Mercurial > repos > dereeper > tassel5
comparison tassel.xml @ 11:75948ef196f9 draft
Uploaded
| 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> |