| Previous changeset 6:f76d842e960f (2020-09-30) Next changeset 8:16d22eee0fe3 (2021-12-02) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6e391fa7267f5225f0bca795c002107821bbac27" |
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modified:
plink.xml |
| b |
| diff -r f76d842e960f -r 66b35562554d plink.xml --- a/plink.xml Wed Sep 30 20:29:06 2020 +0000 +++ b/plink.xml Mon Oct 05 16:08:24 2020 +0000 |
| [ |
| b"@@ -1,7 +1,7 @@\n <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>\n <macros>\n <token name='@TOOL_VERSION@'>1.9.b618</token>\n- <token name='@VERSION_SUFFIX@'>1</token>\n+ <token name='@VERSION_SUFFIX@'>2</token>\n <xml name='template_sanitizer'>\n <sanitizer>\n <valid initial='default'>\n@@ -76,8 +76,8 @@\n #if $inputs.covar_input:\n --covar '$inputs.covar_input'\n #end if\n- #if $inputs.pheno:\n- --pheno $inputs.pheno\n+ #if $inputs.set_pheno.set_pheno == 'Yes':\n+ --pheno $inputs.set_pheno.pheno $inputs.set_pheno.all_pheno\n #end if\n #if $functions.func == 'filtering':\n ##ID list functions\n@@ -381,6 +381,24 @@\n --memory \\${GALAXY_MEMORY_MB:-8192}\n --make-bed\n --out plink_output/plink_output\n+\n+ #if $functions.func == 'association':\n+ #if $functions.logistic.logistic == 'Yes':\n+ && mkdir logistic_out\n+ && mv plink_output/plink_output.*.l* logistic_out\n+ && find ./logistic_out/. -type f -exec mv {} {}.txt ';'\n+ #end if\n+ #if $functions.adjust.adjust == 'Yes':\n+ && mkdir adjust_out\n+ && mv ./plink_output/*.adjuste* adjust_out\n+ && find ./adjust_out/. -type f -exec mv {} {}.txt ';'\n+ #end if\n+ #if $functions.assoc.assoc == 'Yes':\n+ && mkdir assoc_out\n+ && mv ./plink_output/*asso* assoc_out\n+ && find ./assoc_out/. -type f -exec mv {} {}.txt ';'\n+ #end if\n+ #end if\n ]]></command>\n <inputs>\n <section name='inputs' title='Data inputs' expanded='true'>\n@@ -398,7 +416,17 @@\n <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/>\n </when>\n </conditional>\n- <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.' optional='true'/> \n+ <conditional name='set_pheno'>\n+ <param name='set_pheno' type='select' label='Set phenotype'>\n+ <option value=''>No</option>\n+ <option value='Yes'>Yes</option>\n+ </param>\n+ <when value=''/>\n+ <when value='Yes'>\n+ <param name='pheno' type='data' format='txt,tabular' label='Phenotype file' help='Read phenotype values from the 3rd column of the specified space- or tab-delimited file, instead of the .fam or .ped file.'/> \n+ <param name='all_pheno' type='boolean' truevalue='--all-pheno' falsevalue='' label='Allow all phenotypes present in the phenotype file to be subject to the association tests you have requested' checked='false'/>\n+ </when>\n+ </conditional>\n <param name='covar_input' type='data' format='tabular,tsv' label='Input covariate file' optional='true'/>\n </section>\n <conditional name='functions'>\n@@ -998,52 +1026,21 @@\n </data>\n \n <!--Association-->\n- <!--assoc-->\n- <data name='assoc' format='tabular' from_work_dir='plink_output/plink_output.assoc' label='${tool.name}: Association'>\n- <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and not functions['assoc']['fisher']</filter> \n- </data>\n- <data name='perm' format='tabular' from_work_dir='plink_output/plink_output.assoc.perm' label='${tool.name}: Association Monte Carlo'>\n- <filter>functions['func'] == 'association' and functions['assoc']['assoc'] == 'Yes' and functions['assoc']['perm']['perm'] == 'perm' and not functions['assoc']['fisher']</filter>\n- </data>\n- <data name='mperm' format='tabular' from_work_dir='plink_output/plink_output.assoc.mperm' label='${tool.name}: Association "..b'lection>\n+ <!--Adjust-->\n+ <collection name=\'adjust_outfiles\' type=\'list\' label=\'Adjust outfiles\'>\n+ <discover_datasets directory=\'adjust_out\' pattern=\'__name_and_ext__\'/>\n+ <filter>functions[\'func\'] == \'association\' and functions[\'adjust\'][\'adjust\'] == \'Yes\'</filter>\n+ </collection>\n <!--Logistic-->\n- <data name=\'logistic\' format=\'tabular\' from_work_dir=\'plink_output/plink_output.assoc.logistic\' label=\'${tool.name}: Logistic Regression\'>\n- <filter>functions[\'func\'] == \'association\' and functions[\'logistic\'][\'logistic\'] == \'Yes\'</filter>\n- </data>\n- <data name=\'logistic_perm\' format=\'tabular\' from_work_dir=\'plink_output/plink_output.assoc.logistic.perm\' label=\'${tool.name}: Logistic Association Monte Carlo\'>\n- <filter>functions[\'func\'] == \'association\' and functions[\'logistic\'][\'logistic\'] == \'Yes\' and functions[\'logistic\'][\'perm\'][\'perm\'] == \'perm\'</filter>\n- </data>\n- <data name=\'logistic_mperm\' format=\'tabular\' from_work_dir=\'plink_output/plink_output.assoc.logistic.mperm\' label=\'${tool.name}: Logistic Association Max(T) permutation test\'>\n- <filter>functions[\'func\'] == \'association\' and functions[\'logistic\'][\'logistic\'] == \'Yes\' and functions[\'logistic\'][\'perm\'][\'perm\'] == \'mperm\'</filter>\n- </data>\n- \n+ <collection name=\'log_outfiles\' type=\'list\' label=\'Logistic outfiles\'>\n+ <discover_datasets directory=\'logistic_out\' pattern=\'__name_and_ext__\'/>\n+ <filter>functions[\'func\'] == \'association\' and functions[\'logistic\'][\'logistic\'] == \'Yes\'</filter>\n+ </collection> \n <!--Link-->\n <data name=\'prune_in\' format=\'tabular\' from_work_dir=\'plink_output/plink_output.prune.in\' label=\'${tool.name}: Prune In\'>\n <filter>functions[\'func\'] == \'link\' and functions[\'set_indep\'][\'choice\'] == \'Yes\'</filter>\n@@ -1291,7 +1288,7 @@\n <output name=\'eigenvals\' value=\'plink.mds.eigenval\' compare=\'sim_size\'/>\n </test>\n \n- <test expect_num_outputs=\'11\'>\n+ <test expect_num_outputs=\'8\'>\n <section name=\'inputs\'>\n <conditional name=\'inputs\'>\n <param name=\'filetype\' value=\'bfile\'/>\n@@ -1333,12 +1330,18 @@\n <element name=\'plink_bim\' file=\'out.assoc.bim\'/>\n <element name=\'plink_fam\' file=\'out.assoc.fam\'/>\n </output_collection>\n- <output name=\'fisher\' value="out.assoc.fisher"/>\n- <output name=\'adjust_fisher\' value="out.assoc.fisher.adjusted" sort="True" />\n- <output name=\'fisher_mperm\' value="out.assoc.fisher.mperm" compare=\'sim_size\'/>\n- <output name=\'logistic\' value="out.assoc.logistic"/>\n- <output name=\'adjust_logistic\' value="out.assoc.logistic.adjusted"/>\n- <output name=\'logistic_perm\' value="out.assoc.logistic.perm" compare=\'sim_size\'/>\n+ <output_collection name=\'assoc_outfiles\' type=\'list\' count=\'2\'>\n+ <element name=\'plink_output.assoc.fisher.mperm\' value=\'out.assoc.fisher.mperm\' compare=\'sim_size\'/>\n+ <element name=\'plink_output.assoc.fisher\' value=\'out.assoc.fisher\'/>\n+ </output_collection>\n+ <output_collection name=\'adjust_outfiles\' type=\'list\' count=\'1\'>\n+ <element name=\'plink_output.assoc.fisher.adjusted\' value=\'out.assoc.fisher.adjusted\' compare=\'sim_size\' />\n+ </output_collection>\n+ <output_collection name=\'log_outfiles\' type=\'list\' count=\'3\'>\n+ <element name=\'plink_output.assoc.logistic\' value=\'out.assoc.logistic\'/>\n+ <element name=\'plink_output.assoc.logistic.adjusted\' value=\'out.assoc.logistic.adjusted\'/>\n+ <element name=\'plink_output.assoc.logistic.perm\' value=\'out.assoc.logistic.perm\' compare=\'sim_size\'/>\n+ </output_collection>\n </test>\n \n <test expect_num_outputs=\'6\'>\n' |