Mercurial > repos > dereeper > tassel5
diff tassel.xml @ 4:652aafd88060 draft
planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac
| author | dereeper |
|---|---|
| date | Mon, 16 Apr 2018 08:54:41 -0400 |
| parents | 0eebff4180d9 |
| children | 28c0efb3a226 |
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--- a/tassel.xml Thu Nov 02 05:19:30 2017 -0400 +++ b/tassel.xml Mon Apr 16 08:54:41 2018 -0400 @@ -1,8 +1,14 @@ -<tool id="Tassel" name="Tassel" version="5.0"> - <description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description> +<tool id="Tassel" name="Tassel" version="2.0.0"> + <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description> <requirements> - <requirement type="package" version="5.0">tassel</requirement> + <requirement type="package" version="5.2.40">tassel</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$$/ #if $analysis_opts.fonction_selector == "mlm": -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq @@ -62,6 +68,8 @@ <when value="yes"> <param format="txt" name="structure" type="data" label="Structure file"/> </when> + <when value="no"> + </when> </conditional> </when> <when value="mlm"> @@ -75,6 +83,8 @@ <when value="yes"> <param format="txt" name="structure" type="data" label="Structure file"/> </when> + <when value="no"> + </when> </conditional> <param name="mlmVarCompEst" type="select" label="Variance Component Estimation"> <option value="P3D" selected="True">P3D</option> @@ -108,46 +118,64 @@ <data format="txt" name="log" label="Log file"/> </outputs> - <help> + + <tests> + <test> + <param name="hapmap" value="input_hapmap.txt"/> + <conditional name="analysis_opts"> + <param name="fonction_selector" value="glm"/> + <param name="trait" value="phenotyping_DRB.csv"/> + <conditional name="add_structure_file"> + <param name="additional_file_selector" value="yes"/> + <param name="structure" value="Best_K_Output"/> + </conditional> + </conditional> + <param name="filterAlignMinFreq" value="0.05"/> + <output name="output1" value="Tassel_output.txt"/> + <output name="output2" value="Allele_effects.txt"/> + </test> + </tests> + + <help><![CDATA[ + .. class:: infomark -**Program encapsulated in Galaxy by Southgreen** +**Tassel5** version 5.2.40 + +.. class:: infomark + +**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA) .. class:: infomark -**Tassel** - ------ +**Support** For any questions about Galaxy integration, please send an e-mail to alexis.dereeper@ird.fr -========== - Authors: -========== +--------------------------------------------------- -**Terry Casstevens** - ------ +======= +Tassel5 +======= -========== - Overview -========== +----------- +Description +----------- -Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. + | 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/ -For further informations, please visite the website of TASSEL_. - - -.. _TASSEL: http://www.maizegenetics.net/tassel/ +------------ +Dependencies +------------ +Tassel5 + tassel_ 5.2.40, Conda version - </help> -<!-- -<tests> - <test> - <param name="input" value="genotyping_file.inp" /> - <output name="output" file="phase_output" /> - </test> -</tests> ---> +.. _tassel: https://anaconda.org/bioconda/tassel + + ]]></help> + <citations> + <citation type="doi">10.1093/bioinformatics/btm308</citation> + </citations> </tool>