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comparison tassel.xml @ 18:dfbdf8077621 draft

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author dereeper
date Tue, 22 Oct 2024 09:23:33 +0000
parents 93bccb57e4f4
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17:93bccb57e4f4 18:dfbdf8077621
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