Mercurial > repos > iuc > plink
diff plink.xml @ 9:272aca44b3dd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit e4f567640710d5f8447b31bd6d78e7fb2d8fe401"
author | iuc |
---|---|
date | Sun, 19 Dec 2021 15:53:35 +0000 |
parents | 16d22eee0fe3 |
children | 2c0ac05fe240 |
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--- a/plink.xml Thu Dec 02 16:20:30 2021 +0000 +++ b/plink.xml Sun Dec 19 15:53:35 2021 +0000 @@ -1,7 +1,7 @@ <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'> <macros> - <token name='@TOOL_VERSION@'>1.9.b618</token> - <token name='@VERSION_SUFFIX@'>3</token> + <token name='@TOOL_VERSION@'>1.90b6.21</token> + <token name='@VERSION_SUFFIX@'>0</token> <xml name='template_sanitizer'> <sanitizer> <valid initial='default'> @@ -37,12 +37,19 @@ </valid> </sanitizer> </xml> + <xml name="log_out_assert"> + <output name="plink_log"> + <assert_contents> + <has_text text="End time:"/> + </assert_contents> + </output> + </xml> </macros> <xrefs> <xref type="bio.tools">plink</xref> </xrefs> <requirements> - <requirement type='package' version='1.90b6.18'>plink</requirement> + <requirement type='package' version='@TOOL_VERSION@'>plink</requirement> </requirements> <command detect_errors='exit_code'><![CDATA[ @@ -55,17 +62,17 @@ #if $functions.func == 'data_manage': #if $functions.bmerge.set == 'Yes': && mkdir bmerge_files - && ln -s '$functions.bmerge.bed' bmerge_files/bmerge_input.bed - && ln -s '$functions.bmerge.bim' bmerge_files/bmerge_input.bim - && ln -s '$functions.bmerge.fam' bmerge_files/bmerge_input.fam + && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bed bmerge_files/bmerge_input.bed + && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.bim bmerge_files/bmerge_input.bim + && ln -s '$functions.bmerge.bed.extra_files_path'/RgeneticsData.fam bmerge_files/bmerge_input.fam #end if #end if #if $inputs.inputs.filetype == 'bfile': - && ln -s '$inputs.inputs.bed' plink_input/plink_input.bed - && ln -s '$inputs.inputs.bim' plink_input/plink_input.bim - && ln -s '$inputs.inputs.fam' plink_input/plink_input.fam + && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bed plink_input/plink_input.bed + && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.bim plink_input/plink_input.bim + && ln -s '$inputs.inputs.bed.extra_files_path'/RgeneticsData.fam plink_input/plink_input.fam && plink --bfile plink_input/plink_input #elif $inputs.inputs.filetype == 'vcf': #if $inputs.inputs.input.is_of_type('bcf'): @@ -402,6 +409,10 @@ && find ./assoc_out/. -type f -exec mv {} {}.txt ';' #end if #end if + && mkdir '$plink_out.extra_files_path' + && cp plink_output/plink_output.bed '$plink_out.extra_files_path'/RgeneticsData.bed + && cp plink_output/plink_output.bim '$plink_out.extra_files_path'/RgeneticsData.bim + && cp plink_output/plink_output.fam '$plink_out.extra_files_path'/RgeneticsData.fam ]]></command> <inputs> <section name='inputs' title='Data inputs' expanded='true'> @@ -412,8 +423,6 @@ </param> <when value='bfile'> <param format='pbed' name='bed' type='data' label='plink bed file'/> - <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/> - <param format='txt' name='fam' type='data' label='plink fam file'/> </when> <when value='vcf'> <param name='input' format='vcf,vcf_bgzip,bcf' type='data' label='VCF/BCF Input file'/> @@ -671,9 +680,7 @@ </param> <when value='No'/> <when value='Yes'> - <param format='binary' name='bed' type='data' label='plink bed file'/> - <param format='tabular,tsv' name='bim' type='data' label='plink bim file'/> - <param format='tabular,tsv' name='fam' type='data' label='plink fam file'/> + <param format='pbed' name='bed' type='data' label='plink bed file'/> </when> </conditional> <param name='recode' type='boolean' label='Recode' truevalue='--recode' falsevalue='' checked='false' help='Create a new text fileset, after applying sample/variant filters and other operations'/> @@ -802,7 +809,6 @@ <param name='r2' type='float' label='Unphased Hardcall r^2 Threshold' value='0.2' /> </when> </conditional> - </when> <when value='stratification'> <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/> @@ -993,38 +999,35 @@ </inputs> <outputs> <!--Main--> - <collection name='plink_out' type='list' label='Plink main outputs'> - <data name='plink_bed' format='pbed' from_work_dir='plink_output/plink_output.bed'/> - <data name='plink_bim' format='tabular' from_work_dir='plink_output/plink_output.bim'/> - <data name='plink_fam' format='txt' from_work_dir='plink_output/plink_output.fam'/> - <data name='plink_log' format='txt' from_work_dir='plink_output/plink_output.log'/> - </collection> + <data name="plink_out" format="pbed"/> + + <data name="plink_log" format='txt' from_work_dir='plink_output/plink_output.log' label='${tool.name} on ${on_string}: Log'/> <!--Data Manage--> - <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name}: Recode ped'> + <data name='plink_ped' format='txt' from_work_dir='plink_output/plink_output.ped' label='${tool.name} on ${on_string}: Recode ped'> <filter>functions['func'] == 'data_manage' and functions['recode']</filter> </data> - <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name}: Recode map'> + <data name='plink_map' format='txt' from_work_dir='plink_output/plink_output.map' label='${tool.name} on ${on_string}: Recode map'> <filter>functions['func'] == 'data_manage' and functions['recode']</filter> </data> <!--Stats--> - <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name}: freq out'> + <data name='frequency' format='tabular' from_work_dir='plink_output/plink_output.frq' label='${tool.name} on ${on_string}: freq out'> <filter>functions['func'] == 'stats' and functions['freq']</filter> </data> - <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name}: Hardy-Weinberg equilibrium'> + <data name='hardy_out' format='tabular' from_work_dir='plink_output/plink_output.hwe' label='${tool.name} on ${on_string}: Hardy-Weinberg equilibrium'> <filter>functions['func'] == 'stats' and functions['hardy']</filter> </data> - <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name}: imiss'> + <data name='missing_1' format='tabular' from_work_dir='plink_output/plink_output.imiss' label='${tool.name} on ${on_string}: imiss'> <filter>functions['func'] == 'stats' and functions['missing']</filter> </data> - <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name}: lmiss'> + <data name='missing_2' format='tabular' from_work_dir='plink_output/plink_output.lmiss' label='${tool.name} on ${on_string}: lmiss'> <filter>functions['func'] == 'stats' and functions['missing']</filter> </data> - <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name}: Het'> + <data name='het' format='tabular' from_work_dir='plink_output/plink_output.het' label='${tool.name} on ${on_string}: Het'> <filter>functions['func'] == 'stats' and functions['het']</filter> </data> - <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name}: Sex check'> + <data name='sex_check' format='tabular' from_work_dir='plink_output/plink_output.sexcheck' label='${tool.name} on ${on_string}: Sex check'> <filter>functions['func'] == 'stats' and functions['sex']['sex_stats']</filter> </data> @@ -1081,13 +1084,15 @@ </data> </outputs> <tests> - <test expect_num_outputs='5'> + <test expect_num_outputs='2'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='bfile'/> - <param name='bed' value='plink.bed'/> - <param name='bim' value='plink.bim'/> - <param name='fam' value='plink.fam'/> + <param name='bed' value='' ftype="pbed"> + <composite_data value="plink.bim"/> + <composite_data value="plink.bed"/> + <composite_data value="plink.fam"/> + </param> </conditional> </section> <conditional name='functions'> @@ -1133,29 +1138,34 @@ <param name='nonfounders' value='--nonfounders'/> </conditional> </conditional> - <output_collection name='plink_out' type='list'> - <element name='plink_bed' file='test1_out.bed' compare='sim_size'/> - <element name='plink_bim' file='test1_out.bim'/> - <element name='plink_fam' file='test1_out.fam'/> - </output_collection> + <output name="plink_out"> + <extra_files type="file" name="RgeneticsData.bed" value="test1_out.bed" compare='sim_size'/> + <extra_files type="file" name="RgeneticsData.bim" value="test1_out.bim"/> + <extra_files type="file" name="RgeneticsData.fam" value="test1_out.fam"/> + </output> + <expand macro="log_out_assert"/> </test> - <test expect_num_outputs='7'> + <test expect_num_outputs='4'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='bfile'/> - <param name='bed' value='plink.bed'/> - <param name='bim' value='plink.bim'/> - <param name='fam' value='plink.fam'/> + <param name='bed' value='' ftype="pbed"> + <composite_data value="plink.bim"/> + <composite_data value="plink.bed"/> + <composite_data value="plink.fam"/> + </param> </conditional> </section> <conditional name='functions'> <param name='func' value='data_manage'/> <conditional name='bmerge'> <param name='set' value='Yes'/> - <param name='bed' value='plink_2.bed'/> - <param name='bim' value='plink_2.bim'/> - <param name='fam' value='plink_2.fam'/> + <param name='bed' value='' ftype="pbed"> + <composite_data value="plink_2.bim"/> + <composite_data value="plink_2.bed"/> + <composite_data value="plink_2.fam"/> + </param> </conditional> <param name='recode' value='--recode'/> <param name='template' value='@asd#123'/> @@ -1168,36 +1178,40 @@ <param name='skip' value='a'/> </conditional> </conditional> - <output_collection name='plink_out' type='list'> - <element name='plink_bed' file='test2_out.bed' compare='sim_size'/> - <element name='plink_bim' file='test2_out.bim'/> - <element name='plink_fam' file='test2_out.fam'/> - </output_collection> + <output name="plink_out"> + <extra_files type="file" name="RgeneticsData.bed" value="test2_out.bed" compare='sim_size'/> + <extra_files type="file" name="RgeneticsData.bim" value="test2_out.bim"/> + <extra_files type="file" name="RgeneticsData.fam" value="test2_out.fam"/> + </output> + <expand macro="log_out_assert"/> <output name='plink_ped' file='out.ped'/> <output name='plink_map' file='out.map'/> </test> - <test expect_num_outputs='5'> + <test expect_num_outputs='2'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='vcf'/> <param name='input' value='test.vcf'/> </conditional> </section> - <output_collection name='plink_out' type='list'> - <element name='plink_bed' file='vcf_out.bed'/> - <element name='plink_bim' file='vcf_out.bim'/> - <element name='plink_fam' file='vcf_out.fam'/> - </output_collection> + <output name="plink_out"> + <extra_files type="file" name="RgeneticsData.bed" value="vcf_out.bed" compare='sim_size'/> + <extra_files type="file" name="RgeneticsData.bim" value="vcf_out.bim"/> + <extra_files type="file" name="RgeneticsData.fam" value="vcf_out.fam"/> + </output> + <expand macro="log_out_assert"/> </test> - <test expect_num_outputs='11'> + <test expect_num_outputs='8'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='bfile'/> - <param name='bed' value='plink.bed'/> - <param name='bim' value='x_plink.bim'/> - <param name='fam' value='plink.fam'/> + <param name='bed' value='' ftype="pbed"> + <composite_data value="x_plink.bim"/> + <composite_data value="plink.bed"/> + <composite_data value="plink.fam"/> + </param> </conditional> </section> <conditional name='functions'> @@ -1217,12 +1231,12 @@ </conditional> </conditional> </conditional> - <output_collection name='plink_out' type='list'> - <element name='plink_bed' file='stats.bed'/> - <element name='plink_bim' file='stats.bim'/> - <element name='plink_fam' file='stats.fam'/> - <element name='plink_fam' file='stats.fam'/> - </output_collection> + <output name="plink_out"> + <extra_files type="file" name="RgeneticsData.bed" value="stats.bed" compare='sim_size'/> + <extra_files type="file" name="RgeneticsData.bim" value="stats.bim"/> + <extra_files type="file" name="RgeneticsData.fam" value="stats.fam"/> + </output> + <expand macro="log_out_assert"/> <output name='frequency' file='out.freq'/> <output name='hardy_out' file='out.hardy'/> <output name='missing_1' file='out.imiss'/> @@ -1231,13 +1245,15 @@ <output name='sex_check' file='out.sexcheck'/> </test> - <test expect_num_outputs='7'> + <test expect_num_outputs='4'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='bfile'/> - <param name='bed' value='plink.bed'/> - <param name='bim' value='plink.bim'/> - <param name='fam' value='plink.fam'/> + <param name='bed' value='' ftype="pbed"> + <composite_data value="plink.bim"/> + <composite_data value="plink.bed"/> + <composite_data value="plink.fam"/> + </param> </conditional> </section> <conditional name='functions'> @@ -1249,21 +1265,24 @@ <param name='r2' value='0.3'/> </conditional> </conditional> - <output_collection name='plink_out' type='list'> - <element name='plink_bed' file='test5_out.bed' compare='sim_size'/> - <element name='plink_bim' file='test5_out.bim'/> - <element name='plink_fam' file='test5_out.fam'/> - </output_collection> + <output name="plink_out"> + <extra_files type="file" name="RgeneticsData.bed" value="test5_out.bed" compare='sim_size'/> + <extra_files type="file" name="RgeneticsData.bim" value="test5_out.bim"/> + <extra_files type="file" name="RgeneticsData.fam" value="test5_out.fam"/> + </output> + <expand macro="log_out_assert"/> <output name='prune_in' file='plink.prune.in'/> </test> - <test expect_num_outputs='10'> + <test expect_num_outputs='7'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='bfile'/> - <param name='bed' value='plink.bed'/> - <param name='bim' value='plink.bim'/> - <param name='fam' value='plink.fam'/> + <param name='bed' value='' ftype="pbed"> + <composite_data value="plink.bim"/> + <composite_data value="plink.bed"/> + <composite_data value="plink.fam"/> + </param> </conditional> </section> <conditional name='functions'> @@ -1279,11 +1298,12 @@ </conditional> </conditional> </conditional> - <output_collection name='plink_out' type='list'> - <element name='plink_bed' file='test6_out.bed' compare='sim_size'/> - <element name='plink_bim' file='test6_out.bim'/> - <element name='plink_fam' file='test6_out.fam'/> - </output_collection> + <output name="plink_out"> + <extra_files type="file" name="RgeneticsData.bed" value="test6_out.bed" compare='sim_size'/> + <extra_files type="file" name="RgeneticsData.bim" value="test6_out.bim"/> + <extra_files type="file" name="RgeneticsData.fam" value="test6_out.fam"/> + </output> + <expand macro="log_out_assert"/> <output name='mds' value='plink.mds' compare='sim_size'/> <output name='cluster1' value='plink.cluster1' compare='sim_size'/> <output name='cluster2' value='plink.cluster2' compare='sim_size'/> @@ -1291,13 +1311,15 @@ <output name='eigenvals' value='plink.mds.eigenval' compare='sim_size'/> </test> - <test expect_num_outputs='8'> + <test expect_num_outputs='5'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='bfile'/> - <param name='bed' value='plink.bed'/> - <param name='bim' value='plink.bim'/> - <param name='fam' value='plink.fam'/> + <param name='bed' value='' ftype="pbed"> + <composite_data value="plink.bim"/> + <composite_data value="plink.bed"/> + <composite_data value="plink.fam"/> + </param> </conditional> </section> <conditional name='functions'> @@ -1328,11 +1350,12 @@ </conditional> <param name='lambda' value='1.0'/> </conditional> - <output_collection name='plink_out' type='list'> - <element name='plink_bed' file='out.assoc.bed' compare='sim_size'/> - <element name='plink_bim' file='out.assoc.bim'/> - <element name='plink_fam' file='out.assoc.fam'/> - </output_collection> + <output name="plink_out"> + <extra_files type="file" name="RgeneticsData.bed" value="out.assoc.bed" compare='sim_size'/> + <extra_files type="file" name="RgeneticsData.bim" value="out.assoc.bim"/> + <extra_files type="file" name="RgeneticsData.fam" value="out.assoc.fam"/> + </output> + <expand macro="log_out_assert"/> <output_collection name='assoc_outfiles' type='list' count='2'> <element name='plink_output.assoc.fisher.mperm' value='out.assoc.fisher.mperm' compare='sim_size'/> <element name='plink_output.assoc.fisher' value='out.assoc.fisher'/> @@ -1347,13 +1370,15 @@ </output_collection> </test> - <test expect_num_outputs='6'> + <test expect_num_outputs='3'> <section name='inputs'> <conditional name='inputs'> <param name='filetype' value='bfile'/> - <param name='bed' value='plink.bed'/> - <param name='bim' value='plink.bim'/> - <param name='fam' value='plink.fam'/> + <param name='bed' value='' ftype="pbed"> + <composite_data value="plink.bim"/> + <composite_data value="plink.bed"/> + <composite_data value="plink.fam"/> + </param> </conditional> </section> <conditional name='functions'> @@ -1365,6 +1390,7 @@ <param name='modifiers' value='full,unbounded,nudge'/> </conditional> </conditional> + <expand macro="log_out_assert"/> <output name='genome' file='out.genome'/> </test> </tests>