Mercurial > repos > iuc > stacks_populations
changeset 4:d0b325dfe508 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit 643293a896a2ccfac10fe995f48c7f01c1a89a7f
| author | iuc |
|---|---|
| date | Mon, 26 Sep 2016 11:44:41 -0400 |
| parents | 2ac5c9616748 |
| children | b3ea05f1490b |
| files | macros.xml stacks_populations.xml test-data/populations/batch_1.vcf tool_dependencies.xml |
| diffstat | 4 files changed, 123 insertions(+), 29 deletions(-) [+] |
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--- a/macros.xml Sat Jun 25 17:28:14 2016 -0400 +++ b/macros.xml Mon Sep 26 11:44:41 2016 -0400 @@ -2,14 +2,14 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.40">stacks</requirement> + <requirement type="package" version="1.42">stacks</requirement> <requirement type="package" version="1.2.10">velvet</requirement> - <container type="docker">quay.io/mulled/stacks:1.40--1</container> + <container type="docker">quay.io/mulled/stacks:1.42--2</container> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">1.40</token> + <token name="@WRAPPER_VERSION@">1.42</token> <xml name="stdio"> <stdio> @@ -86,6 +86,10 @@ <option value="taqI">taqI</option> <option value="xbaI">xbaI</option> <option value="xhoI">xhoI</option> + <option value="csp6I">csp6I</option> + <option value="bsaHI">bsaHI</option> + <option value="hpaII">hpaII</option> + <option value="ncoI">ncoI</option> </xml> <xml name="cross_types">
--- a/stacks_populations.xml Sat Jun 25 17:28:14 2016 -0400 +++ b/stacks_populations.xml Mon Sep 26 11:44:41 2016 -0400 @@ -1,4 +1,4 @@ -<tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.1"> +<tool id="stacks_populations" name="Stacks: populations" version="@WRAPPER_VERSION@.0"> <description>analyze a population of individual samples ('populations' program)</description> <macros> <import>macros.xml</import> @@ -12,21 +12,29 @@ && - #for $input_file in $options_usage.input_col: - #set $filename = str($input_file.element_identifier) - #if not $filename.endswith('.tsv'): - #set $filename = $filename + ".tsv" - #end if - #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename): - ln -s "${input_file}" "stacks_outputs/${filename}" && - #end if - #end for + #if str($options_usage.input_type) == 'stacks': + #for $input_file in $options_usage.input_col: + #set $filename = str($input_file.element_identifier) + #if not $filename.endswith('.tsv'): + #set $filename = $filename + ".tsv" + #end if + #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename): + ln -s "${input_file}" "stacks_outputs/${filename}" && + #end if + #end for + #end if populations -t \${GALAXY_SLOTS:-1} - -P stacks_outputs + #if str($options_usage.input_type) == 'vcf': + -V "$options_usage.input_vcf" + #else: + -P stacks_outputs + -b $advanced_options.batchid + #end if + -M "$options_usage.popmap" ## Data filtering @@ -111,14 +119,23 @@ #if $advanced_options.whitelist: -W "$advanced_options.whitelist" #end if - -b $advanced_options.batchid ]]></command> <inputs> - <section name="options_usage" title="Input" expanded="true"> - <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" /> - <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" /> - </section> + <conditional name="options_usage"> + <param name="input_type" type="select" label="Input type" help="select input file type" > + <option value="stacks">Stacks output</option> + <!--option value="vcf">VCF file</option--> <!-- broken in 1.42 --> + </param> + <when value="stacks"> + <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map or refmap)" argument="-P" /> + <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" /> + </when> + <when value="vcf"> + <param name="input_vcf" format="vcf" type="data" label="VCF file" argument="-V" /> + <param name="popmap" type="data" format="tabular,txt" label="Specify a population map" argument="-M" /> + </when> + </conditional> <section name="options_filtering" title="Data filtering options" expanded="true"> @@ -225,6 +242,7 @@ <tests> <test> + <param name="options_usage|input_type" value="stacks" /> <param name="options_usage|input_col"> <collection type="list"> <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" /> @@ -292,7 +310,7 @@ </output> <output name="out_vcf"> <assert_contents> - <has_text text="fileformat=VCFv4.0" /> + <has_text text="fileformat=VCFv4.2" /> </assert_contents> </output> <output name="out_treemix_pop"> @@ -306,6 +324,75 @@ </assert_contents> </output> </test> + <!--test> + <param name="options_usage|input_type" value="vcf" /> + <param name="options_usage|input_vcf" value="populations/batch_1.vcf" /> + <param name="options_usage|popmap" ftype="tabular" value="denovo_map/popmap.tsv" /> + <param name="options_filtering|correction_select|correction" value="p_value" /> + + <param name="populations_output|ordered_export" value="true" /> + <param name="populations_output|vcf" value="true" /> + <param name="populations_output|vcf_haplotypes" value="true" /> + <param name="populations_output|genepop" value="true" /> + <param name="populations_output|structure" value="true" /> + <param name="populations_output|fasta" value="true" /> + <param name="populations_output|fasta_strict" value="true" /> + <param name="populations_output|hzar" value="true" /> + <param name="populations_output|phase" value="true" /> + <param name="populations_output|fastphase" value="true" /> + <param name="populations_output|beagle" value="true" /> + <param name="populations_output|beagle_phased" value="true" /> + <param name="populations_output|plink" value="true" /> + <param name="populations_output|phylip" value="true" /> + <param name="populations_output|phylip_var" value="true" /> + <param name="populations_output|phylip_var_all" value="true" /> + <param name="populations_output|treemix" value="true" /> + + <param name="populations_output|options_genomic|genomic" value="true" /> + <param name="populations_output|options_genomic|enzyme" value="ecoRI" /--> + + <!-- populations --> + <!--output name="out_haplotypes"> + <assert_contents> + <has_text text="PopA_01" /> + </assert_contents> + </output> + <output name="out_hapstats"> + <assert_contents> + <has_text text="Smoothed Gene Diversity" /> + </assert_contents> + </output> + <output name="out_populations_log"> + <assert_contents> + <has_text text="populations version" /> + </assert_contents> + </output> + <output name="out_sumstats_sum"> + <assert_contents> + <has_text text="Polymorphic Sites" /> + </assert_contents> + </output> + <output name="out_sumstats"> + <assert_contents> + <has_text text="Smoothed Pi" /> + </assert_contents> + </output> + <output name="out_vcf"> + <assert_contents> + <has_text text="fileformat=VCFv4.2" /> + </assert_contents> + </output> + <output name="out_treemix_pop"> + <assert_contents> + <has_text text="TreeMix v1.1;" /> + </assert_contents> + </output> + <output name="out_fasta"> + <assert_contents> + <has_text text="AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGCGAGAC" /> + </assert_contents> + </output> + </test--> <!-- broken in 1.42 --> </tests> <help> <![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/batch_1.vcf Mon Sep 26 11:44:41 2016 -0400 @@ -0,0 +1,12 @@ +##fileformat=VCFv4.2 +##fileDate=20160926 +##source="Stacks v1.42" +##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> +##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> +##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Allele Depth"> +##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihood"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT PopA_01 PopA_02 +un 35 1_33 A C . PASS NS=2;AF=0.500 GT:DP:AD:GL 0/1:18:9,9:.,19.78,. 0/1:10:6,4:.,13.18,. +un 90 1_88 A C . PASS NS=2;AF=0.500 GT:DP:AD:GL 0/1:18:9,9:.,19.78,. 0/1:10:4,6:.,13.18,.
--- a/tool_dependencies.xml Sat Jun 25 17:28:14 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,9 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="stacks" version="1.40"> - <repository changeset_revision="51d4ab2c4dcf" name="package_stacks_1_40" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="velvet" version="1.2.10"> - <repository changeset_revision="93d32326537b" name="package_velvet_1_2_10" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>