| Next changeset 1:228d0cbc14f9 (2015-06-29) |
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Commit message:
Uploaded |
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added:
process_radtags.xml process_radtags_macros.xml process_radtags_rename.sh test-data/barcodes.tbl test-data/input-se-inline.fastqsanger tool_dependencies.xml |
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| diff -r 000000000000 -r af879fc0d734 process_radtags.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/process_radtags.xml Fri Jun 26 16:48:45 2015 -0400 |
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| b'@@ -0,0 +1,252 @@\n+<?xml version="1.0"?>\n+<tool id="process_radtags" name="process_radtags" version="0.1.0">\n+\n+ <description>from Stacks toolbox</description>\n+\n+ <macros>\n+ <import>process_radtags_macros.xml</import>\n+ </macros>\n+\n+ <requirements>\n+ <requirement type="package" version="1.32">stacks</requirement>\n+ </requirements>\n+\n+ <command>\n+ <![CDATA[\n+\n+ mkdir output &&\n+\n+ process_radtags\n+ \n+ #if $analysis_type.analysis_type_select == \'se\'\n+ -f ${analysis_type.fastq_input1}\n+ #elif $analysis_type.analysis_type_select == \'pe\'\n+ -1 ${analysis_type.fastq_input1}\n+ -2 ${analysis_type.fastq_input2}\n+ #end if\n+\n+ -b ${barcode_file}\n+ -o output\n+\n+ #if $analysis_type.fastq_input1.is_of_type(\'fastqsanger\')\n+ -E "phred33"\n+ #elif $analysis_type.fastq_input1.is_of_type(\'fastqillumina\')\n+ -E "phred64"\n+ #end if\n+\n+ #if $double_digest.double_digest_enabled\n+ --renz_1 ${enzyme}\n+ --renz_2 ${double_digest.enzyme}\n+ #else\n+ -e ${enzyme}\n+ #end if\n+ \n+ ${c} ${q} ${r}\n+\n+ #if $t > 0\n+ -t ${t}\n+ #end if\n+ -w ${w}\n+ -s ${s}\n+\n+ -D\n+\n+ #if $analysis_type.adapter_options.adapter_options_enabled\n+ #if $analysis_type.analysis_type_select == \'se\'\n+ --adapter_1 ${$analysis_type.adapter_options.adapter_1}\n+ #elif $analysis_type.analysis_type_select == \'pe\'\n+ --adapter_1 ${$analysis_type.adapter_options.adapter_1}\n+ --adapter_2 ${$analysis_type.adapter_options.adapter_2}\n+ #end if\n+ --adapter_mm ${$analysis_type.adapter_options.adapter_mm}\n+ #end if\n+\n+ #if $advanced_options.advanced_options_enabled\n+ ${advanced_options.filter_illumina}\n+ ${advanced_options.disable_rad_check}\n+ --barcode_dist_1 ${advanced_options.barcode_dist}\n+ #end if\n+\n+ > ${log_file} 2>&1 &&\n+\n+ bash $__tool_directory__/process_radtags_rename.sh ${analysis_type.fastq_input1.ext}\n+\n+ ]]>\n+ </command>\n+\n+ <inputs>\n+ <conditional name="analysis_type">\n+ <param name="analysis_type_select" type="select" label="Analysis type">\n+ <option value="se" selected="true">Single End Reads</option>\n+ <option value="pe">Paired End Reads (NOT IMPLEMENTED)</option>\n+ </param>\n+\n+ <when value="se">\n+ <param name="fastq_input1" type="data" format="fasta,fastqsanger,fastqillumina" label="Select the fastq/a file" help="Specify fastq/a file with reads"/>\n+ \n+ <param name="barcode_type" type="select" label="Barcode type">\n+ <option value="--inline_null">inline barcode</option>\n+ <option value="--index_null">barcode in header</option>\n+ </param>\n+\n+ <expand macro="macro_adapter_options_se"/>\n+ </when>\n+\n+ <when value="pe">\n+ <param name="fastq_input1" type="data" format="fasta,fastqsanger,fastqillumina" label="Select first fastq/a file" help="Specify fastq/a file with forward reads"/>\n+ <param name="fastq_input2" type="data" format="fasta,fastqsanger,fastqillumina" label="Select second fastq/a file" help="Specify fastq/a file with reverse reads"/>\n+\n+ <param name="barcode_type" type="select" label="Barcode type">\n+ <option value="--inline_inline">inline barcode</option>\n+ <option value="--index_index">barcode in header</option>\n+ <option value="--inline_index">forward read: inline; reverse read: header</option>\n+ <option value="--index_inline">forward read: header; reverse read: inline</option>\n+ </param>\n+\n+ <expand macro="macro_adapter_options_pe"/>\n+ </when>\n+ </conditional>\n+ \n+ <param name="barcode_file" type="data" format="tabular" label="Select t'..b"[\n+\n+**Tool website (with examples)**:\n+\n+http://catchenlab.life.illinois.edu/stacks/comp/process_radtags.php\n+\n+----\n+\n+**Tool help output**::\n+\n+ process_radtags 1.32\n+ 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]\n+ f: path to the input file if processing single-end sequences.\n+ i: input file type, either 'bustard' for the Illumina BUSTARD format, 'bam', 'fastq' (default), or 'gzfastq' for gzipped FASTQ.\n+ y: output type, either 'fastq', 'gzfastq', 'fasta', or 'gzfasta' (default is to match the input file type).\n+ p: path to a directory of files.\n+ P: files contained within directory specified by '-p' are paired.\n+ I: specify that the paired-end reads are interleaved in single files.\n+ 1: first input file in a set of paired-end sequences.\n+ 2: second input file in a set of paired-end sequences.\n+ o: path to output the processed files.\n+ b: path to a file containing barcodes for this run.\n+ c: clean data, remove any read with an uncalled base.\n+ q: discard reads with low quality scores.\n+ r: rescue barcodes and RAD-Tags.\n+ t: truncate final read length to this value.\n+ E: specify how quality scores are encoded, 'phred33' (Illumina 1.8+, Sanger, default) or 'phred64' (Illumina 1.3 - 1.5).\n+ D: capture discarded reads to a file.\n+ w: set the size of the sliding window as a fraction of the read length, between 0 and 1 (default 0.15).\n+ s: set the score limit. If the average score within the sliding window drops below this value, the read is discarded (default 10).\n+ h: display this help messsage.\n+\n+ Barcode options:\n+ --inline_null: barcode is inline with sequence, occurs only on single-end read (default).\n+ --index_null: barcode is provded in FASTQ header, occurs only on single-end read.\n+ --inline_inline: barcode is inline with sequence, occurs on single and paired-end read.\n+ --index_index: barcode is provded in FASTQ header, occurs on single and paired-end read.\n+ --inline_index: barcode is inline with sequence on single-end read, occurs in FASTQ header for paired-end read.\n+ --index_inline: barcode occurs in FASTQ header for single-end read, is inline with sequence on paired-end read.\n+\n+ Restriction enzyme options:\n+ -e <enz>, --renz_1 <enz>: provide the restriction enzyme used (cut site occurs on single-end read)\n+ --renz_2 <enz>: if a double digest was used, provide the second restriction enzyme used (cut site occurs on the paired-end read).\n+ Currently supported enzymes include:\n+ 'aluI', 'apeKI', 'apoI', 'bamHI', 'bgIII', 'bstYI', 'claI', 'ddeI', \n+ 'dpnII', 'eaeI', 'ecoRI', 'ecoRV', 'ecoT22I', 'hindIII', 'kpnI', 'mluCI', \n+ 'mseI', 'mspI', 'ndeI', 'nheI', 'nlaIII', 'notI', 'nsiI', 'pstI', \n+ 'rsaI', 'sacI', 'sau3AI', 'sbfI', 'sexAI', 'sgrAI', 'speI', 'sphI', \n+ 'taqI', 'xbaI', or 'xhoI'\n+ Adapter options:\n+ --adapter_1 <sequence>: provide adaptor sequence that may occur on the single-end read for filtering.\n+ --adapter_2 <sequence>: provide adaptor sequence that may occur on the paired-read for filtering.\n+ --adapter_mm <mismatches>: number of mismatches allowed in the adapter sequence.\n+\n+ Output options:\n+ --merge: if no barcodes are specified, merge all input files into a single output file.\n+\n+ Advanced options:\n+ --filter_illumina: discard reads that have been marked by Illumina's chastity/purity filter as failing.\n+ --disable_rad_check: disable checking if the RAD site is intact.\n+ --len_limit <limit>: specify a minimum sequence length (useful if your data has already been trimmed).\n+ --barcode_dist_1: the number of allowed mismatches when rescuing single-end barcodes (default 1).\n+ --barcode_dist_2: the number of allowed mismatches when rescuing paired-end barcodes (defaults to --barcode_dist_1).\n+\n+]]>\n+ </help>\n+</tool>\n" |
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| diff -r 000000000000 -r af879fc0d734 process_radtags_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/process_radtags_macros.xml Fri Jun 26 16:48:45 2015 -0400 |
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| @@ -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> |
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| diff -r 000000000000 -r af879fc0d734 process_radtags_rename.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/process_radtags_rename.sh Fri Jun 26 16:48:45 2015 -0400 |
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| @@ -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 |
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| diff -r 000000000000 -r af879fc0d734 test-data/barcodes.tbl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/barcodes.tbl Fri Jun 26 16:48:45 2015 -0400 |
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| @@ -0,0 +1,9 @@ +TAGCAG +CCTTGCCATT +ACTGCGAT +GCAAGCCAT +AACGTGCCT +GAAGTG +TCTTGG +AACTGG +ATGAGCAA |
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| diff -r 000000000000 -r af879fc0d734 test-data/input-se-inline.fastqsanger --- /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 |
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| @@ -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@ |
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| diff -r 000000000000 -r af879fc0d734 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 26 16:48:45 2015 -0400 |
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| @@ -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> |