# HG changeset patch
# User devteam
# Date 1390498245 18000
# Node ID a03a7ee6cdff0563ea43729a10ab5f3917a4e740
Imported from capsule None
diff -r 000000000000 -r a03a7ee6cdff bowtie2_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/bowtie2_wrapper.xml Thu Jan 23 12:30:45 2014 -0500
@@ -0,0 +1,383 @@
+
+
+ is a short-read aligner
+ bowtie2 --version
+
+ bowtie2
+ samtools
+
+
+
+ ## prepare bowtie2 index
+ #set index_path = ''
+ #if str($reference_genome.source) == "history":
+ bowtie2-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
+ #set index_path = 'genome'
+ #else:
+ #set index_path = $reference_genome.index.fields.path
+ #end if
+
+ ## execute bowtie2
+ bowtie2
+
+ ## number of threads
+ -p \${GALAXY_SLOTS:-4}
+
+ ## index file path
+ -x $index_path
+
+ ## check for single/pair-end
+ #if str( $library.type ) == "single"
+ ## prepare inputs
+ -U $library.input_1
+
+ #if $output_unaligned_reads_l
+ --un $output_unaligned_reads_l
+ #end if
+ #else
+ ## prepare inputs
+ -1 $library.input_1
+ -2 $library.input_2
+ -I $library.min_insert
+ -X $library.max_insert
+
+ #if $output_unaligned_reads_l
+ --un-conc $output_unaligned_reads_l
+ #end if
+ #end if
+
+ ## configure settings
+ #if str($params.full) == "yes":
+ ## add alignment type
+ $params.align_type
+
+ ## add performance
+ $params.performance
+
+ ## add time flag
+ $params.time
+
+ ## add nofw/norc
+ $params.nofw_norc
+
+ ## set gbar
+ --gbar $params.gbar
+
+ ## check skip
+ #if str($params.skip) != "0":
+ -s $params.skip
+ #end if
+
+ ## check upto
+ #if str($params.upto) != "0":
+ -u $params.upto
+ #end if
+
+ ## check trim5
+ #if str($params.trim5) != "0":
+ -5 $params.trim5
+ #end if
+
+ ## check trim3
+ #if str($params.trim3) != "0":
+ -3 $params.trim3
+ #end if
+ #end if
+
+ ## read group information
+ #if str($read_group.selection) == "yes":
+ #if $read_group.rgid and $read_group.rglb and $read_group.rgpl and $read_group.rgsm:
+ --rg-id "$read_group.rgid"
+ --rg "LB:$read_group.rglb"
+ --rg "PL:$read_group.rgpl"
+ --rg "SM:$read_group.rgsm"
+ #end if
+ #end if
+
+ ## view/sort and output file
+ | samtools view -Su - | samtools sort -o - - > $output
+
+ ## rename unaligned sequence files
+ #if $library.type == "paired" and $output_unaligned_reads_l and $output_unaligned_reads_r:
+ #set left = str($output_unaligned_reads_l).replace( '.dat', '.1.dat' )
+ #set right = str($output_unaligned_reads_l).replace( '.dat', '.2.dat' )
+
+ ; mv $left $output_unaligned_reads_l;
+ mv $right $output_unaligned_reads_r
+ #end if
+
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+ unaligned_file is True
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+ library['type'] == "paired" and unaligned_file is True
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+**Bowtie2 Overview**
+
+Bowtie_ is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters to relatively long (e.g. mammalian) genomes. Bowtie 2 supports gapped, local, and paired-end alignment modes. Bowtie 2 outputs alignments in SAM format, enabling interoperation with a large number of other tools.
+
+*Please cite:* Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25 (2009)
+
+.. _Bowtie: http://bowtie-bio.sourceforge.net/bowtie2/
+
+------
+
+**Inputs**
+
+Bowtie 2 accepts files in Sanger FASTQ format (single or pair-end). Use the FASTQ Groomer to prepare your files.
+
+------
+
+**Outputs**
+
+The mapped sequence reads are provided as BAM file, while unmapped reads are optionally available as SAM records. When Bowtie 2 finishes running, it prints messages summarizing what happened. These messages are printed to the "standard error" ("stderr") filehandle. For datasets consisting of unpaired reads, the summary might look like this::
+
+ 20000 reads; of these:
+ 20000 (100.00%) were unpaired; of these:
+ 1247 (6.24%) aligned 0 times
+ 18739 (93.69%) aligned exactly 1 time
+ 14 (0.07%) aligned >1 times
+ 93.77% overall alignment rate
+
+------
+
+**Alignment options**
+
+*--end-to-end/--local*
+
+By default, Bowtie 2 performs end-to-end read alignment. That is, it searches for alignments involving all of the read characters. This is also called an "untrimmed" or "unclipped" alignment. When the --local option is specified, Bowtie 2 performs local read alignment. In this mode, Bowtie 2 might "trim" or "clip" some read characters from one or both ends of the alignment if doing so maximizes the alignment score.
+
+End-to-end alignment example::
+
+ Read GACTGGGCGATCTCGACTTCG
+ ||||| ||||||||||||||
+ Reference GACTG--CGATCTCGACATCG
+
+Local alignment example::
+
+ Read ACGGTTGCGTTAA-TCCGCCACG
+ ||||||||| ||||||
+ Reference TAACTTGCGTTAAATCCGCCTGG
+
+*-s/--skip (default: 0)*
+
+Skip (i.e. do not align) the first n-reads or pairs in the input.
+
+*-u/--qupto (default: no limit)*
+
+Align the first n-reads or read pairs from the input (after the -s/--skip reads or pairs have been skipped), then stop.
+
+*-5/--trim5 (default: 0)*
+
+Trim n-bases from 5' (left) end of each read before alignment.
+
+*-3/--trim3 (default: 0)*
+
+Trim n-bases from 3' (right) end of each read before alignment.
+
+*--nofw/--norc (default: both strands enabled)*
+
+If --nofw is specified, Bowtie 2 will not attempt to align unpaired reads to the forward (Watson) reference strand. If --norc is specified, bowtie2 will not attempt to align unpaired reads against the reverse-complement (Crick) reference strand. In paired-end mode, --nofw and --norc pertain to the fragments; i.e. specifying --nofw causes Bowtie 2 to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand. Default: both strands enabled.
+
+*--gbar (default: 4)*
+
+Disallow gaps within n-positions of the beginning or end of the read.
+
+------
+
+**Paired-end options**
+
+*-I/--minins (default: 0)*
+
+The minimum fragment length for valid paired-end alignments. E.g. if -I 60 is specified and a paired-end alignment consists of two 20-bp alignments in the appropriate orientation with a 20-bp gap between them, that alignment is considered valid (as long as -X is also satisfied). A 19-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -I constraint is applied with respect to the untrimmed mates.
+
+The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.
+
+*-X/--maxins (default: 0)*
+
+The maximum fragment length for valid paired-end alignments. E.g. if -X 100 is specified and a paired-end alignment consists of two 20-bp alignments in the proper orientation with a 60-bp gap between them, that alignment is considered valid (as long as -I is also satisfied). A 61-bp gap would not be valid in that case. If trimming options -3 or -5 are also used, the -X constraint is applied with respect to the untrimmed mates, not the trimmed mates.
+
+The larger the difference between -I and -X, the slower Bowtie 2 will run. This is because larger differences bewteen -I and -X require that Bowtie 2 scan a larger window to determine if a concordant alignment exists. For typical fragment length ranges (200 to 400 nucleotides), Bowtie 2 is very efficient.
+
+------
+
+**SAM options**
+
+*--rg-id [text]*
+
+Set the read group ID to [text]. This causes the SAM @RG header line to be printed, with [text] as the value associated with the ID: tag. It also causes the RG:Z: extra field to be attached to each SAM output record, with value set to [text].
+
+*--rg [text]*
+
+Add [text] as a field on the @RG header line. Note: in order for the @RG line to appear, --rg-id must also be specified. This is because the ID tag is required by the SAM Spec. Specify --rg multiple times to set multiple fields. See the SAM Spec for details about what fields are legal.
+
+------
+
+**Output options**
+
+*--un/--un-conc*
+
+Write reads that fail to align concordantly to file(s). These reads correspond to the SAM records.
+
+*-t/--time (default: off)*
+
+Print the wall-clock time required to load the index files and align the reads. This is printed to the "standard error" ("stderr") filehandle.
+
+
+
diff -r 000000000000 -r a03a7ee6cdff test-data/bowtie2/phix_genome.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2/phix_genome.fasta Thu Jan 23 12:30:45 2014 -0500
@@ -0,0 +1,78 @@
+>gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174, complete genome
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
\ No newline at end of file
diff -r 000000000000 -r a03a7ee6cdff test-data/bowtie2/phix_mapped.bam
Binary file test-data/bowtie2/phix_mapped.bam has changed
diff -r 000000000000 -r a03a7ee6cdff test-data/bowtie2/phix_reads.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bowtie2/phix_reads.fastq Thu Jan 23 12:30:45 2014 -0500
@@ -0,0 +1,260 @@
+@HWI-EAS210R_0001:4:10:890:1882#0/1
+AATCTCATCTCTCTTTTTGCGTTCTGCTTCAATATCTG
++HWI-EAS210R_0001:4:10:890:1882#0/1
+fcceeggggggggggggffghggggggggggggggggg
+@HWI-EAS210R_0001:4:10:890:1010#0/1
+GTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGA
++HWI-EAS210R_0001:4:10:890:1010#0/1
+gggggggggggggghgggggggggfggggggggggggg
+@HWI-EAS210R_0001:4:10:890:1780#0/1
+GAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTAT
++HWI-EAS210R_0001:4:10:890:1780#0/1
+ggfhggggggggggggggggghgggggfggggggdggg
+@HWI-EAS210R_0001:4:10:890:1348#0/1
+TTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT
++HWI-EAS210R_0001:4:10:890:1348#0/1
+ggggggggggggggggggggggggghfggeggggggdg
+@HWI-EAS210R_0001:4:10:890:1707#0/1
+AAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCC
++HWI-EAS210R_0001:4:10:890:1707#0/1
+gfgfgfgggggggfggeggggffgcgggdfggfggdgg
+@HWI-EAS210R_0001:4:10:890:1527#0/1
+CGTACTTATTCGCCACCATGATTATGACCAGTGTTTCC
++HWI-EAS210R_0001:4:10:890:1527#0/1
+gggggggggggggggggggggggggggggggggggggg
+@HWI-EAS210R_0001:4:10:890:781#0/1
+CGGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCAT
++HWI-EAS210R_0001:4:10:890:781#0/1
+gggggggggggggggggggggggggggggggghggggg
+@HWI-EAS210R_0001:4:10:890:568#0/1
+GTTTATCGCAATCTGCCGACCACTCGCGATTCAATCAT
++HWI-EAS210R_0001:4:10:890:568#0/1
+gggggggfgggggggggggggggggggggggggggggg
+@HWI-EAS210R_0001:4:10:890:1365#0/1
+CCAACATAAACATTATTGCCCGGCGTACGAGGAAGGAC
++HWI-EAS210R_0001:4:10:890:1365#0/1
+eggggdggfghggggggggghgfgfegghfggfgggge
+@HWI-EAS210R_0001:4:10:890:161#0/1
+GTGATTATCTTGCTGCTGCATTTCCTGAGCTTAATGCT
++HWI-EAS210R_0001:4:10:890:161#0/1
+ggggfg_gggfegggfgeggaefefdbfddeedgcgg`
+@HWI-EAS210R_0001:4:10:890:1920#0/1
+TTTATCAATACCATGAAAAATATCAACCACACCAGAAG
++HWI-EAS210R_0001:4:10:890:1920#0/1
+gggggggggggggggggggggffggggggggggggggg
+@HWI-EAS210R_0001:4:10:890:61#0/1
+GTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAAGCA
++HWI-EAS210R_0001:4:10:890:61#0/1
+eede[egfggfggggggggggggegggggfgggggggg
+@HWI-EAS210R_0001:4:10:890:1284#0/1
+AAGCGCAAGAGTAAACATAGTGCCATGCTCAGGAACAA
++HWI-EAS210R_0001:4:10:890:1284#0/1
+gggggggggggggggggggggggggggggggggggggg
+@HWI-EAS210R_0001:4:10:890:208#0/1
+CAGACCTATAAACATTCTGTGCCGCGTTTCTTTGTTCC
++HWI-EAS210R_0001:4:10:890:208#0/1
+gggeggggggggggggggggggggggggggggddgggg
+@HWI-EAS210R_0001:4:10:890:859#0/1
+CAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGC
++HWI-EAS210R_0001:4:10:890:859#0/1
+ggggcgggggggggggdgfggggggggfggggghgggh
+@HWI-EAS210R_0001:4:10:890:1947#0/1
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGAT
++HWI-EAS210R_0001:4:10:890:1947#0/1
+ggggggggggggggggggeggggggggggggfgfgggg
+@HWI-EAS210R_0001:4:10:890:416#0/1
+AATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTG
++HWI-EAS210R_0001:4:10:890:416#0/1
+eggggggggggdcgggggfggfgggggfcgfggggggg
+@HWI-EAS210R_0001:4:10:890:654#0/1
+GCAGCAAGGTCCATATCTGACTTTTTGTTAACGTATTT
++HWI-EAS210R_0001:4:10:890:654#0/1
+ggggghggggghggggghgfggggfgdfffgggggggg
+@HWI-EAS210R_0001:4:10:890:269#0/1
+CTTGAAGGCTTCCCATTCATTCAGGAACCGCCTTCTGG
++HWI-EAS210R_0001:4:10:890:269#0/1
+eecaadggggggggggggggggdgg\ffffgggggggg
+@HWI-EAS210R_0001:4:10:890:657#0/1
+TACCAGCTTTAGCCATAGCACCAGAAACAAAACTAGGG
++HWI-EAS210R_0001:4:10:890:657#0/1
+ggggghggggffgggfggggggfggfggggfffgfggg
+@HWI-EAS210R_0001:4:10:890:1449#0/1
+TTCAAGATTGCTGGAGGCCTCCACTATGAAATCGCGTA
++HWI-EAS210R_0001:4:10:890:1449#0/1
+ggggggggggggggggfgggghgggggggggggghhfh
+@HWI-EAS210R_0001:4:10:890:305#0/1
+CACGTTGGCTGACGACCGATTAGAGGCGTTTTATGATA
++HWI-EAS210R_0001:4:10:890:305#0/1
+gggegggfgggfggggggdgggdggfgffggggggfhg
+@HWI-EAS210R_0001:4:10:890:1190#0/1
+AATAAGCAATGACGGCAGCAATAAACTCAACAGGAGCA
++HWI-EAS210R_0001:4:10:890:1190#0/1
+bbecb_gggggggggggggggggggcgggfVgggeggg
+@HWI-EAS210R_0001:4:10:890:1586#0/1
+ATTAGCTGTACCATACTCAGGCACACAAAAATACTGAT
++HWI-EAS210R_0001:4:10:890:1586#0/1
+eggWgaa^O[\`[\_]J_^][`W`\]K^BBBBBBBBBB
+@HWI-EAS210R_0001:4:10:890:617#0/1
+AAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGG
++HWI-EAS210R_0001:4:10:890:617#0/1
+gggggggggggggggggggggggggggggggggggggg
+@HWI-EAS210R_0001:4:10:890:1562#0/1
+GTGGACTGCTGGCGGAAAATGAGAAAATTCGACCTATC
++HWI-EAS210R_0001:4:10:890:1562#0/1
+hggffggggdgggggaageef`Waegggbgggcgddgg
+@HWI-EAS210R_0001:4:10:890:1410#0/1
+CATAAAAAAGCCTCCAAGATTTGGAGGCATGAAAACAT
++HWI-EAS210R_0001:4:10:890:1410#0/1
+\geedggfffcd\gd`\edeggY_Zda`gggXgadeeg
+@HWI-EAS210R_0001:4:10:890:465#0/1
+AGCGTTGACCCTAATTTTGGTCGTCGGGTACGCAATCG
++HWI-EAS210R_0001:4:10:890:465#0/1
+gggggfgggggggfgggeggggbgggggagf^ffefea
+@HWI-EAS210R_0001:4:10:890:1323#0/1
+ATGACAAGTAAAGGACGGTTGTCAGCGTCATAAGAGGT
++HWI-EAS210R_0001:4:10:890:1323#0/1
+gggggggfggdggggggggggggggggggggfgghggg
+@HWI-EAS210R_0001:4:10:890:1064#0/1
+TTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAA
++HWI-EAS210R_0001:4:10:890:1064#0/1
+gggggggcegggfgfggfgfgggdgggggghfggggdf
+@HWI-EAS210R_0001:4:10:890:637#0/1
+ATAGTGCCATGCTCAGGAACAAAGAAACGCGGCACAGA
++HWI-EAS210R_0001:4:10:890:637#0/1
+ggggggggggggggggggeggggggfddgggcgggggd
+@HWI-EAS210R_0001:4:10:890:1825#0/1
+TCCATCTGAATGCAATGAAGAAAACCACCATTACCAGC
++HWI-EAS210R_0001:4:10:890:1825#0/1
+gggggggghgggffgggggegggffgghgggggggggg
+@HWI-EAS210R_0001:4:10:890:1697#0/1
+ACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCAT
++HWI-EAS210R_0001:4:10:890:1697#0/1
+eecaadeffedeggcabebeagggdecL_aNTTTTeg_
+@HWI-EAS210R_0001:4:10:890:1479#0/1
+ATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCC
++HWI-EAS210R_0001:4:10:890:1479#0/1
+ggggggggggggggggggggfggggggggghgbgggfg
+@HWI-EAS210R_0001:4:10:890:1838#0/1
+ATGTGACCGTTTATCGCAATCTGCCGACCACTCGCGAT
++HWI-EAS210R_0001:4:10:890:1838#0/1
+ggfgfggfggggggfgggggggaggggfegfhggdggg
+@HWI-EAS210R_0001:4:10:890:988#0/1
+CATTCAGTCGGCGACTTCACGCCAGAATACGAAAGACC
++HWI-EAS210R_0001:4:10:890:988#0/1
+ggghggfggggggegghgfggfgggggggggggggggg
+@HWI-EAS210R_0001:4:10:890:1902#0/1
+CTTCCTCGTACGCCGGGCAATAATGTTTATGTTGGTTT
++HWI-EAS210R_0001:4:10:890:1902#0/1
+gggggggegggggggggggggggggggggfgggggggg
+@HWI-EAS210R_0001:4:10:890:1983#0/1
+TTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAA
++HWI-EAS210R_0001:4:10:890:1983#0/1
+ffdfbaQa_c_Y\]Yeceeeege_gYR^VS]ZW[\Lcc
+@HWI-EAS210R_0001:4:10:890:1058#0/1
+GCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACTAA
++HWI-EAS210R_0001:4:10:890:1058#0/1
+ggggdgggggggggggggggggggggggggggfggggg
+@HWI-EAS210R_0001:4:10:890:287#0/1
+GTATCCAACCTGCAGAGTTTTATCGCTTCCATGACGCA
++HWI-EAS210R_0001:4:10:890:287#0/1
+ggggggfcggggg^fbe``egggggggdgg`dddfggg
+@HWI-EAS210R_0001:4:10:890:335#0/1
+AAGAGGTTTTACCTCCAAATGAAGAAATAACATCATGG
++HWI-EAS210R_0001:4:10:890:335#0/1
+`^_``Q[cccggfgggggggbddg\dXdbegggddfg`
+@HWI-EAS210R_0001:4:10:891:149#0/1
+TTTAAGAGCCTCGATACGCTCAAAGTCAAAATAATCAG
++HWI-EAS210R_0001:4:10:891:149#0/1
+ggggghgggggghggggggggggggfgggggggffggg
+@HWI-EAS210R_0001:4:10:891:445#0/1
+ATATTTTTCATGGTATTGATAAAGCTGTTGCCGATACT
++HWI-EAS210R_0001:4:10:891:445#0/1
+gggggggddggggggggggggggggggggggggggggg
+@HWI-EAS210R_0001:4:10:891:1476#0/1
+GGCGACTCCTTCGAGATGGACGCCGTTGGCGCTCTCCG
++HWI-EAS210R_0001:4:10:891:1476#0/1
+ggegggffghhggfhggfgeggffgggffggagfggfg
+@HWI-EAS210R_0001:4:10:891:323#0/1
+TGTAAAACAGGTGCCGAAGAAGCTGGAGTAACAGAAGT
++HWI-EAS210R_0001:4:10:891:323#0/1
+gggcgfefghgggghgfgfgggggggggegaaeeagge
+@HWI-EAS210R_0001:4:10:891:69#0/1
+CTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTAC
++HWI-EAS210R_0001:4:10:891:69#0/1
+gggefgggfgafP_Vdbacbgegebd`fbaeggaggQd
+@HWI-EAS210R_0001:4:10:891:1379#0/1
+GACCCTGTTTTGTATGGCAACTTGCCGCCGCGTGAAAT
++HWI-EAS210R_0001:4:10:891:1379#0/1
+gggggggggggggggggggggggggggggfgefggggg
+@HWI-EAS210R_0001:4:10:891:608#0/1
+CTTATGCTAATTTGCATACTGACCAAGAACGTGATTAC
++HWI-EAS210R_0001:4:10:891:608#0/1
+ggggggggggggggggggggggggfggggggggggggg
+@HWI-EAS210R_0001:4:10:891:1831#0/1
+GTGGATTACTATCTGAGTCCGATGCTGTTCAACCACTA
++HWI-EAS210R_0001:4:10:891:1831#0/1
+ggggggggggggggggghggggggggghgggggfgggg
+@HWI-EAS210R_0001:4:10:891:412#0/1
+TAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACG
++HWI-EAS210R_0001:4:10:891:412#0/1
+gggggggggggggggggggggggggggggggggggggg
+@HWI-EAS210R_0001:4:10:891:346#0/1
+AATTCATCCATTAACTTCTCATCAACATATACAAACTC
++HWI-EAS210R_0001:4:10:891:346#0/1
+^W][_b^be_cRgaggdgdgbL_^_\ZN\R]]`W]cYe
+@HWI-EAS210R_0001:4:10:891:174#0/1
+AGTGGAGGCCTCCAGCAATCTTGAACACTCATCCTTAA
++HWI-EAS210R_0001:4:10:891:174#0/1
+ggggggggggggggggggggggcgggggfgggghghcg
+@HWI-EAS210R_0001:4:10:891:1415#0/1
+ACCAACCATCAGCATGAGCCTGTCGCATTGCATTCATC
++HWI-EAS210R_0001:4:10:891:1415#0/1
+gggggggggggdghgggggggggggggggggggggggg
+@HWI-EAS210R_0001:4:10:891:705#0/1
+TTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTC
++HWI-EAS210R_0001:4:10:891:705#0/1
+gfgggggggggfgggggggggggfgddgggggggeggg
+@HWI-EAS210R_0001:4:10:891:1398#0/1
+GCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAA
++HWI-EAS210R_0001:4:10:891:1398#0/1
+ebehggdhdfgffdda`e\ecgfggedgegeggdfdfg
+@HWI-EAS210R_0001:4:10:891:971#0/1
+TAGCTTTAAGCGGCTCACCTTTAGCATCAACAGGCCAC
++HWI-EAS210R_0001:4:10:891:971#0/1
+ggfgggghggggggfggfgghggfggggfghggffghg
+@HWI-EAS210R_0001:4:10:891:627#0/1
+GTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAA
++HWI-EAS210R_0001:4:10:891:627#0/1
+dfdffaeaaagggg[bgggghgghgggfgg\efefggd
+@HWI-EAS210R_0001:4:10:891:1822#0/1
+GAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCA
++HWI-EAS210R_0001:4:10:891:1822#0/1
+gggeggfggegggggdggggghgfgedgggggcfgdcg
+@HWI-EAS210R_0001:4:10:891:1103#0/1
+AAGGGTAATAAGAACGAACCATAAAAAAGCCTCCAAGA
++HWI-EAS210R_0001:4:10:891:1103#0/1
+ggeggfggggggggghggggggggggfffgdggggggb
+@HWI-EAS210R_0001:4:10:891:586#0/1
+TATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGC
++HWI-EAS210R_0001:4:10:891:586#0/1
+ggggggggggggegfgggfcgggggffggggggggggg
+@HWI-EAS210R_0001:4:10:891:1620#0/1
+TTTTGTGTGCCTGAGTATGGTACAGCTAATGGCCGTCT
++HWI-EAS210R_0001:4:10:891:1620#0/1
+gggggfggggghgggggghcgggdgggegggefgfT``
+@HWI-EAS210R_0001:4:10:891:42#0/1
+CTAAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTA
++HWI-EAS210R_0001:4:10:891:42#0/1
+ggefggggggfggggfaf_fggggdfggggfaYbfd]b
+@HWI-EAS210R_0001:4:10:891:1609#0/1
+GCCATAGCACCAGAAACAAAACTAGGGGCGGCCTCATC
++HWI-EAS210R_0001:4:10:891:1609#0/1
+gggghgggghfgghgggggfffggggcgggfdggfggf
+@HWI-EAS210R_0001:4:10:891:1028#0/1
+AATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAAT
++HWI-EAS210R_0001:4:10:891:1028#0/1
+gfgggggggdgbggfgegeeggggggggdggegggddg
+@HWI-EAS210R_0001:4:10:891:902#0/1
+ATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCG
++HWI-EAS210R_0001:4:10:891:902#0/1
+ggggggfgggggggggggggggggfddggggggggggg
diff -r 000000000000 -r a03a7ee6cdff tool-data/bowtie2_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie2_indices.loc.sample Thu Jan 23 12:30:45 2014 -0500
@@ -0,0 +1,37 @@
+# bowtie2_indices.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a bowtie_indices.loc file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample),
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+#
+#
+# So, for example, if you had hg18 indexes stored in:
+#
+# /depot/data2/galaxy/hg19/bowtie2/
+#
+# containing hg19 genome and hg19.*.bt2 files, such as:
+# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa
+# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2
+# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2
+# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2
+# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2
+#
+# then the bowtie2_indices.loc entry could look like this:
+#
+#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon
+#
+#More examples:
+#
+#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10
+#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3
+#
+#
diff -r 000000000000 -r a03a7ee6cdff tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Jan 23 12:30:45 2014 -0500
@@ -0,0 +1,8 @@
+
+
+
+