| Previous changeset 16:d9c73778f0e2 (2024-01-22) Next changeset 18:dfbdf8077621 (2024-10-22) |
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modified:
tassel.xml |
| b |
| diff -r d9c73778f0e2 -r 93bccb57e4f4 tassel.xml --- a/tassel.xml Mon Jan 22 13:31:02 2024 +0000 +++ b/tassel.xml Mon Jan 22 13:31:24 2024 +0000 |
| [ |
| @@ -7,44 +7,23 @@ <!-- [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>$__tool_directory__/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 - + <command> +#if $analysis_opts.fonction_selector == "ck": + mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1; +#else if $analysis_opts.fonction_selector == "ld": + mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1; #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 + #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; + #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; #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 +#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$$/output6.txt $output3; + #else if $analysis_opts.add_structure_file.additional_file_selector == "yes": + mkdir tmpdir$$;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; + #end if #end if </command> <inputs> @@ -116,7 +95,6 @@ <data format="txt" name="log" label="Log file"/> </outputs> - <tests> <test> <param name="hapmap" value="input_hapmap.txt"/> |