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comparison tassel.xml @ 17:93bccb57e4f4 draft default tip

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author dereeper
date Mon, 22 Jan 2024 13:31:24 +0000
parents 88ea6f8f664e
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16:d9c73778f0e2 17:93bccb57e4f4
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>$__tool_directory__/tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/ 10 <command>
11 #if $analysis_opts.fonction_selector == "mlm": 11 #if $analysis_opts.fonction_selector == "ck":
12 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq 12 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ck -export tmpdir$$/output1.txt -runfork1 >>$log;mv tmpdir$$/output1.txt $output1;
13 -fork2 -r $analysis_opts.trait 13 #else if $analysis_opts.fonction_selector == "ld":
14 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": 14 mkdir tmpdir$$;run_pipeline.pl -fork1 -h $hapmap -ld -ldType All -ldd png -ldplotsize 3000 -o tmpdir$$/output1.png -runfork1 >>$log;mv tmpdir$$/output1.png $output1;
15 -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait 15 #else if $analysis_opts.fonction_selector == "glm":
16 #if $analysis_opts.add_file.additional_file_selector == "no":
17 mkdir tmpdir$$;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$$/output2.txt $output2;
18 #else if $analysis_opts.add_file.additional_file_selector == "yes":
19 mkdir tmpdir$$;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$$/output2.txt $output2;
16 #end if 20 #end if
17 -fork4 -k $analysis_opts.kinship 21 #else if $analysis_opts.fonction_selector == "mlm":
18 -combineA -input1 -input2 22 #if $analysis_opts.add_structure_file.additional_file_selector == "no":
19 #if $analysis_opts.add_structure_file.additional_file_selector == "yes": 23 mkdir tmpdir$$;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;
20 -input3 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$$/output6.txt $output3;
21 #end if 26 #end if
22 -intersect -combineB -inputA -input4 -mlm -mlmVarCompEst $analysis_opts.mlmVarCompEst -mlmCompressionLevel $analysis_opts.mlmCompressionLevel -export tmpdir$$/TASSELMLM -runfork1 -runfork2
23 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":
24 -runfork3
25 #end if
26 -runfork4
27
28 #else if $analysis_opts.fonction_selector == "glm":
29 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
30 -fork2 -r $analysis_opts.trait
31 #if $analysis_opts.add_file.additional_file_selector == "yes":
32 -fork3 -q $analysis_opts.add_file.structure -excludeLastTrait
33 #end if
34 -combineA -input1 -input2
35 #if $analysis_opts.add_file.additional_file_selector == "yes":
36 -input3
37 #end if
38 -intersect -glm -export tmpdir$$/TASSELGLM -runfork1 -runfork2
39 #if $analysis_opts.add_file.additional_file_selector == "yes":
40 -runfork3
41 #end if
42 #else if $analysis_opts.fonction_selector == "ld":
43 -fork1 -h $hapmap
44 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
45 #else if $analysis_opts.fonction_selector == "ck":
46 -fork1 -h $hapmap
47 -ck -export tmpdir$$/kinship -runfork1
48 #end if 27 #end if
49 </command> 28 </command>
50 <inputs> 29 <inputs>
51 <param format="txt" name="hapmap" type="data" label="HapMap file"/> 30 <param format="txt" name="hapmap" type="data" label="HapMap file"/>
52 <conditional name="analysis_opts"> 31 <conditional name="analysis_opts">
114 <filter>analysis_opts['fonction_selector'] == "mlm"</filter> 93 <filter>analysis_opts['fonction_selector'] == "mlm"</filter>
115 </data> 94 </data>
116 95
117 <data format="txt" name="log" label="Log file"/> 96 <data format="txt" name="log" label="Log file"/>
118 </outputs> 97 </outputs>
119 ​
120 <tests> 98 <tests>
121 <test> 99 <test>
122 <param name="hapmap" value="input_hapmap.txt"/> 100 <param name="hapmap" value="input_hapmap.txt"/>
123 <conditional name="analysis_opts"> 101 <conditional name="analysis_opts">
124 <param name="fonction_selector" value="glm"/> 102 <param name="fonction_selector" value="glm"/>