Mercurial > repos > iuc > stacks_procrad
changeset 8:bec1f08cdfcc draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e
| author | iuc |
|---|---|
| date | Thu, 27 Apr 2017 04:19:34 -0400 |
| parents | f1f715f5d2f3 |
| children | 57910d476be9 |
| files | macros.xml stacks_procrad.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, 140 insertions(+), 24 deletions(-) [+] |
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--- a/macros.xml Fri Apr 07 11:49:00 2017 -0400 +++ b/macros.xml Thu Apr 27 04:19:34 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_procrad.xml Fri Apr 07 11:49:00 2017 -0400 +++ b/stacks_procrad.xml Thu Apr 27 04:19:34 2017 -0400 @@ -7,29 +7,29 @@ <expand macro="stdio"/> <command><![CDATA[ - #if $input_type.options_type_selector == "single": + #if $input_type.options_type_selector == "single" - #if $input_type.input_single.is_of_type('fastqsanger'): + #if $input_type.input_single.is_of_type('fastqsanger') #set $ext = ".fq" #set inputype = "fastq" - #else: + #else #set $ext = ".fq.gz" #set inputype = "gzfastq" #end if - ln -s "$input_type.input_single" R1$ext && + ln -s '$input_type.input_single' R1$ext && #else - #if $input_type.inputs_paired1.is_of_type('fastqsanger'): + #if $input_type.inputs_paired1.is_of_type('fastqsanger') #set $ext = ".fq" #set inputype = "fastq" - #else: + #else #set $ext = ".fq.gz" #set inputype = "gzfastq" #end if - ln -s "$input_type.inputs_paired1" R1$ext && - ln -s "$input_type.inputs_paired2" R2$ext && + ln -s '$input_type.inputs_paired1' R1$ext && + ln -s '$input_type.inputs_paired2' R2$ext && #end if mkdir stacks_outputs @@ -38,31 +38,33 @@ process_radtags - #if $input_type.options_type_selector == "single": + #if $input_type.options_type_selector == "single" -f R1$ext - #else: + #else -1 R1$ext -2 R2$ext #end if -i $inputype - -b "$barcode" + -b '$barcode' $input_type.barcode_encoding - #if str( $options_enzyme.options_enzyme_selector ) == "1": + #if str( $options_enzyme.options_enzyme_selector ) == "1" -e $options_enzyme.enzyme - #else: + #else --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2 #end if - -y $outype + #if str( $outype ) != "auto" + -y $outype + #end if $capture $options_advanced.retain_header - #if str($options_advanced.truncate): + #if str($options_advanced.truncate) -t $options_advanced.truncate #end if @@ -85,7 +87,7 @@ <option value="paired">Paired-end files</option> </param> <when value="single"> - <param name="input_single" argument="-f" format="fastqsanger,fastq.gz" type="data" label="singles-end reads infile(s)" help="input files" /> + <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" /> <param name="barcode_encoding" type="select" label="Barcode location"> <option value="--inline_null" selected="True">Barcode is inline with sequence</option> @@ -93,8 +95,8 @@ </param> </when> <when value="paired"> - <param name="inputs_paired1" argument="-1" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> - <param name="inputs_paired2" argument="-2" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> + <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" /> + <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" /> <param name="barcode_encoding" type="select" label="Barcode location"> <option value="--inline_null" selected="True">Barcode is inline with sequence, only on the single-end read (read 1)</option> @@ -141,10 +143,11 @@ <param name="retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" argument="--retain_header" label="Retain unmodified FASTQ headers in the output" /> </section> - <!-- Stacks can produce fastq.gz and fasta.gz output but we don't propose it as they are not very common datatypes in galaxy --> - <param name="outype" argument="-y" type="select" label="Output format" help="output type, either 'fastq' or 'fasta'" > - <option value="fastq" selected="True">fastq</option> + <param name="outype" argument="-y" type="select" label="Output format" > + <option value="auto" selected="True">Same as input</option> + <option value="fastq">fastq</option> <option value="fasta">fasta</option> + <option value="gzfastq">gzipped fastq</option> </param> </inputs> @@ -153,16 +156,19 @@ <collection name="demultiplexed" type="list" label="Demultiplexed reads from ${on_string}"> <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>.+(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> </collection> <collection name="remaining" type="list" label="Remaining orphan reads from ${on_string}"> <filter>input_type['options_type_selector'] == "paired"</filter> <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fq.gz$" ext="fastqsanger.gz" directory="stacks_outputs" /> <discover_datasets pattern="(?P<name>.+\.rem(\.[12])?)\.fa$" ext="fasta" directory="stacks_outputs" /> </collection> <collection name="discarded" type="list" label="${tool.name}: discarded reads from ${on_string}"> <filter>capture is True</filter> <discover_datasets pattern="(?P<name>.+)\.fq\.discards$" ext="fastqsanger" directory="stacks_outputs" /> + <discover_datasets pattern="(?P<name>.+)\.fq\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped --> <discover_datasets pattern="(?P<name>.+)\.fa\.discards$" ext="fasta" directory="stacks_outputs" /> </collection> </outputs> @@ -189,6 +195,23 @@ </output_collection> </test> <test> + <param name="options_type_selector" value="single"/> + <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/> + <param name="barcode" value="procrad/barcodes"/> + <param name="options_enzyme_selector" value="1"/> + <param name="enzyme" value="ecoRI"/> + <param name="discard" value="true"/> + <param name="capture" value="true"/> + <param name="outype" value="gzfastq"/> + <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> + <output_collection name="demultiplexed"> + <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/> + </output_collection> + <output_collection name="discarded"> + <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/> + </output_collection> + </test> + <test> <param name="options_type_selector" value="paired"/> <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/> <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/> @@ -262,6 +285,43 @@ </element> </output_collection> </test> + <test> + <param name="options_type_selector" value="single"/> + <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/> + <param name="barcode" value="procrad/barcodes"/> + <param name="options_enzyme_selector" value="1"/> + <param name="enzyme" value="ecoRI"/> + <param name="discard" value="true"/> + <param name="capture" value="true"/> + <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> + <output_collection name="demultiplexed"> + <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/> + </output_collection> + <output_collection name="discarded"> + <element name="R1"> + <assert_contents> + <has_text text="lane1_fakedata0_11" /> + </assert_contents> + </element> + </output_collection> + </test> + <test> + <param name="options_type_selector" value="single"/> + <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/> + <param name="barcode" value="procrad/barcodes"/> + <param name="options_enzyme_selector" value="1"/> + <param name="enzyme" value="ecoRI"/> + <param name="discard" value="true"/> + <param name="capture" value="true"/> + <param name="outype" value="gzfastq"/> + <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/> + <output_collection name="demultiplexed"> + <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/> + </output_collection> + <output_collection name="discarded"> + <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/> + </output_collection> + </test> </tests>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/popmap_cstacks.tsv Thu Apr 27 04:19:34 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 04:19:34 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.