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Commit message:
Deleted selected files |
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removed:
tassel.xml |
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| diff -r e2608e112f2a -r 7ec8715bedc2 tassel.xml --- a/tassel.xml Thu Dec 21 16:00:45 2023 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,182 +0,0 @@ -<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="5.2.89">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 detect_errors="exit_code"><![CDATA[./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ -#if $analysis_opts.fonction_selector == "mlm": - -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq - -fork2 -r $analysis_opts.trait - #if $analysis_opts.add_structure_file.additional_file_selector == "yes": - -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait - #end if - -fork4 -k $analysis_opts.kinship - -combineA -input1 -input2 - #if $analysis_opts.add_structure_file.additional_file_selector == "yes": - -input3 - #end if - -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2 - #if $analysis_opts.add_structure_file.additional_file_selector == "yes": - -runfork3 - #end if - -runfork4 - -#else if $analysis_opts.fonction_selector == "glm": - -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq - -fork2 -r $analysis_opts.trait - #if $analysis_opts.add_file.additional_file_selector == "yes": - -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait - #end if - -combineA -input1 -input2 - #if $analysis_opts.add_file.additional_file_selector == "yes": - -input3 - #end if - -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2 - #if $analysis_opts.add_file.additional_file_selector == "yes": - -runfork3 - #end if -#else if $analysis_opts.fonction_selector == "ld": - -fork1 -h $hapmap - -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1 -#else if $analysis_opts.fonction_selector == "ck": - -fork1 -h $hapmap - -ck -export tmpdir$$/kinship -runfork1 -#end if - ]]></command> - <inputs> - <param format="txt" name="hapmap" type="data" label="HapMap file"/> - <conditional name="analysis_opts"> - <param name="fonction_selector" type="select" label="Type of analysis"> - <option value="mlm" selected="True">MLM</option> - <option value="glm">GLM</option> - <option value="ld">Linkage Disequilibrium</option> - <option value="ck">Kinship</option> - </param> - <when value="glm"> - <param format="txt" name="trait" type="data" label="Trait file"/> - <conditional name="add_file"> - <param name="additional_file_selector" type="select" label="Add structure file"> - <option value="no" selected="True">no</option> - <option value="yes">yes</option> - </param> - <when value="yes"> - <param format="txt" name="structure" type="data" label="Structure file"/> - </when> - <when value="no"> - </when> - </conditional> - </when> - <when value="mlm"> - <param format="txt" name="trait" type="data" label="Trait file"/> - <param format="txt" name="kinship" type="data" label="Kinship file"/> - <conditional name="add_structure_file"> - <param name="additional_file_selector" type="select" label="Add structure file"> - <option value="no" selected="True">no</option> - <option value="yes">yes</option> - </param> - <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> - <option value="EachMarker">EachMarker</option> - </param> - <param name="mlmCompressionLevel" type="select" label="Compression Level"> - <option value="Optimum" selected="True">Optimum</option> - <option value="Custom">Custom</option> - <option value="None">None</option> - </param> - </when> - <when value="ld"></when> - <when value="ck"></when> - </conditional> - <param type="text" name="filterAlignMinFreq" label="Filter minimal frequency allele" value="0.05"/> - </inputs> - <outputs> - <data format="txt" name="output1" label="Tassel output"> - <change_format> - <when input="analysis_opts['fonction_selector']" value="ld" format="png"/> - </change_format> - </data> - - <data format="txt" name="output2" label="Allele effects"> - <filter>analysis_opts['fonction_selector'] == "glm" or analysis_opts['fonction_selector'] == "mlm"</filter> - </data> - - <data format="txt" name="output3" label="Compression file"> - <filter>analysis_opts['fonction_selector'] == "mlm"</filter> - </data> - - <data format="txt" name="log" label="Log file"/> - </outputs> - - <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 - -**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> \ No newline at end of file |