| Previous changeset 5:e94b8b64929c (2018-08-24) Next changeset 7:e2608e112f2a (2023-12-21) |
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tassel.xml |
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| diff -r e94b8b64929c -r 28c0efb3a226 tassel.xml --- a/tassel.xml Fri Aug 24 08:33:49 2018 -0400 +++ b/tassel.xml Mon Dec 11 15:12:25 2023 +0000 |
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| @@ -2,14 +2,15 @@ <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description> <requirements> <requirement type="package" version="5.2.40">tassel</requirement> + <requirement type="package" version="1.8">openjdk</requirement> </requirements> - + <stdio> <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> <exit_code range="1:" level="fatal" /> </stdio> - - <command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ + + <command detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ #if $analysis_opts.fonction_selector == "mlm": -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait @@ -48,7 +49,7 @@ -fork1 -h $hapmap -ck -export tmpdir$$/kinship -runfork1 #end if - </command> + ]]></command> <inputs> <param format="txt" name="hapmap" type="data" label="HapMap file"/> <conditional name="analysis_opts"> @@ -118,7 +119,7 @@ <data format="txt" name="log" label="Log file"/> </outputs> - + <tests> <test> <param name="hapmap" value="input_hapmap.txt"/> @@ -135,47 +136,47 @@ <output name="output2" value="Allele_effects.txt"/> </test> </tests> - + <help><![CDATA[ - - + + .. class:: infomark - + **Tassel5** version 5.2.40 - + .. class:: infomark - + **Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) - + .. class:: infomark - + **Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr - + --------------------------------------------------- - + ======= Tassel5 ======= - + ----------- Description ----------- - + | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. | For further informations on tassel, please visit the website_. - + .. _website: http://www.maizegenetics.net/tassel/ - + ------------ Dependencies ------------ Tassel5 tassel_ 5.2.40, Conda version - + .. _tassel: https://anaconda.org/bioconda/tassel - + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btm308</citation> </citations> -</tool> +</tool> \ No newline at end of file |