Mercurial > repos > dereeper > tassel5
comparison tassel.xml @ 18:dfbdf8077621 draft
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| author | dereeper |
|---|---|
| date | Tue, 22 Oct 2024 09:23:33 +0000 |
| parents | 93bccb57e4f4 |
| children |
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| 17:93bccb57e4f4 | 18:dfbdf8077621 |
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| 1 <tool id="Tassel" name="Tassel" version="2.0.0"> | 1 <tool id="Tassel" name="Tassel" version="3.0.0"> |
| 2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description> | 2 <description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="5.2.89">tassel</requirement> | 4 <requirement type="package" version="5.2.89">tassel</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 <stdio> | 6 <stdio> |
| 7 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> | 7 <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR --> |
| 8 <exit_code range="1:" level="fatal" /> | 8 <exit_code range="1:" level="fatal" /> |
| 9 </stdio> | 9 </stdio> |
| 10 <command> | 10 <command> |
| 11 #if $analysis_opts.fonction_selector == "ck": | 11 #if $analysis_opts.fonction_selector == "ck": |
| 12 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1; | 12 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1; |
| 13 #else if $analysis_opts.fonction_selector == "ld": | 13 #else if $analysis_opts.fonction_selector == "ld": |
| 14 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1; | 14 mkdir tmpdir$$;run_pipeline.pl -fork1 -vcf $vcffile -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1; |
| 15 #else if $analysis_opts.fonction_selector == "glm": | 15 #else if $analysis_opts.fonction_selector == "glm": |
| 16 #if $analysis_opts.add_file.additional_file_selector == "no": | 16 #if $analysis_opts.add_file.additional_file_selector == "no": |
| 17 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; | 17 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; |
| 18 #else if $analysis_opts.add_file.additional_file_selector == "yes": | 18 #else if $analysis_opts.add_file.additional_file_selector == "yes": |
| 19 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; | 19 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; |
| 20 #end if | 20 #end if |
| 21 #else if $analysis_opts.fonction_selector == "mlm": | 21 #else if $analysis_opts.fonction_selector == "mlm": |
| 22 #if $analysis_opts.add_structure_file.additional_file_selector == "no": | 22 #if $analysis_opts.add_structure_file.additional_file_selector == "no": |
| 23 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$$/output6.txt $output3; | 23 mkdir tmpdir$$;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; |
| 24 #else if $analysis_opts.add_structure_file.additional_file_selector == "yes": | 24 #else if $analysis_opts.add_structure_file.additional_file_selector == "yes": |
| 25 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$$/output6.txt $output3; | 25 mkdir tmpdir$$;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; |
| 26 #end if | 26 #end if |
| 27 #end if | 27 #end if |
| 28 </command> | 28 </command> |
| 29 <inputs> | 29 <inputs> |
| 30 <param format="txt" name="hapmap" type="data" label="HapMap file"/> | 30 <param format="vcf" name="vcffile" type="data" label="VCF file"/> |
| 31 <conditional name="analysis_opts"> | 31 <conditional name="analysis_opts"> |
| 32 <param name="fonction_selector" type="select" label="Type of analysis"> | 32 <param name="fonction_selector" type="select" label="Type of analysis"> |
| 33 <option value="mlm" selected="True">MLM</option> | 33 <option value="mlm" selected="True">MLM</option> |
| 34 <option value="glm">GLM</option> | 34 <option value="glm">GLM</option> |
| 35 <option value="ld">Linkage Disequilibrium</option> | 35 <option value="ld">Linkage Disequilibrium</option> |
| 95 | 95 |
| 96 <data format="txt" name="log" label="Log file"/> | 96 <data format="txt" name="log" label="Log file"/> |
| 97 </outputs> | 97 </outputs> |
| 98 <tests> | 98 <tests> |
| 99 <test> | 99 <test> |
| 100 <param name="hapmap" value="input_hapmap.txt"/> | 100 <param name="vcffile" value="input.vcf"/> |
| 101 <conditional name="analysis_opts"> | 101 <conditional name="analysis_opts"> |
| 102 <param name="fonction_selector" value="glm"/> | 102 <param name="fonction_selector" value="glm"/> |
| 103 <param name="trait" value="phenotyping_DRB.csv"/> | 103 <param name="trait" value="phenotyping_xantho.tsv"/> |
| 104 <conditional name="add_structure_file"> | 104 <conditional name="add_structure_file"> |
| 105 <param name="additional_file_selector" value="yes"/> | 105 <param name="additional_file_selector" value="yes"/> |
| 106 <param name="structure" value="Best_K_Output"/> | 106 <param name="structure" value="Best_K_Output2"/> |
| 107 </conditional> | 107 </conditional> |
| 108 </conditional> | 108 </conditional> |
| 109 <param name="filterAlignMinFreq" value="0.05"/> | 109 <param name="filterAlignMinFreq" value="0.05"/> |
| 110 <output name="output1" value="Tassel_output.txt"/> | 110 <output name="output1" value="statistics_output.txt"/> |
| 111 <output name="output2" value="Allele_effects.txt"/> | 111 <output name="output2" value="Allele_effects_output.txt"/> |
| 112 </test> | 112 </test> |
| 113 </tests> | 113 </tests> |
| 114 <help><![CDATA[ | 114 <help><![CDATA[ |
| 115 .. class:: infomark | 115 .. class:: infomark |
| 116 | 116 |