if $analysis_opts.fonction_selector == "ck":
49 -fork1 -h $hapmap 49 -fork1 -h $hapmap
50 -ck -export tmpdir$$/kinship -runfork1 50 -ck -export tmpdir$$/kinship -runfork1
51 #end if 51 #end if
52 ]]></command> 52 </command>
53 <inputs> 53 <inputs>
54 <param format="txt" name="hapmap" type="data" label="HapMap file"/> 54 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
55 <conditional name="analysis_opts"> 55 <conditional name="analysis_opts">
56 <param name="fonction_selector" type="select" label="Type of analysis"> 56 <param name="fonction_selector" type="select" label="Type of analysis">
57 <option value="mlm" selected="True">MLM</option> 57 <option value="mlm" selected="True">MLM</option>