| Previous changeset 7:c541e62d6c56 (2017-04-07) Next changeset 9:ff1f282d731e (2017-05-21) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e |
|
modified:
macros.xml stacks_cstacks.xml |
|
added:
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 |
| b |
| diff -r c541e62d6c56 -r 759ba5c7faca macros.xml --- a/macros.xml Fri Apr 07 11:48:00 2017 -0400 +++ b/macros.xml Thu Apr 27 04:18:23 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) |
| b |
| diff -r c541e62d6c56 -r 759ba5c7faca stacks_cstacks.xml --- a/stacks_cstacks.xml Fri Apr 07 11:48:00 2017 -0400 +++ b/stacks_cstacks.xml Thu Apr 27 04:18:23 2017 -0400 |
| [ |
| b'@@ -13,28 +13,33 @@\n &&\n \n #set $samples = ""\n- #for $input_file in $input_col:\n+ #for $input_file in $input_col\n #set $filename = str($input_file.element_identifier)\n- #if not filename.endswith(\'.tsv\'):\n+ #if not filename.endswith(\'.tsv\')\n #set $filename = $filename + ".tsv"\n #end if\n- #if not re.search(\'catalog\\.[a-z]+(\\.tsv)?$\', $filename):\n- ln -s "${input_file}" "stacks_inputs/$filename" &&\n+ #if not re.search(\'catalog\\.[a-z]+(\\.tsv)?$\', $filename)\n+ ln -s \'${input_file}\' \'stacks_inputs/$filename\' &&\n \n- #if $filename.endswith(\'.tags.tsv\'):\n- #set samples += " -s \\"stacks_inputs/" + $filename[:-9] + "\\""\n+ #if $filename.endswith(\'.tags.tsv\')\n+ #set samples += " -s \'stacks_inputs/" + $filename[:-9] + "\'"\n #end if\n #end if\n #end for\n \n cstacks\n \n+ ## Batch description\n+ -b 1\n+\n -p \\${GALAXY_SLOTS:-1}\n \n- $samples\n-\n- ## Batch description\n- -b 1\n+ #if $popmap\n+ -P stacks_inputs -M \'$popmap\'\n+ #else\n+ $samples\n+ -o stacks_outputs\n+ #end if\n \n $g\n \n@@ -42,20 +47,29 @@\n \n $include_multiple\n \n- #if $gapped.use_gapped:\n+ #if $gapped.use_gapped == "yes"\n --gapped\n --max_gaps $gapped.max_gaps\n --min_aln_len $gapped.min_aln_len\n #end if\n \n- -o stacks_outputs\n+ 2>&1 | tee cstacks.log\n \n- > cstacks.log 2>&1\n+ #if $popmap\n+ ## When using a popmap, stacks write to the input dir\n+ && mv stacks_inputs/batch_1.catalog.*.tsv stacks_outputs/\n+ #end if\n+\n+ &&\n+\n+ stacks_summary.py --stacks-prog cstacks --res-dir stacks_outputs --logfile cstacks.log --summary stacks_outputs/summary.html\n ]]></command>\n \n <inputs>\n <param name="input_col" format="tabular,txt" type="data_collection" collection_type="list" label="Output from previous Stacks pipeline steps (e.g. denovo_map, refmap, ustacks or pstacks)" />\n \n+ <param name="popmap" type="data" format="tabular,txt" label="Population map" help="If set, the catalog will be built from samples listed in this file" optional="true" argument="-M" />\n+\n <param name="g" argument="-g" type="boolean" checked="false" truevalue="-g" falsevalue="" label="Base catalog matching on genomic location, not sequence identity" />\n \n <param name="n" argument="-n" type="integer" value="1" label="Number of mismatches allowed between sample tags when building the catalog"/>\n@@ -63,9 +77,12 @@\n <param name="include_multiple" argument="-m" type="boolean" checked="false" truevalue="-m" falsevalue="" label="Include tags in the catalog that match to more than one entry" />\n \n <conditional name="gapped">\n- <param name="use_gapped" argument="--gapped" type="boolean" checked="false" label="Perform gapped alignments between stacks" />\n- <when value="false"></when>\n- <when value="true">\n+ <param name="use_gapped" argument="--gapped" type="select" label="Perform gapped alignments between stacks">\n+ <option value="no" selected="true">No</option>\n+ <option value="yes">Yes</option>\n+ </param>\n+ <when value="no"/>\n+ <when value="yes">\n <param name="max_gaps" argument="--max_gaps" type="integer" value="2" label="Number of gaps allowed between stacks before merging"/>\n <param name="min_aln_len" argument="--min_aln_len" type="float" value="0.8" min="0.0" max="1.0" label="Minimum length of aligned sequence in a gapped alignment"/>\n </when'..b'abel="Catalog model calls (snps) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.snps.tsv" />\n <data format="tabular" name="catalogalleles" label="Catalog haplotypes (alleles) with ${tool.name} on ${on_string}" from_work_dir="stacks_outputs/batch_1.catalog.alleles.tsv" />\n@@ -103,6 +122,11 @@\n <has_text text="done." />\n </assert_contents>\n </output>\n+ <output name="output_summary">\n+ <assert_contents>\n+ <has_text text="Stacks Statistics" />\n+ </assert_contents>\n+ </output>\n \n <!-- catalog -->\n <output name="catalogtags">\n@@ -138,13 +162,66 @@\n <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />\n </collection>\n </param>\n- <param name="gapped|use_gapped" value="true" />\n+ <param name="gapped|use_gapped" value="yes" />\n \n <output name="output_log">\n <assert_contents>\n <has_text text="done." />\n </assert_contents>\n </output>\n+ <output name="output_summary">\n+ <assert_contents>\n+ <has_text text="Stacks Statistics" />\n+ </assert_contents>\n+ </output>\n+\n+ <!-- catalog -->\n+ <output name="catalogtags">\n+ <assert_contents>\n+ <has_text text="catalog generated on" />\n+ </assert_contents>\n+ </output>\n+ <output name="catalogsnps">\n+ <assert_contents>\n+ <has_text text="catalog generated on" />\n+ </assert_contents>\n+ </output>\n+ <output name="catalogalleles">\n+ <assert_contents>\n+ <has_text text="catalog generated on" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ <test>\n+ <param name="input_col">\n+ <collection type="list">\n+ <element name="batch_1.catalog.alleles.tsv" ftype="tabular" value="genotypes/batch_1.catalog.alleles.tsv" />\n+ <element name="batch_1.catalog.snps.tsv" ftype="tabular" value="genotypes/batch_1.catalog.snps.tsv" />\n+ <element name="batch_1.catalog.tags.tsv" ftype="tabular" value="genotypes/batch_1.catalog.tags.tsv" />\n+ <element name="PopA_01.alleles.tsv" ftype="tabular" value="genotypes/PopA_01.alleles.tsv" />\n+ <element name="PopA_01.matches.tsv" ftype="tabular" value="genotypes/PopA_01.matches.tsv" />\n+ <element name="PopA_01.snps.tsv" ftype="tabular" value="genotypes/PopA_01.snps.tsv" />\n+ <element name="PopA_01.tags.tsv" ftype="tabular" value="genotypes/PopA_01.tags.tsv" />\n+ <element name="PopA_02.alleles.tsv" ftype="tabular" value="genotypes/PopA_02.alleles.tsv" />\n+ <element name="PopA_02.matches.tsv" ftype="tabular" value="genotypes/PopA_02.matches.tsv" />\n+ <element name="PopA_02.snps.tsv" ftype="tabular" value="genotypes/PopA_02.snps.tsv" />\n+ <element name="PopA_02.tags.tsv" ftype="tabular" value="genotypes/PopA_02.tags.tsv" />\n+ </collection>\n+ </param>\n+\n+ <param name="popmap" ftype="tabular" value="denovo_map/popmap_cstacks.tsv" />\n+\n+ <output name="output_log">\n+ <assert_contents>\n+ <has_text text="done." />\n+ </assert_contents>\n+ </output>\n+ <output name="output_summary">\n+ <assert_contents>\n+ <has_text text="Stacks Statistics" />\n+ </assert_contents>\n+ </output>\n \n <!-- catalog -->\n <output name="catalogtags">\n' |
| b |
| diff -r c541e62d6c56 -r 759ba5c7faca test-data/demultiplexed/PopA_01.1.fq.gzip |
| b |
| Binary file test-data/demultiplexed/PopA_01.1.fq.gzip has changed |
| b |
| diff -r c541e62d6c56 -r 759ba5c7faca test-data/denovo_map/popmap_cstacks.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/popmap_cstacks.tsv Thu Apr 27 04:18:23 2017 -0400 |
| b |
| @@ -0,0 +1,1 @@ +PopA_01 myPopA |
| b |
| diff -r c541e62d6c56 -r 759ba5c7faca test-data/procrad/R1.fq.gzip |
| b |
| Binary file test-data/procrad/R1.fq.gzip has changed |
| b |
| diff -r c541e62d6c56 -r 759ba5c7faca test-data/ustacks/ustacks.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/ustacks.out Thu Apr 27 04:18:23 2017 -0400 |
| b |
| @@ -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. |