# HG changeset patch
# User avowinkel
# Date 1435351725 14400
# Node ID af879fc0d7348099c9c1fbe15ad49492873eabaf
Uploaded
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
@@ -0,0 +1,252 @@
+
+
+
+ from Stacks toolbox
+
+
+ process_radtags_macros.xml
+
+
+
+ stacks
+
+
+
+ 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}
+
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ 0 and value < 1]]>
+
+
+ = 0 and value <= 40]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+, --renz_1 : provide the restriction enzyme used (cut site occurs on single-end read)
+ --renz_2 : 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 : provide adaptor sequence that may occur on the single-end read for filtering.
+ --adapter_2 : provide adaptor sequence that may occur on the paired-read for filtering.
+ --adapter_mm : 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).
+
+]]>
+
+
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
@@ -0,0 +1,108 @@
+
+
+ ${tool.name}
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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
@@ -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
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
@@ -0,0 +1,9 @@
+TAGCAG
+CCTTGCCATT
+ACTGCGAT
+GCAAGCCAT
+AACGTGCCT
+GAAGTG
+TCTTGG
+AACTGG
+ATGAGCAA
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
@@ -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>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?DDB??ACDDB0
+
+
+
+
+