Mercurial > repos > iuc > stacks_sstacks
changeset 8:db683c98e455 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
| author | iuc |
|---|---|
| date | Thu, 27 Apr 2017 04:17:14 -0400 |
| parents | b185c3e3f1dc |
| children | 95e37a28704b |
| files | macros.xml stacks_sstacks.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, 147 insertions(+), 23 deletions(-) [+] |
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--- a/macros.xml Fri Apr 07 11:47:12 2017 -0400 +++ b/macros.xml Thu Apr 27 04:17:14 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_sstacks.xml Fri Apr 07 11:47:12 2017 -0400 +++ b/stacks_sstacks.xml Thu Apr 27 04:17:14 2017 -0400 @@ -13,45 +13,49 @@ && #set $catalog = "" - #for $input_file in $input_cat: + #for $input_file in $input_cat #set $filename = str($input_file.element_identifier) - #if not filename.endswith('.tsv'): + #if not filename.endswith('.tsv') #set $filename = $filename + ".tsv" #end if - #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename): - ln -s "${input_file}" "stacks_inputs/$filename" && + #if re.search('catalog\.[a-z]+(\.tsv)?$', $filename) + ln -s '${input_file}' 'stacks_inputs/$filename' && - #if $filename.endswith('.tags.tsv'): - #set catalog += " -c \"stacks_inputs/"+$filename[:-17] + "\"" + #if $filename.endswith('.tags.tsv') + #set catalog += " -c 'stacks_inputs/"+$filename[:-17] + "'" #end if #end if #end for #set $samples = "" - #for $input_file in $input_tags: + #for $input_file in $input_tags #set $filename = str($input_file.element_identifier) - #if not filename.endswith('.tsv'): + #if not filename.endswith('.tsv') #set $filename = $filename + ".tsv" #end if - #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename): - ln -s "${input_file}" "stacks_inputs/$filename" && + #if not re.search('catalog\.[a-z]+(\.tsv)?$', $filename) + ln -s '${input_file}' 'stacks_inputs/$filename' && - #if $filename.endswith('.tags.tsv'): - #set samples += " -s \"stacks_inputs/"+$filename[:-9] + "\"" + #if $filename.endswith('.tags.tsv') + #set samples += " -s 'stacks_inputs/"+$filename[:-9] + "'" #end if #end if #end for sstacks + ## Batch description + -b 1 + -p \${GALAXY_SLOTS:-1} - $catalog - - $samples - - ## Batch description - -b 1 + #if $popmap + -P stacks_inputs -M '$popmap' + #else + $catalog + $samples + -o stacks_outputs + #end if $g @@ -59,15 +63,24 @@ $gapped - -o stacks_outputs + 2>&1 | tee sstacks.log - > sstacks.log 2>&1 + #if $popmap + ## When using a popmap, stacks write to the input dir + && mv stacks_inputs/*matches.tsv stacks_outputs/ + #end if + + && + + stacks_summary.py --stacks-prog sstacks --res-dir stacks_outputs --logfile sstacks.log --summary stacks_outputs/summary.html ]]></command> <inputs> <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog files" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" /> <param name="input_tags" format="tabular,txt" type="data_collection" collection_type="list" label="Samples stacks" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks/pstacks" /> + <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, matching will be done only for samples listed in this file" optional="true" argument="-M" /> + <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" /> <param name="check_haplo" argument="-x" type="boolean" checked="false" truevalue="-x" falsevalue="" label="Don't verify haplotype of matching locus" /> @@ -78,6 +91,8 @@ <outputs> <data format="txt" name="output_log" label="sstacks.log with ${tool.name} on ${on_string}" from_work_dir="sstacks.log" /> + <data format="html" name="output_summary" label="Summary from ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/summary.html" /> + <collection name="matches" type="list" label="Matches to the catalog on ${on_string}"> <discover_datasets pattern="(?P<name>.+\.matches)\.tsv$" ext="tabular" directory="stacks_outputs" /> </collection> @@ -110,6 +125,11 @@ <has_text text="Outputing to file" /> </assert_contents> </output> + <output name="output_summary"> + <assert_contents> + <has_text text="Stacks Statistics" /> + </assert_contents> + </output> <output_collection name="matches"> <element name="PopA_01.matches"> @@ -148,6 +168,54 @@ <has_text text="Outputing to file" /> </assert_contents> </output> + <output name="output_summary"> + <assert_contents> + <has_text text="Stacks Statistics" /> + </assert_contents> + </output> + + <output_collection name="matches"> + <element name="PopA_01.matches"> + <assert_contents> + <has_text text="generated on " /> + </assert_contents> + </element> + </output_collection> + </test> + + <test> + <param name="input_cat"> + <collection type="list"> + <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" /> + <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" /> + <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" /> + </collection> + </param> + <param name="input_tags"> + <collection type="list"> + <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" /> + <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" /> + <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" /> + <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" /> + <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" /> + <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" /> + <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" /> + <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" /> + </collection> + </param> + + <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" /> + + <output name="output_log"> + <assert_contents> + <has_text text="Outputing to file" /> + </assert_contents> + </output> + <output name="output_summary"> + <assert_contents> + <has_text text="Stacks Statistics" /> + </assert_contents> + </output> <output_collection name="matches"> <element name="PopA_01.matches">
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/popmap_cstacks.tsv Thu Apr 27 04:17:14 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 04:17:14 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.