| Previous changeset 7:f1f715f5d2f3 (2017-04-07) Next changeset 9:57910d476be9 (2017-05-21) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks commit dc23703c260d004a28fe24a2a7c00cb4371bc32e |
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modified:
macros.xml stacks_procrad.xml |
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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 |
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| diff -r f1f715f5d2f3 -r bec1f08cdfcc macros.xml --- a/macros.xml Fri Apr 07 11:49:00 2017 -0400 +++ b/macros.xml Thu Apr 27 04:19:34 2017 -0400 |
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| @@ -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) |
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| diff -r f1f715f5d2f3 -r bec1f08cdfcc stacks_procrad.xml --- a/stacks_procrad.xml Fri Apr 07 11:49:00 2017 -0400 +++ b/stacks_procrad.xml Thu Apr 27 04:19:34 2017 -0400 |
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| b'@@ -7,29 +7,29 @@\n <expand macro="stdio"/>\n <command><![CDATA[\n \n- #if $input_type.options_type_selector == "single":\n+ #if $input_type.options_type_selector == "single"\n \n- #if $input_type.input_single.is_of_type(\'fastqsanger\'):\n+ #if $input_type.input_single.is_of_type(\'fastqsanger\')\n #set $ext = ".fq"\n #set inputype = "fastq"\n- #else:\n+ #else\n #set $ext = ".fq.gz"\n #set inputype = "gzfastq"\n #end if\n \n- ln -s "$input_type.input_single" R1$ext &&\n+ ln -s \'$input_type.input_single\' R1$ext &&\n #else\n \n- #if $input_type.inputs_paired1.is_of_type(\'fastqsanger\'):\n+ #if $input_type.inputs_paired1.is_of_type(\'fastqsanger\')\n #set $ext = ".fq"\n #set inputype = "fastq"\n- #else:\n+ #else\n #set $ext = ".fq.gz"\n #set inputype = "gzfastq"\n #end if\n \n- ln -s "$input_type.inputs_paired1" R1$ext &&\n- ln -s "$input_type.inputs_paired2" R2$ext &&\n+ ln -s \'$input_type.inputs_paired1\' R1$ext &&\n+ ln -s \'$input_type.inputs_paired2\' R2$ext &&\n #end if\n \n mkdir stacks_outputs\n@@ -38,31 +38,33 @@\n \n process_radtags\n \n- #if $input_type.options_type_selector == "single":\n+ #if $input_type.options_type_selector == "single"\n -f R1$ext\n- #else:\n+ #else\n -1 R1$ext\n -2 R2$ext\n #end if\n \n -i $inputype\n- -b "$barcode"\n+ -b \'$barcode\'\n \n $input_type.barcode_encoding\n \n- #if str( $options_enzyme.options_enzyme_selector ) == "1":\n+ #if str( $options_enzyme.options_enzyme_selector ) == "1"\n -e $options_enzyme.enzyme\n- #else:\n+ #else\n --renz_1 $options_enzyme.enzyme --renz_2 $options_enzyme.enzyme2\n #end if\n \n- -y $outype\n+ #if str( $outype ) != "auto"\n+ -y $outype\n+ #end if\n \n $capture\n \n $options_advanced.retain_header\n \n- #if str($options_advanced.truncate):\n+ #if str($options_advanced.truncate)\n -t $options_advanced.truncate\n #end if\n \n@@ -85,7 +87,7 @@\n <option value="paired">Paired-end files</option>\n </param>\n <when value="single">\n- <param name="input_single" argument="-f" format="fastqsanger,fastq.gz" type="data" label="singles-end reads infile(s)" help="input files" />\n+ <param name="input_single" argument="-f" format="fastqsanger,fastqsanger.gz" type="data" label="singles-end reads infile(s)" help="input files" />\n \n <param name="barcode_encoding" type="select" label="Barcode location">\n <option value="--inline_null" selected="True">Barcode is inline with sequence</option>\n@@ -93,8 +95,8 @@\n </param>\n </when>\n <when value="paired">\n- <param name="inputs_paired1" argument="-1" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" />\n- <param name="inputs_paired2" argument="-2" format="fastqsanger,fastq.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_001.fastq" />\n+ <param name="inputs_paired1" argument="-1" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 1" help="Files must have this syntax : name_R1_001.fastq" />\n+ <param name="inputs_paired2" argument="-2" format="fastqsanger,fastqsanger.gz" type="data" label="paired-end reads infile(s) 2" help="Files must have this syntax : name_R2_'..b'type="list" label="${tool.name}: discarded reads from ${on_string}">\n <filter>capture is True</filter>\n <discover_datasets pattern="(?P<name>.+)\\.fq\\.discards$" ext="fastqsanger" directory="stacks_outputs" />\n+ <discover_datasets pattern="(?P<name>.+)\\.fq\\.gz.discards$" ext="fastqsanger" directory="stacks_outputs" /> <!-- discards are never gzipped -->\n <discover_datasets pattern="(?P<name>.+)\\.fa\\.discards$" ext="fasta" directory="stacks_outputs" />\n </collection>\n </outputs>\n@@ -189,6 +195,23 @@\n </output_collection>\n </test>\n <test>\n+ <param name="options_type_selector" value="single"/>\n+ <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq"/>\n+ <param name="barcode" value="procrad/barcodes"/>\n+ <param name="options_enzyme_selector" value="1"/>\n+ <param name="enzyme" value="ecoRI"/>\n+ <param name="discard" value="true"/>\n+ <param name="capture" value="true"/>\n+ <param name="outype" value="gzfastq"/>\n+ <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>\n+ <output_collection name="demultiplexed">\n+ <element name="PopA_01" ftype="fastqsanger.gz" md5="c7250f50138cbca747b85223aaae9565"/>\n+ </output_collection>\n+ <output_collection name="discarded">\n+ <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>\n+ </output_collection>\n+ </test>\n+ <test>\n <param name="options_type_selector" value="paired"/>\n <param name="inputs_paired1" ftype="fastqsanger" value="procrad/R1.fq"/>\n <param name="inputs_paired2" ftype="fastqsanger" value="procrad/R2.fq"/>\n@@ -262,6 +285,43 @@\n </element>\n </output_collection>\n </test>\n+ <test>\n+ <param name="options_type_selector" value="single"/>\n+ <param name="input_single" ftype="fastqsanger" value="procrad/R1.fq.gzip"/>\n+ <param name="barcode" value="procrad/barcodes"/>\n+ <param name="options_enzyme_selector" value="1"/>\n+ <param name="enzyme" value="ecoRI"/>\n+ <param name="discard" value="true"/>\n+ <param name="capture" value="true"/>\n+ <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>\n+ <output_collection name="demultiplexed">\n+ <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq"/>\n+ </output_collection>\n+ <output_collection name="discarded">\n+ <element name="R1">\n+ <assert_contents>\n+ <has_text text="lane1_fakedata0_11" />\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ <test>\n+ <param name="options_type_selector" value="single"/>\n+ <param name="input_single" ftype="fastqsanger.gz" value="procrad/R1.fq.gzip"/>\n+ <param name="barcode" value="procrad/barcodes"/>\n+ <param name="options_enzyme_selector" value="1"/>\n+ <param name="enzyme" value="ecoRI"/>\n+ <param name="discard" value="true"/>\n+ <param name="capture" value="true"/>\n+ <param name="outype" value="gzfastq"/>\n+ <output name="output_log" file="procrad/process_radtags.out" compare="sim_size"/>\n+ <output_collection name="demultiplexed">\n+ <element name="PopA_01" compare="sim_size" file="demultiplexed/PopA_01.1.fq.gzip"/>\n+ </output_collection>\n+ <output_collection name="discarded">\n+ <element name="R1" ftype="fastqsanger" md5="786b30d864332a2d56d9179f0a53add4"/>\n+ </output_collection>\n+ </test>\n </tests>\n \n \n' |
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| diff -r f1f715f5d2f3 -r bec1f08cdfcc test-data/demultiplexed/PopA_01.1.fq.gzip |
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| Binary file test-data/demultiplexed/PopA_01.1.fq.gzip has changed |
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| diff -r f1f715f5d2f3 -r bec1f08cdfcc 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 04:19:34 2017 -0400 |
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| @@ -0,0 +1,1 @@ +PopA_01 myPopA |
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| diff -r f1f715f5d2f3 -r bec1f08cdfcc test-data/procrad/R1.fq.gzip |
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| Binary file test-data/procrad/R1.fq.gzip has changed |
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| diff -r f1f715f5d2f3 -r bec1f08cdfcc test-data/ustacks/ustacks.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ustacks/ustacks.out Thu Apr 27 04:19:34 2017 -0400 |
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| @@ -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. |