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tassel.xml |
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| diff -r 7ec8715bedc2 -r b2f196d098cb tassel.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tassel.xml Wed Jan 03 09:30:12 2024 +0000 |
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| @@ -0,0 +1,182 @@ +<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 |