| Previous changeset 17:93bccb57e4f4 (2024-01-22) Next changeset 19:55cb63deadfe (2024-10-22) |
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tassel.xml |
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| diff -r 93bccb57e4f4 -r dfbdf8077621 tassel.xml --- a/tassel.xml Mon Jan 22 13:31:24 2024 +0000 +++ b/tassel.xml Tue Oct 22 09:23:33 2024 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="Tassel" name="Tassel" version="2.0.0"> +<tool id="Tassel" name="Tassel" version="3.0.0"> <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description> <requirements> <requirement type="package" version="5.2.89">tassel</requirement> @@ -9,25 +9,25 @@ </stdio> <command> #if $analysis_opts.fonction_selector == "ck": - mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1; + mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1; #else if $analysis_opts.fonction_selector == "ld": - mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1; + mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1; #else if $analysis_opts.fonction_selector == "glm": #if $analysis_opts.add_file.additional_file_selector == "no": - mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -combineA -input1 -input2 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2; + mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -combineA -input1 -input2 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2; #else if $analysis_opts.add_file.additional_file_selector == "yes": - mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait -combineA -input1 -input2 -input3 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 -runfork3 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2; + mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait -combineA -input1 -input2 -input3 -intersect -glm -export tmpdir$$/output -runfork1 -runfork2 -runfork3 >>$log;mv tmpdir$$/output1.txt $output1;mv tmpdir$$/output2.txt $output2; #end if #else if $analysis_opts.fonction_selector == "mlm": #if $analysis_opts.add_structure_file.additional_file_selector == "no": - mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork4 >>$log;mv tmpdir$$/output4.txt $output1;mv tmpdir$$/output5.txt $output2;mv tmpdir$$/output6.txt $output3; + mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork4 >>$log;mv tmpdir$$/output2.txt $output1;mv tmpdir$$/output3.txt $output2;mv tmpdir$$/output4.txt $output3; #else if $analysis_opts.add_structure_file.additional_file_selector == "yes": - mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -input3 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork3 -runfork4 >>$log;mv tmpdir$$/output4.txt $output1;mv tmpdir$$/output5.txt $output2;mv tmpdir$$/output6.txt $output3; + mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -filterAlign -filterAlignMinFreq $filterAlignMinFreq -fork2 -r $analysis_opts.trait -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait -fork4 -k $analysis_opts.kinship -combineA -input1 -input2 -input3 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/output -runfork1 -runfork2 -runfork3 -runfork4 >>$log;mv tmpdir$$/output2.txt $output1;mv tmpdir$$/output3.txt $output2;mv tmpdir$$/output4.txt $output3; #end if #end if </command> <inputs> - <param format="txt" name="hapmap" type="data" label="HapMap file"/> + <param format="vcf" name="vcffile" type="data" label="VCF file"/> <conditional name="analysis_opts"> <param name="fonction_selector" type="select" label="Type of analysis"> <option value="mlm" selected="True">MLM</option> @@ -97,18 +97,18 @@ </outputs> <tests> <test> - <param name="hapmap" value="input_hapmap.txt"/> + <param name="vcffile" value="input.vcf"/> <conditional name="analysis_opts"> <param name="fonction_selector" value="glm"/> - <param name="trait" value="phenotyping_DRB.csv"/> + <param name="trait" value="phenotyping_xantho.tsv"/> <conditional name="add_structure_file"> <param name="additional_file_selector" value="yes"/> - <param name="structure" value="Best_K_Output"/> + <param name="structure" value="Best_K_Output2"/> </conditional> </conditional> <param name="filterAlignMinFreq" value="0.05"/> - <output name="output1" value="Tassel_output.txt"/> - <output name="output2" value="Allele_effects.txt"/> + <output name="output1" value="statistics_output.txt"/> + <output name="output2" value="Allele_effects_output.txt"/> </test> </tests> <help><![CDATA[ |