| Previous changeset 9:272aca44b3dd (2021-12-19) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit 6d29c051fe8a6564805da7a13668d067c31f0e86 |
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modified:
plink.xml |
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added:
test-data/scores_file.tab test-data/scores_results.tab |
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| diff -r 272aca44b3dd -r 2c0ac05fe240 plink.xml --- a/plink.xml Sun Dec 19 15:53:35 2021 +0000 +++ b/plink.xml Tue Nov 14 17:51:25 2023 +0000 |
| [ |
| b"@@ -1,7 +1,8 @@\n <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>\n+ <description>genome association analysis toolset</description>\n <macros>\n <token name='@TOOL_VERSION@'>1.90b6.21</token>\n- <token name='@VERSION_SUFFIX@'>0</token>\n+ <token name='@VERSION_SUFFIX@'>1</token>\n <xml name='template_sanitizer'>\n <sanitizer>\n <valid initial='default'>\n@@ -50,6 +51,7 @@\n </xrefs>\n <requirements>\n <requirement type='package' version='@TOOL_VERSION@'>plink</requirement>\n+ <requirement type='package' version='5.3.0'>gawk</requirement>\n </requirements>\n <command detect_errors='exit_code'><![CDATA[\n \n@@ -62,17 +64,17 @@\n #if $functions.func == 'data_manage':\n #if $functions.bmerge.set == 'Yes':\n && mkdir bmerge_files\n- && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bed bmerge_files/bmerge_input.bed\n- && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bim bmerge_files/bmerge_input.bim\n- && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.fam bmerge_files/bmerge_input.fam\n+ && ln -s '$functions.bmerge.bed.extra_files_path/RgeneticsData.bed' 'bmerge_files/bmerge_input.bed'\n+ && ln -s '$functions.bmerge.bed.extra_files_path/RgeneticsData.bim' 'bmerge_files/bmerge_input.bim'\n+ && ln -s '$functions.bmerge.bed.extra_files_path/RgeneticsData.fam' 'bmerge_files/bmerge_input.fam'\n #end if\n #end if\n \n \n #if $inputs.inputs.filetype == 'bfile':\n- && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bed plink_input/plink_input.bed\n- && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bim plink_input/plink_input.bim\n- && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.fam plink_input/plink_input.fam\n+ && ln -s '$inputs.inputs.bed.extra_files_path/RgeneticsData.bed' 'plink_input/plink_input.bed'\n+ && ln -s '$inputs.inputs.bed.extra_files_path/RgeneticsData.bim' 'plink_input/plink_input.bim'\n+ && ln -s '$inputs.inputs.bed.extra_files_path/RgeneticsData.fam' 'plink_input/plink_input.fam'\n && plink --bfile plink_input/plink_input\n #elif $inputs.inputs.filetype == 'vcf':\n #if $inputs.inputs.input.is_of_type('bcf'):\n@@ -84,7 +86,7 @@\n \n ## Plink commands by section\n #if $inputs.covar_input:\n- --covar '$inputs.covar_input'\n+ --covar '$inputs.covar_input'\n #end if\n #if $inputs.set_pheno.set_pheno == 'Yes':\n --pheno $inputs.set_pheno.pheno $inputs.set_pheno.all_pheno\n@@ -232,7 +234,6 @@\n #end if\n \n #elif $functions.func == 'data_manage':\n-\n #if $functions.bmerge.set == 'Yes':\n --bmerge bmerge_files/bmerge_input\n #end if\n@@ -285,8 +286,6 @@\n #end if\n #end if\n #end if\n-\n-\n #elif $functions.func == 'link':\n #if $functions.set_indep.choice == 'Yes':\n --indep-pairwise $functions.set_indep.window $functions.set_indep.step $functions.set_indep.r2\n@@ -382,8 +381,8 @@\n #end if\n #end if\n \n-## #elif $functions.func == 'scoring':\n-##\n+ #elif $functions.func == 'scoring':\n+ --score '$functions.score_file' $functions.variant_id_i $functions.allel_codes_j $functions.scores_k $functions.header $functions.sum\n ## #else:\n ## --rerun $functions.logfile\n ## \n@@ -410,9 +409,12 @@\n #end if\n #end if\n && mkdir '$plink_out.extra_files_path'\n- && cp plink_output/plink_output.bed '$plink_out.extra_files_path'/RgeneticsData.bed\n- && cp plink_output/plink_output.bim '$plink_out.extra_files_path'/RgeneticsData.bim\n- && cp plink_output/plink_output.fam '$plink_out.extra_files_path'/RgeneticsData.fam\n+ && cp plink_output/plink_output.bed '$plink_out.extra_files_path/RgeneticsData.bed'\n+ && cp plink_output/plink_outp"..b'\' label=\'Lambda value\' optional=\'true\'/>\n </when>\n- <!-- <when value=\'scoring\'>\n- </when> -->\n+ <when value=\'scoring\'>\n+ <!-- this implements a part of the -\\-score parameter -->\n+ <param name=\'score_file\' format=\'tabular\' type=\'data\' label=\'Scoring system which should be applied to all samples\'/>\n+ <param name="variant_id_i" type="data_column" data_ref="score_file" label="Variant ID column"/>\n+ <param name="allel_codes_j" type="data_column" data_ref="score_file" label="Allel column"/>\n+ <param name="scores_k" type="data_column" data_ref="score_file" label="Score column"/>\n+ <param name=\'header\' type=\'boolean\' truevalue=\'header\' falsevalue=\'\' checked=\'false\' label=\'Is a header line present in the scores file?\'/>\n+\n+ <param name="sum" type="select" label="How to combine the valid per-variant scores?" help="Average is the default, but it can be changed to sum.">\n+ <option value="">Final scores are averages of the valid per-variant scores</option>\n+ <option value="sum">Report sums (sum; can not be used with \'no-mean-imputation\'; is automatically on with dosage data)</option>\n+ <option value="no-sum">Disable sum (no-sum)</option>\n+ </param>\n+ </when>\n <when value=\'ibd\'>\n <conditional name=\'genome\'>\n <param name=\'output_genome\' type=\'select\' help=\'Perform and return results of IBS/IBD computation\'>\n@@ -1060,6 +1075,11 @@\n <filter>functions[\'func\'] == \'ibd\' and functions[\'genome\'][\'output_genome\']</filter>\n </data>\n \n+ <!--scores-->\n+ <data name=\'scores\' format=\'tabular\' from_work_dir=\'plink_output/plink_output.profile.tab\' label=\'${tool.name}: Scores\'>\n+ <filter>functions[\'func\'] == \'scoring\'</filter>\n+ </data>\n+\n <!--Stratifiction-->\n <data name=\'mds\' format=\'txt\' from_work_dir=\'plink_output/plink_output.mds\' label=\'${tool.name}: MDS\'>\n <filter>functions[\'func\'] == \'stratification\' and functions[\'cluster\'][\'cluster\'] == \'Yes\' and functions[\'cluster\'][\'mds\'][\'mds_scaling\'] == \'Yes\'</filter>\n@@ -1203,6 +1223,7 @@\n <expand macro="log_out_assert"/>\n </test>\n \n+ \n <test expect_num_outputs=\'8\'>\n <section name=\'inputs\'>\n <conditional name=\'inputs\'>\n@@ -1393,6 +1414,30 @@\n <expand macro="log_out_assert"/>\n <output name=\'genome\' file=\'out.genome\'/>\n </test>\n+ <!-- scoring function test-->\n+ <test expect_num_outputs=\'3\'>\n+ <section name=\'inputs\'>\n+ <conditional name=\'inputs\'>\n+ <param name=\'filetype\' value=\'bfile\'/>\n+ <param name=\'bed\' value=\'\' ftype="pbed">\n+ <composite_data value="plink.bim"/>\n+ <composite_data value="plink.bed"/>\n+ <composite_data value="plink.fam"/>\n+ </param>\n+ </conditional>\n+ </section>\n+ <conditional name=\'functions\'>\n+ <param name=\'func\' value=\'scoring\'/>\n+ <param name=\'score_file\' value=\'scores_file.tab\'/>\n+ <param name=\'variant_id_i\' value=\'1\'/>\n+ <param name=\'allel_codes_j\' value=\'2\'/>\n+ <param name=\'scores_k\' value=\'3\'/>\n+ <param name=\'header\' value=\'true\'/>\n+ <param name=\'sum\' value=\'sum\'/>\n+ </conditional>\n+ <expand macro="log_out_assert"/>\n+ <output name=\'scores\' file=\'scores_results.tab\'/>\n+ </test>\n </tests>\n <help><![CDATA[\n PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.\n' |
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| diff -r 272aca44b3dd -r 2c0ac05fe240 test-data/scores_file.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scores_file.tab Tue Nov 14 17:51:25 2023 +0000 |
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| @@ -0,0 +1,10 @@ +variant effect_allele beta +snp1 T -0.078507 +snp2 A 0.16488 +snp3 C -0.043171 +snp18 C -0.37606 +snp19 T -0.039295 +snp20 A 0.033082 +snp21 T 0.13057 +snp22 C 0.02329 +snp23 G 0.027248 |
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| diff -r 272aca44b3dd -r 2c0ac05fe240 test-data/scores_results.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/scores_results.tab Tue Nov 14 17:51:25 2023 +0000 |
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| @@ -0,0 +1,201 @@ +FID IID PHENO CNT CNT2 SCORESUM +per0 per0 1 4 0 0 +per1 per1 2 4 2 0.066164 +per2 per2 1 4 3 0.231044 +per3 per3 1 4 2 0.197962 +per4 per4 1 4 2 0.197962 +per5 per5 1 4 1 0.16488 +per6 per6 2 4 2 0.32976 +per7 per7 2 4 2 0.197962 +per8 per8 1 4 2 0.197962 +per9 per9 1 4 2 0.197962 +per10 per10 1 4 2 0.197962 +per11 per11 2 4 1 0.16488 +per12 per12 1 4 0 0 +per13 per13 2 4 3 0.362842 +per14 per14 2 4 3 0.231044 +per15 per15 1 4 1 0.16488 +per16 per16 2 4 2 0.197962 +per17 per17 2 4 1 0.16488 +per18 per18 1 4 2 0.197962 +per19 per19 2 4 3 0.231044 +per20 per20 2 4 3 0.362842 +per21 per21 2 4 2 0.197962 +per22 per22 2 4 1 0.033082 +per23 per23 2 4 0 0 +per24 per24 1 4 2 0.32976 +per25 per25 1 4 4 0.395924 +per26 per26 2 4 1 0.033082 +per27 per27 2 4 1 0.16488 +per28 per28 2 4 1 0.033082 +per29 per29 2 4 3 0.231044 +per30 per30 2 4 2 0.197962 +per31 per31 2 4 2 0.197962 +per32 per32 2 4 0 0 +per33 per33 1 4 2 0.32976 +per34 per34 1 4 2 0.197962 +per35 per35 1 4 4 0.395924 +per36 per36 2 4 1 0.033082 +per37 per37 2 4 3 0.231044 +per38 per38 2 4 1 0.033082 +per39 per39 1 4 2 0.197962 +per40 per40 1 4 2 0.197962 +per41 per41 1 4 2 0.197962 +per42 per42 2 4 2 0.197962 +per43 per43 2 4 2 0.32976 +per44 per44 2 4 4 0.395924 +per45 per45 2 4 4 0.395924 +per46 per46 2 4 2 0.066164 +per47 per47 2 4 2 0.197962 +per48 per48 1 4 3 0.231044 +per49 per49 1 4 4 0.395924 +per50 per50 2 4 3 0.231044 +per51 per51 1 4 2 0.197962 +per52 per52 2 4 1 0.033082 +per53 per53 1 4 3 0.362842 +per54 per54 2 4 1 0.033082 +per55 per55 1 4 2 0.32976 +per56 per56 2 4 1 0.033082 +per57 per57 2 4 2 0.32976 +per58 per58 2 4 2 0.066164 +per59 per59 1 4 2 0.197962 +per60 per60 2 4 2 0.32976 +per61 per61 2 4 1 0.16488 +per62 per62 2 4 1 0.033082 +per63 per63 1 4 2 0.197962 +per64 per64 1 4 3 0.231044 +per65 per65 2 4 3 0.362842 +per66 per66 2 4 4 0.395924 +per67 per67 1 4 2 0.066164 +per68 per68 2 4 3 0.231044 +per69 per69 1 4 1 0.16488 +per70 per70 2 4 2 0.197962 +per71 per71 2 4 2 0.197962 +per72 per72 2 4 2 0.32976 +per73 per73 1 4 1 0.033082 +per74 per74 2 4 1 0.16488 +per75 per75 1 4 2 0.066164 +per76 per76 2 4 1 0.16488 +per77 per77 2 4 3 0.231044 +per78 per78 1 4 2 0.066164 +per79 per79 2 4 3 0.362842 +per80 per80 1 4 3 0.362842 +per81 per81 2 4 3 0.231044 +per82 per82 1 4 2 0.197962 +per83 per83 1 4 3 0.362842 +per84 per84 1 4 2 0.197962 +per85 per85 2 4 0 0 +per86 per86 1 4 3 0.362842 +per87 per87 2 4 1 0.033082 +per88 per88 1 4 2 0.32976 +per89 per89 2 4 2 0.32976 +per90 per90 2 4 1 0.16488 +per91 per91 1 4 2 0.197962 +per92 per92 2 4 3 0.231044 +per93 per93 1 4 3 0.231044 +per94 per94 2 4 1 0.16488 +per95 per95 2 4 3 0.362842 +per96 per96 2 4 3 0.362842 +per97 per97 1 4 2 0.197962 +per98 per98 2 4 1 0.16488 +per99 per99 2 4 0 0 +per100 per100 2 4 1 0.033082 +per101 per101 2 4 1 0.16488 +per102 per102 1 4 0 0 +per103 per103 1 4 2 0.197962 +per104 per104 1 4 1 0.16488 +per105 per105 2 4 1 0.033082 +per106 per106 2 4 2 0.197962 +per107 per107 2 4 1 0.16488 +per108 per108 2 4 2 0.32976 +per109 per109 1 4 3 0.362842 +per110 per110 1 4 2 0.066164 +per111 per111 1 4 2 0.197962 +per112 per112 2 4 4 0.395924 +per113 per113 1 4 0 0 +per114 per114 2 4 3 0.231044 +per115 per115 1 4 2 0.197962 +per116 per116 1 4 1 0.16488 +per117 per117 2 4 2 0.197962 +per118 per118 2 4 2 0.066164 +per119 per119 2 4 0 0 +per120 per120 2 4 1 0.16488 +per121 per121 1 4 3 0.231044 +per122 per122 2 4 0 0 +per123 per123 1 4 4 0.395924 +per124 per124 1 4 2 0.197962 +per125 per125 1 4 3 0.362842 +per126 per126 2 4 2 0.066164 +per127 per127 1 4 2 0.066164 +per128 per128 2 4 1 0.16488 +per129 per129 2 4 2 0.197962 +per130 per130 2 4 1 0.16488 +per131 per131 2 4 1 0.033082 +per132 per132 2 4 3 0.362842 +per133 per133 2 4 2 0.066164 +per134 per134 1 4 2 0.197962 +per135 per135 1 4 1 0.033082 +per136 per136 1 4 0 0 +per137 per137 1 4 3 0.362842 +per138 per138 1 4 2 0.32976 +per139 per139 1 4 1 0.033082 +per140 per140 1 4 0 0 +per141 per141 1 4 3 0.362842 +per142 per142 1 4 1 0.16488 +per143 per143 1 4 2 0.197962 +per144 per144 2 4 2 0.066164 +per145 per145 2 4 2 0.197962 +per146 per146 1 4 3 0.362842 +per147 per147 2 4 2 0.197962 +per148 per148 2 4 2 0.197962 +per149 per149 2 4 3 0.362842 +per150 per150 1 4 2 0.066164 +per151 per151 2 4 1 0.033082 +per152 per152 1 4 1 0.16488 +per153 per153 2 4 3 0.231044 +per154 per154 2 4 1 0.16488 +per155 per155 1 4 3 0.231044 +per156 per156 1 4 2 0.32976 +per157 per157 1 4 3 0.362842 +per158 per158 2 4 1 0.16488 +per159 per159 1 4 2 0.066164 +per160 per160 2 4 3 0.231044 +per161 per161 1 4 2 0.197962 +per162 per162 2 4 2 0.197962 +per163 per163 1 4 2 0.197962 +per164 per164 2 4 3 0.231044 +per165 per165 2 4 4 0.395924 +per166 per166 1 4 2 0.197962 +per167 per167 1 4 2 0.197962 +per168 per168 1 4 2 0.197962 +per169 per169 1 4 1 0.033082 +per170 per170 2 4 1 0.16488 +per171 per171 1 4 1 0.033082 +per172 per172 1 4 3 0.231044 +per173 per173 1 4 3 0.362842 +per174 per174 1 4 1 0.033082 +per175 per175 2 4 2 0.197962 +per176 per176 2 4 0 0 +per177 per177 2 4 2 0.197962 +per178 per178 1 4 1 0.033082 +per179 per179 1 4 2 0.197962 +per180 per180 1 4 2 0.066164 +per181 per181 1 4 1 0.033082 +per182 per182 1 4 3 0.362842 +per183 per183 1 4 4 0.395924 +per184 per184 1 4 3 0.362842 +per185 per185 1 4 2 0.197962 +per186 per186 2 4 3 0.231044 +per187 per187 1 4 1 0.16488 +per188 per188 1 4 3 0.231044 +per189 per189 2 4 2 0.197962 +per190 per190 1 4 1 0.033082 +per191 per191 1 4 4 0.395924 +per192 per192 1 4 2 0.197962 +per193 per193 2 4 1 0.033082 +per194 per194 2 4 2 0.197962 +per195 per195 1 4 2 0.32976 +per196 per196 1 4 2 0.197962 +per197 per197 1 4 3 0.231044 +per198 per198 1 4 3 0.231044 +per199 per199 2 4 4 0.395924 |