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author | dereeper |
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date | Fri, 24 Aug 2018 08:33:49 -0400 |
parents | 652aafd88060 |
children | 28c0efb3a226 |
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<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="5.2.40">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$$/ #if $analysis_opts.fonction_selector == "mlm": -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait #if $analysis_opts.add_structure_file.additional_file_selector == "yes": -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait #end if -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": -input3 #end if -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/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>