Mercurial > repos > avowinkel > stacks
changeset 0:af879fc0d734 draft
Uploaded
| author | avowinkel |
|---|---|
| date | Fri, 26 Jun 2015 16:48:45 -0400 |
| parents | |
| children | 228d0cbc14f9 |
| files | process_radtags.xml process_radtags_macros.xml process_radtags_rename.sh test-data/barcodes.tbl test-data/input-se-inline.fastqsanger tool_dependencies.xml |
| diffstat | 6 files changed, 429 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/process_radtags.xml Fri Jun 26 16:48:45 2015 -0400 @@ -0,0 +1,252 @@ +<?xml version="1.0"?> +<tool id="process_radtags" name="process_radtags" version="0.1.0"> + + <description>from Stacks toolbox</description> + + <macros> + <import>process_radtags_macros.xml</import> + </macros> + + <requirements> + <requirement type="package" version="1.32">stacks</requirement> + </requirements> + + <command> + <![CDATA[ + + mkdir output && + + process_radtags + + #if $analysis_type.analysis_type_select == 'se' + -f ${analysis_type.fastq_input1} + #elif $analysis_type.analysis_type_select == 'pe' + -1 ${analysis_type.fastq_input1} + -2 ${analysis_type.fastq_input2} + #end if + + -b ${barcode_file} + -o output + + #if $analysis_type.fastq_input1.is_of_type('fastqsanger') + -E "phred33" + #elif $analysis_type.fastq_input1.is_of_type('fastqillumina') + -E "phred64" + #end if + + #if $double_digest.double_digest_enabled + --renz_1 ${enzyme} + --renz_2 ${double_digest.enzyme} + #else + -e ${enzyme} + #end if + + ${c} ${q} ${r} + + #if $t > 0 + -t ${t} + #end if + -w ${w} + -s ${s} + + -D + + #if $analysis_type.adapter_options.adapter_options_enabled + #if $analysis_type.analysis_type_select == 'se' + --adapter_1 ${$analysis_type.adapter_options.adapter_1} + #elif $analysis_type.analysis_type_select == 'pe' + --adapter_1 ${$analysis_type.adapter_options.adapter_1} + --adapter_2 ${$analysis_type.adapter_options.adapter_2} + #end if + --adapter_mm ${$analysis_type.adapter_options.adapter_mm} + #end if + + #if $advanced_options.advanced_options_enabled + ${advanced_options.filter_illumina} + ${advanced_options.disable_rad_check} + --barcode_dist_1 ${advanced_options.barcode_dist} + #end if + + > ${log_file} 2>&1 && + + bash $__tool_directory__/process_radtags_rename.sh ${analysis_type.fastq_input1.ext} + + ]]> + </command> + + <inputs> + <conditional name="analysis_type"> + <param name="analysis_type_select" type="select" label="Analysis type"> + <option value="se" selected="true">Single End Reads</option> + <option value="pe">Paired End Reads (NOT IMPLEMENTED)</option> + </param> + + <when value="se"> + <param name="fastq_input1" type="data" format="fasta,fastqsanger,fastqillumina" label="Select the fastq/a file" help="Specify fastq/a file with reads"/> + + <param name="barcode_type" type="select" label="Barcode type"> + <option value="--inline_null">inline barcode</option> + <option value="--index_null">barcode in header</option> + </param> + + <expand macro="macro_adapter_options_se"/> + </when> + + <when value="pe"> + <param name="fastq_input1" type="data" format="fasta,fastqsanger,fastqillumina" label="Select first fastq/a file" help="Specify fastq/a file with forward reads"/> + <param name="fastq_input2" type="data" format="fasta,fastqsanger,fastqillumina" label="Select second fastq/a file" help="Specify fastq/a file with reverse reads"/> + + <param name="barcode_type" type="select" label="Barcode type"> + <option value="--inline_inline">inline barcode</option> + <option value="--index_index">barcode in header</option> + <option value="--inline_index">forward read: inline; reverse read: header</option> + <option value="--index_inline">forward read: header; reverse read: inline</option> + </param> + + <expand macro="macro_adapter_options_pe"/> + </when> + </conditional> + + <param name="barcode_file" type="data" format="tabular" label="Select the barcode file" /> + + <expand macro="macro_enzyme_selector"/> + + <conditional name="double_digest"> + <param name="double_digest_enabled" type="boolean" label="Double Digest was used?" /> + <when value="true"> + <expand macro="macro_enzyme_selector2"/> + </when> + <when value="false" /> + </conditional> + + <param name="c" type="boolean" truevalue="-c" falsevalue="" label="clean data, remove any read with an uncalled base" help="-c" /> + <param name="q" type="boolean" truevalue="-q" falsevalue="" label="discard reads with low quality scores" help="-q" /> + <param name="r" type="boolean" truevalue="-r" falsevalue="" label="rescue barcodes and RAD-Tags" help="-r" /> + <param name="t" type="integer" value="0" size="4" label="truncate final read length to this value" help="0 = don't truncate; -t &lt;len&gt;" /> + <param name="w" type="float" value="0.15" label="set the size of the sliding window" help="... as a fraction of the read length, between 0 and 1 (default 0.15); -w &lt;size&gt;"> + <validator type="expression" message="Window size is a fraction between 0 and 1."><![CDATA[value > 0 and value < 1]]></validator> + </param> + <param name="s" type="integer" value="10" label="set the score limit" help="If the average score within the sliding window drops below this value, the read is discarded (default 10); -s &lt;lim&gt;"> + <validator type="expression" message="Score limit must be between 0 and 40."><![CDATA[value >= 0 and value <= 40]]></validator> + </param> + + <conditional name="advanced_options"> + <param name="advanced_options_enabled" type="boolean" label="Specify advanced options?" /> + <when value="true"> + <param name="filter_illumina" type="boolean" truevalue="--filter_illumina" falsevalue="" label="discard reads that have been marked by Illumina’s chastity/purity filter as failing" /> + <param name="disable_rad_check" type="boolean" truevalue="--disable_rad_check" falsevalue="" label="disable checking if the RAD site is intact" /> + <param name="barcode_dist" type="integer" value="2" size="1" label="distance between barcodes to allow for barcode rescue (default 2)" /> + </when> + <when value="false" /> + </conditional> + + </inputs> + + <outputs> + <collection name="split_output" type="list" label="@OUTPUT_NAME_PREFIX@ on ${on_string} (Fastq Collection)"> + <discover_datasets pattern="sample_(?P<designation>.+)\.(?P<ext>.+)" directory="splits" /> + </collection> + <data format="txt" name="log_file" label="@OUTPUT_NAME_PREFIX@ on ${on_string} (log)"> + <discover_datasets pattern="(?P<designation>.+)\.log" ext="txt" directory="output" visible="true" /> + <discover_datasets pattern="(?P<designation>.+)\.(?P<ext>.+)\.discards" directory="output" visible="true" /> + </data> + </outputs> + + <tests> + <test> + <param name="analysis_type_select" value="se" /> + <param name="fastq_input1" value="input-se-inline.fastqsanger" /> + <param name="barcode_type" value="--inline_null" /> + <param name="adapter_options_enabled" value="false" /> + <param name="barcode_file" value="barcodes.tbl" /> + <param name="enzyme" value="ecoT22I" /> + <param name="double_digest_enabled" value="false" /> + <output name="log_file"> + <assert_contents> + <has_line line="Processing single-end data." /> + <has_line line="Using Phred+33 encoding for quality scores." /> + <has_line line="Found 1 input file(s)." /> + <has_line line="Searching for single-end, inlined barcodes." /> + <has_line line="Loaded 9 barcodes (6-10bp)." /> + <not_has_text text="Will attempt to recover barcodes" /> + <has_line line=" 11 total reads; -4 ambiguous barcodes; -0 ambiguous RAD-Tags; +0 recovered; -0 low quality reads; 7 retained reads." /> + </assert_contents> + <discovered_dataset designation="Report"> + <assert_contents> + <has_line_matching expression="process_radtags version 1.32 executed \d{4}-\d{2}-\d{2} \d{2}:\d{2}:\d{2}" /> + <has_line_matching expression="dataset_1.dat 7 0 4 0 11" /> + </assert_contents> + </discovered_dataset> + </output> + </test> + + </tests> + + <help> +<![CDATA[ + +**Tool website (with examples)**: + +http://catchenlab.life.illinois.edu/stacks/comp/process_radtags.php + +---- + +**Tool help output**:: + + process_radtags 1.32 + process_radtags [-f in_file | -p in_dir [-P] [-I] | -1 pair_1 -2 pair_2] -b barcode_file -o out_dir -e enz [-c] [-q] [-r] [-t len] [-D] [-w size] [-s lim] [-h] + f: path to the input file if processing single-end sequences. + i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ. + y: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default is to match the input file type). + p: path to a directory of files. + P: files contained within directory specified by '-p' are paired. + I: specify that the paired-end reads are interleaved in single files. + 1: first input file in a set of paired-end sequences. + 2: second input file in a set of paired-end sequences. + o: path to output the processed files. + b: path to a file containing barcodes for this run. + c: clean data, remove any read with an uncalled base. + q: discard reads with low quality scores. + r: rescue barcodes and RAD-Tags. + t: truncate final read length to this value. + E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+, Sanger, default) or 'phred64' (Illumina 1.3 - 1.5). + D: capture discarded reads to a file. + w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15). + s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10). + h: display this help messsage. + + Barcode options: + --inline_null: barcode is inline with sequence, occurs only on single-end read (default). + --index_null: barcode is provded in FASTQ header, occurs only on single-end read. + --inline_inline: barcode is inline with sequence, occurs on single and paired-end read. + --index_index: barcode is provded in FASTQ header, occurs on single and paired-end read. + --inline_index: barcode is inline with sequence on single-end read, occurs in FASTQ header for paired-end read. + --index_inline: barcode occurs in FASTQ header for single-end read, is inline with sequence on paired-end read. + + Restriction enzyme options: + -e <enz>, --renz_1 <enz>: provide the restriction enzyme used (cut site occurs on single-end read) + --renz_2 <enz>: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read). + Currently supported enzymes include: + 'aluI', 'apeKI', 'apoI', 'bamHI', 'bgIII', 'bstYI', 'claI', 'ddeI', + 'dpnII', 'eaeI', 'ecoRI', 'ecoRV', 'ecoT22I', 'hindIII', 'kpnI', 'mluCI', + 'mseI', 'mspI', 'ndeI', 'nheI', 'nlaIII', 'notI', 'nsiI', 'pstI', + 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 'speI', 'sphI', + 'taqI', 'xbaI', or 'xhoI' + Adapter options: + --adapter_1 <sequence>: provide adaptor sequence that may occur on the single-end read for filtering. + --adapter_2 <sequence>: provide adaptor sequence that may occur on the paired-read for filtering. + --adapter_mm <mismatches>: number of mismatches allowed in the adapter sequence. + + Output options: + --merge: if no barcodes are specified, merge all input files into a single output file. + + Advanced options: + --filter_illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing. + --disable_rad_check: disable checking if the RAD site is intact. + --len_limit <limit>: specify a minimum sequence length (useful if your data has already been trimmed). + --barcode_dist_1: the number of allowed mismatches when rescuing single-end barcodes (default 1). + --barcode_dist_2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode_dist_1). + +]]> + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/process_radtags_macros.xml Fri Jun 26 16:48:45 2015 -0400 @@ -0,0 +1,108 @@ +<macros> + + <token name="@OUTPUT_NAME_PREFIX@">${tool.name}</token> + + <xml name="macro_enzyme_selector"> + <param name="enzyme" type="select" label="Select Enzyme"> + <option value="aluI">aluI</option> + <option value="apeKI">apeKI</option> + <option value="apoI">apoI</option> + <option value="bamHI">bamHI</option> + <option value="bgIII">bgIII</option> + <option value="bstYI">bstYI</option> + <option value="claI">claI</option> + <option value="ddeI">ddeI</option> + <option value="dpnII">dpnII</option> + <option value="eaeI">eaeI</option> + <option value="ecoRI">ecoRI</option> + <option value="ecoRV">ecoRV</option> + <option value="ecoT22I">ecoT22I</option> + <option value="hindIII">hindIII</option> + <option value="kpnI">kpnI</option> + <option value="mluCI">mluCI</option> + <option value="mseI">mseI</option> + <option value="mspI">mspI</option> + <option value="ndeI">ndeI</option> + <option value="nheI">nheI</option> + <option value="nlaIII">nlaIII</option> + <option value="notI">notI</option> + <option value="nsiI">nsiI</option> + <option value="pstI">pstI</option> + <option value="rsaI">rsaI</option> + <option value="sacI">sacI</option> + <option value="sau3AI">sau3AI</option> + <option value="sbfI">sbfI</option> + <option value="sexAI">sexAI</option> + <option value="sgrAI">sgrAI</option> + <option value="speI">speI</option> + <option value="sphI">sphI</option> + <option value="taqI">taqI</option> + <option value="xbaI">xbaI</option> + <option value="xhoI">xhoI</option> + </param> + </xml> + + <xml name="macro_enzyme_selector2"> + <param name="enzyme2" type="select" label="Select Second Enzyme (on reverse end only)"> + <option value="aluI">aluI</option> + <option value="apeKI">apeKI</option> + <option value="apoI">apoI</option> + <option value="bamHI">bamHI</option> + <option value="bgIII">bgIII</option> + <option value="bstYI">bstYI</option> + <option value="claI">claI</option> + <option value="ddeI">ddeI</option> + <option value="dpnII">dpnII</option> + <option value="eaeI">eaeI</option> + <option value="ecoRI">ecoRI</option> + <option value="ecoRV">ecoRV</option> + <option value="ecoT22I">ecoT22I</option> + <option value="hindIII">hindIII</option> + <option value="kpnI">kpnI</option> + <option value="mluCI">mluCI</option> + <option value="mseI">mseI</option> + <option value="mspI">mspI</option> + <option value="ndeI">ndeI</option> + <option value="nheI">nheI</option> + <option value="nlaIII">nlaIII</option> + <option value="notI">notI</option> + <option value="nsiI">nsiI</option> + <option value="pstI">pstI</option> + <option value="rsaI">rsaI</option> + <option value="sacI">sacI</option> + <option value="sau3AI">sau3AI</option> + <option value="sbfI">sbfI</option> + <option value="sexAI">sexAI</option> + <option value="sgrAI">sgrAI</option> + <option value="speI">speI</option> + <option value="sphI">sphI</option> + <option value="taqI">taqI</option> + <option value="xbaI">xbaI</option> + <option value="xhoI">xhoI</option> + </param> + </xml> + + <xml name="macro_adapter_options_se"> + <expand macro="macro_adapter_options"> + <param name="adapter_1" type="text" label="provide adaptor sequence that may occur on the read for filtering" /> + </expand> + </xml> + + <xml name="macro_adapter_options_pe"> + <expand macro="macro_adapter_options"> + <param name="adapter_1" type="text" label="provide adaptor sequence that may occur on the single-end read for filtering" /> + <param name="adapter_2" type="text" label="provide adaptor sequence that may occur on the paired-read for filtering" /> + </expand> + </xml> + + <xml name="macro_adapter_options"> + <conditional name="adapter_options"> + <param name="adapter_options_enabled" type="boolean" label="Specify adapter options?" /> + <when value="true"> + <yield /> + <param name="adapter_mm" type="integer" value="1" size="2" label="number of mismatches allowed in the adapter sequence" /> + </when> + <when value="false" /> + </conditional> + </xml> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/process_radtags_rename.sh Fri Jun 26 16:48:45 2015 -0400 @@ -0,0 +1,10 @@ +#!/bin/bash + +EXT=$1 + +mv output/process_radtags.log output/Report.log +mv output/*.discards output/Discards.${EXT}.discards +mkdir splits +mv output/sample_* splits +#ls -lah output splits +for i in splits/*.fq; do mv "$i" "${i/.fq}".${EXT}; done
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes.tbl Fri Jun 26 16:48:45 2015 -0400 @@ -0,0 +1,9 @@ +TAGCAG +CCTTGCCATT +ACTGCGAT +GCAAGCCAT +AACGTGCCT +GAAGTG +TCTTGG +AACTGG +ATGAGCAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input-se-inline.fastqsanger Fri Jun 26 16:48:45 2015 -0400 @@ -0,0 +1,44 @@ +@HWI-ST397:425:C563WACXX:1:1101:3568:2226 1:N:0: +CCACTCATGCATAGAGAGTGCTGACATAGAGCAACAGATTTTAAGTTCCTTATTACTTTGCTAAGCCTAGTGGCATTGTTGGAATTTCAGCACTAGAATGG ++ +@@@DDBD;DDACFH@GDD3A?<@@AFIGCEH@3CDCFIIGIIEBHFIGGHG9FC@FHIIHEEFIFFHHGG=CCEGCHBECHFEEED;C@DCCCC:CCCCCA +@HWI-ST397:425:C563WACXX:1:1101:3702:2227 1:N:0: +TAGCAGTGCATTGCACAATTGTAGCTTAGGGTTGCTTATGTGATAGTTCTATTATGATGATATGATCTTGGTATGTAATTATGCAAGATCGGAAGAGCGGT ++ +@CCFFFFFHHHHHJJJJJJJJHJJJJJJIJJFHIIIJIJIBFDHEHIIGJGIJFIIGIJIJJJJIJJJJJJHIIJJHGJJJJJJJJHHHHHFFFDEEEDDB +@HWI-ST397:425:C563WACXX:1:1101:3652:2228 1:N:0: +ACTGCGATTGCATTCCCAAAATCAAAAGAGTGGGATCATGCAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCT ++ +@B@FDFFFHHHHHJJIJIIJJJJJJJJIGG:EGGGJJJCGEHIJIGGGIIIGAEEGIAHHFHG@DDBE:@CEDBDBDBDD><BCBDDCDDDD9@<BCCCCD +@HWI-ST397:425:C563WACXX:1:1101:3631:2229 1:N:0: +CCTTGCCATTTGCATTGCTGAGTGTTTCAGTTTTTTATGCAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTT ++ +CCCFFFFFHHHHGJJJJJJJIJFEEJJJJJIIIIJJIIJJJJIJJJJJGGGHJFJJ5AEHHJHHHFFFFFFDDDDDBDB@BDDDBDDDDDD>BDDAC@CCC +@HWI-ST397:425:C563WACXX:1:1101:3672:2229 1:N:0: +GCAAGCCATTGCATGACTACTTAACGGGGGGATTCACCGCAAATACTACCTTGGCTCATTATTGCCGAGATAATGGTCTACTTCTTCACATCCACCGTGCA ++ +@@@FFFFFHHGHHJIJJJJJJJIJIJIJJJDBBDDDDDDDDDDDDDDDDDDDCCDCDDDEEEEDDDDBD>BDDDDCCCDDDEDDDDDDDCCDDDCDDDDDD +@HWI-ST397:425:C563WACXX:1:1101:3742:2234 1:N:0: +GCAAGCCATTGCATGAATTTTTCCTCTTGCAATGTATGAATTTTTTCCAGCAATGCAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGT ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJHJJJHIIJJJJJJJJJIJJJJJJJJJJJJIJJJJIJJJJDHF@DDECEEDDDDDDDDDDDDB@BBDDDDDD +@HWI-ST397:425:C563WACXX:1:1101:3538:2245 1:N:0: +GGAAGACATTGCATGTCCTTTTGATGAGATTGATGTAAATGAAGTTAGGGATGCAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTAT ++ +CCCFFFFFHHHHHJJHIJJJJJJIJJJJIJJJIJJGGGJJJIIJIIEIJJIGIHIJJJJJJJIJJJJJJJBHFFFEFFDDEEDDDDDBD:?BBDDDDDDDC +@HWI-ST397:425:C563WACXX:1:1101:3974:2048 1:N:0: +NACGTGCCTTGCATTGTTTGGTTTGATCCATTAAAAATAGAATGCAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTC ++ +#1=DDDDFHHHHFJJJHIJIJFGHIIIJJJJIIIIJJEIIIJGIGIJJIGDGIGIGGHGII;AAEHEFFFFECECCBDBB?<B35>DDB??ACDDB0<AB: +@HWI-ST397:425:C563WACXX:1:1101:3920:2053 1:N:0: +NAAGTGTGCATCAACTATCTCAAACACAATTTGTATCCAAAACCATCATTCTAACATGCAAGGATCAATATATGACATCTCATTACTCACAGCCGACCATG ++ +#1=DDFDFHHHHHJJJJJJJJIJJJJJJJJJJJGIIJJIIJJJJJJJIJJIJJJJIJJJJJJJGIJJJJJJJJJIHJJHHHHHHFFFFFFEEDDDDDDDDD +@HWI-ST397:425:C563WACXX:1:1101:3945:2061 1:Y:0: +NCTTGGTGCATCAAAAACTCCGGGATCCTCGGGGCAAATGAAAGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCT ++ +#08@9@@@@@@??######################################################################################## +@HWI-ST397:425:C563WACXX:1:1101:3801:2062 1:N:0: +NACTGGTGCATGTATTAGTTATGTAGGATTTAGTAATGCAGGGTTTAATTATGCAAGTATTAGTTATGCAAGATCGGAAGAGCGGTTCAGCAGGAATGCCG ++ +#1:DDDFFHHHFFIIIEGCEEFHEEHGGFEHIICFHHGHEHGG1CFGGEHIGDHIIIBEHIIIGGHIIIIIIGGGFHIGFFHEDC=ABCCCCBB?B@CCC@
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 26 16:48:45 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="stacks" version="1.32"> + <repository changeset_revision="1e53d7d44ed6" name="package_stacks_1_32" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>