Mercurial > repos > iuc > stacks_genotypes
changeset 8:8dc6a3afbe83 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
| author | iuc |
|---|---|
| date | Thu, 27 Apr 2017 04:19:10 -0400 |
| parents | 639f2db87df0 |
| children | 5af94af9ec8f |
| files | macros.xml stacks_genotypes.xml test-data/demultiplexed/PopA_01.1.fq.gzip test-data/denovo_map/popmap_cstacks.tsv test-data/procrad/R1.fq.gzip test-data/ustacks/ustacks.out |
| diffstat | 6 files changed, 89 insertions(+), 18 deletions(-) [+] |
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--- a/macros.xml Fri Apr 07 11:48:36 2017 -0400 +++ b/macros.xml Thu Apr 27 04:19:10 2017 -0400 @@ -2,14 +2,14 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="1.42">stacks</requirement> + <requirement type="package" version="1.46">stacks</requirement> <requirement type="package" version="1.2.10">velvet</requirement> - <container type="docker">quay.io/biocontainers/stacks:1.42--2</container> + <requirement type="package" version="1.1">stacks_summary</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">1.42</token> + <token name="@WRAPPER_VERSION@">1.46</token> <xml name="stdio"> <stdio> @@ -90,6 +90,7 @@ <option value="bsaHI">bsaHI</option> <option value="hpaII">hpaII</option> <option value="ncoI">ncoI</option> + <option value="ApaLI">ApaLI</option> </xml> <xml name="cross_types"> @@ -100,6 +101,19 @@ <option value="GEN">GEN (generic, unspecific to any map type)</option> </xml> + <token name="@CLEAN_EXT@"> + <![CDATA[ + #from os.path import splitext + #import re + #def clean_ext($identifier) + #while $identifier.endswith(('.1', '.fa', '.fq', '.fasta', '.fastq', '.gz', '.gzip', '.sam', '.bam')) + #set $identifier = splitext($identifier)[0] + #end while +$identifier#slurp + #end def + ]]> + </token> + <token name="@NORM_GENOTYPES_OUTPUT_LIGHT@"> <![CDATA[ ## We need to do this as the output file names contains the value of an option (min progeny)
--- a/stacks_genotypes.xml Fri Apr 07 11:48:36 2017 -0400 +++ b/stacks_genotypes.xml Thu Apr 27 04:19:10 2017 -0400 @@ -12,13 +12,13 @@ && - #for $input_file in $input_col: + #for $input_file in $input_col #set $filename = str($input_file.element_identifier) - #if not $filename.endswith('.tsv'): + #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/${filename}" && + #if re.search('\.(tags|snps|alleles|matches)(\.tsv)?$', $filename) + ln -s '${input_file}' 'stacks_outputs/${filename}' && #end if #end for @@ -30,34 +30,34 @@ -t $options_usage.cross_type -o $options_usage.map_out.map_out_type - #if str( $options_usage.map_out.map_out_type ) == "genomic": + #if str( $options_usage.map_out.map_out_type ) == "genomic" -e ${options_usage.map_out.enzyme} #end if - #if str($advanced_options.minprogeny): + #if str($advanced_options.minprogeny) -r $advanced_options.minprogeny #end if - #if str($advanced_options.mindepth): + #if str($advanced_options.mindepth) -m $advanced_options.mindepth #end if - #if str($advanced_options.lnl): + #if str($advanced_options.lnl) --lnl_lim $advanced_options.lnl #end if - #if $advanced_options.blacklist: - -B "$advanced_options.blacklist" + #if $advanced_options.blacklist + -B '$advanced_options.blacklist' #end if - #if $advanced_options.whitelist: - -W "$advanced_options.whitelist" + #if $advanced_options.whitelist + -W '$advanced_options.whitelist' #end if - #if $advanced_options.manual_cor: - --corr_path "$advanced_options.manual_cor" + #if $advanced_options.manual_cor + --corr_path '$advanced_options.manual_cor' #end if - #if $options_autocorr.corrections: + #if $options_autocorr.corrections -c --min_hom_seqs $options_autocorr.hom --min_het_seqs $options_autocorr.het @@ -68,6 +68,10 @@ -s @NORM_GENOTYPES_OUTPUT_FULL@ + + && + + stacks_summary.py --stacks-prog genotypes --res-dir stacks_outputs --summary stacks_outputs/summary.html ]]></command> <inputs> <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)" /> @@ -85,6 +89,9 @@ <option value="rqtl">R/QTL</option> <option value="genomic">Genomic</option> </param> + <when value="joinmap"/> + <when value="onemap"/> + <when value="rqtl"/> <when value="genomic"> <param name="enzyme" argument="-e" type="select" label="Restriction enzyme used" help="Only needed for Genomic output format"> <expand macro="enzymes"/> @@ -120,6 +127,8 @@ </inputs> <outputs> <expand macro="genotypes_output_full"/> + + <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> </outputs> <tests> @@ -143,6 +152,12 @@ <param name="cross_type" value="CP" /> <param name="advanced_options|minprogeny" value="1" /> + <output name="output_summary"> + <assert_contents> + <has_text text="Stacks Statistics" /> + </assert_contents> + </output> + <!-- genotypes --> <output name="out_generic_haplo"> <assert_contents>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/popmap_cstacks.tsv Thu Apr 27 04:19:10 2017 -0400 @@ -0,0 +1,1 @@ +PopA_01 myPopA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/ustacks.out Thu Apr 27 04:19:10 2017 -0400 @@ -0,0 +1,41 @@ +ustacks parameters selected: + Sample ID: 1 + Min depth of coverage to create a stack: 2 + Max distance allowed between stacks: 2 + Max distance allowed to align secondary reads: 4 + Max number of stacks allowed per de novo locus: 3 + Deleveraging algorithm: disabled + Removal algorithm: enabled + Model type: SNP + Alpha significance level for model: 0.05 + Gapped alignments: disabled +Parsing stacks_inputs/PopA_01.fq +Loading RAD-Tags...done +Loaded 66 RAD-Tags. + Inserted 7 elements into the RAD-Tags hash map. + 0 reads contained uncalled nucleotides that were modified. +4 initial stacks were populated; 3 stacks were set aside as secondary reads. +Initial coverage mean: 15.75; Std Dev: 7.46241; Max: 27 +Deleveraging trigger: 23; Removal trigger: 31 +Calculating distance for removing repetitive stacks. + Distance allowed between stacks: 1; searching with a k-mer length of 47 (48 k-mers per read); 1 k-mer hits required. +Removing repetitive stacks. + Removed 0 stacks. + 4 stacks remain for merging. +Post-Repeat Removal, coverage depth Mean: 15.75; Std Dev: 7.46241; Max: 27 +Calculating distance between stacks... + Distance allowed between stacks: 2; searching with a k-mer length of 31 (64 k-mers per read); 2 k-mer hits required. +Merging stacks, maximum allowed distance: 2 nucleotide(s) + 4 stacks merged into 3 loci; deleveraged 0 loci; blacklisted 0 loci. +After merging, coverage depth Mean: 21; Std Dev: 4.24264; Max: 27 +Merging remainder radtags + 3 remainder sequences left to merge. + Distance allowed between stacks: 4; searching with a k-mer length of 17 (78 k-mers per read); 10 k-mer hits required. + Matched 3 remainder reads; unable to match 0 remainder reads. +After remainders merged, coverage depth Mean: 22; Std Dev: 4.32049; Max: 28 +Calling final consensus sequences, invoking SNP-calling model... +Number of utilized reads: 66 +Writing loci, SNPs, and alleles to 'stacks_outputs/'... + Refetching sequencing IDs from stacks_inputs/PopA_01.fq... read 66 sequence IDs. +done. +ustacks is done.