# HG changeset patch
# User artbio
# Date 1504363925 14400
# Node ID de9cd399857131ff25e7d3e8248c00efb3788da3
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
diff -r 000000000000 -r de9cd3998571 sRbowtie.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/sRbowtie.xml Sat Sep 02 10:52:05 2017 -0400
@@ -0,0 +1,283 @@
+
+ for small RNA short reads
+
+ bowtie
+ samtools
+
+ $output
+ #elif $output_format == "sam":
+ bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output'
+ #elif $output_format == "bam":
+ bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output
+ #end if
+ ##### | samtools view -uS
+ ]]>
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+ additional_fasta == "al" or additional_fasta == "al_and_unal"
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+ additional_fasta == "unal" or additional_fasta == "al_and_unal"
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+**What it does**
+
+Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25.
+
+.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml
+
+A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.
+
+However, this Bowtie wrapper tool only takes FASTQ files as inputs.
+
+The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis.
+
+------
+
+**OPTIONS**
+
+.. class:: infomark
+
+This script uses Bowtie to match reads on a reference index.
+
+Depending on the type of matching, different bowtie options are used:
+
+**Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**
+
+Align on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches:
+
+*-v [0,1,2,3] -M 1 --best --strata -p 12 --norc*
+
+**Match unique mappers on DNA reference index**
+
+Align ONLY unique mappers on DNA reference index
+
+*-v [0,1,2,3] -m 1 -p 12*
+
+Note that using this option with -v values other than 0 is questionnable...
+
+**Match on DNA, multiple mappers randomly matched at a single position**
+
+Align multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:
+
+*-v [0,1,2,3] -M 1 --best --strata -p 12*
+
+**Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**
+
+Align with highest speed, not guaranteeing best hit for speed gain:
+
+*-v [0,1,2,3] -k 1 --best -p 12*
+
+**Match on DNA - RNAseq mode (-n bowtie option)**
+
+Align reads in as for RNAseq data alignment
+
+*-n [0,1,2,3] -M 1 --best -p 12*
+
+**Match and report all valid alignments**
+
+Align reads and report all valid alignments
+
+*-v [0,1,2,3] -a --best -p 12*
+
+
+
+-----
+
+**Input formats**
+
+.. class:: warningmark
+
+*Lists of reads, in fasta or fastq format, clipped from their adapter sequence*
+
+-----
+
+**OUTPUTS**
+
+If you choose tabular as the output format, you will obtain the matched reads in tabular bowtie output format (--suppress 6,7,8), having the following columns::
+
+ Column Description
+ -------- --------------------------------------------------------
+ 1 FastaID fasta identifier
+ 2 polarity + or - depending whether the match was reported on the forward or reverse strand
+ 3 target name of the matched target
+ 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence
+ 5 Seq sequence of the matched Read
+
+If you choose SAM, you will get the output in unordered SAM format.
+
+.. class:: warningmark
+
+if you choose BAM, the output will be in sorted BAM format.
+To be viewable in Trackster, several condition must be fulfilled:
+
+.. class:: infomark
+
+Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes
+
+.. class:: infomark
+
+the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.
+
+Please contact the Galaxy instance administrator if your genome is not referenced
+
+**Matched and unmatched fasta reads can be retrieved, for further analyses**
+
+
+
+ 10.1186/gb-2009-10-3-r25
+
+
diff -r 000000000000 -r de9cd3998571 test-data/297_reference.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/297_reference.fa Sat Sep 02 10:52:05 2017 -0400
@@ -0,0 +1,118 @@
+>FBgn0000005_297
+AGTGACGTATTTGGGTGGTCCAAACCAGCCACTTCCATTATTTCAAAGAAATCAGTAATG
+CACTCTAGTAATTTTCCATAACTGTATCCCAGCTGCGCAGACTCGTTTATCTTTTGCAGC
+GCAGCGTTCTTTGTAAACATCCTAAAGACCTGCCTAAGCAGATTTGACTGCCCTCTTTCA
+ACGCTACCTAATCTTAAGAACCCAAGAGCGAGGCTCTCCCGAAATACAAATATTGTTCAA
+ATACTGAGGCTTCTCCTCAATCCAATTTGCATTTGATTTTTAGTCTTAAGCTGAGATCCA
+AAGAATAAAGTCGTGAAACTATTTCTCCTAAAAACTATTTTTTATTTCTTGGCGTTGTCC
+TTAGTCAACTGACGGGACATTAGTTCGACTCATAAATAAAACAACAATTTTACTGGCGCA
+GTCGGTAGGATACAAAAGTATCCGAAAAAAAAGAACCTTCGAATGGAAAATAAGTTAAAT
+TTTATAGTCCTGTGCTCGAAACATCTCCCAAAATAAATTCGTGAAAACTCTTCAACTTCA
+ATTATAATTCCAATTCGGTTATCCAATAATAAGTGGAAGTGAAATACGAAACAAAAATAT
+TAAGTCCAAAGGCAACTAAGTTTTAAAACCAACATATAAAAATAAAAAATTAAAACAATA
+TAGAATTTTAATAATACAACACAAAAATTTACAAAACAAAAAAACAAACAAGTGAAACTA
+GAAAGCTTAAAAATAATAATAACATTGAATCCGAAACAAAACAAAAAAATAAAACACAAA
+AGTTAAAAATTTTACAATAAAAATGTCACAACCAATTATTGCGCTGAGCGACATAAACCT
+TGCCGAAGCCCGTCGGCAGCTTAAAGACATTATGCCATTCAAGGGTGATCCAGAAACCCT
+TCACACCTTTATCAGCAGAGTGGATTACGTAATTTCGCTCTACCAAACAAATGATGTCCG
+ACAACAGAGGATTCTACTGGGAGCCATCGAAAGGAACTTGGACGGACAAATTACACGATC
+TTTGGGACTTCCGAACGTCGAAGATTGGCCTACCCTTAAAGCAAGACTCATCGCGGAATT
+TAAAATTCAAACACCAAACTACAAACTTCTGGAGAACTTCAGGGAGACACCATACAGAGG
+AAGCCTAAGAGCATTCTGCGAAGAAGCGGAGAGACGACGTCAATTACTAATTTCGAAACT
+ACACCTGGAAGGTAACCAATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT
+TAAGATACTGATAAGGAAACTACCAATACAATTATTCACTATTTTAGCCCATCACGATAT
+TACAGACTTAAGATCCTTAATTACCATTGCACAAAATGAGGGAATTTATGAAGAACACAT
+TAATTTTGAATTTTATGAAAAACCAGAATATCGTAATAAAAATTCAAATTCTAACCAGAA
+TTCGAAAACACAAAAATTCAATACAAATGTTCAAACTCAAAATCGACCAAGTTACTCACA
+ATATTCCCAACCCTTCCAACCTAATTTTAATCAATACATTCAACCATTTAGACCTAGCTA
+TACACAGCAGATAACTAACAACCCACCCATGTGGCACGCACCTAATTATTTCAGACCCAA
+CCAATACATAAACCCACAACCCATTATTCAAAAAAATCATTTCCAACAATATCCCAACAA
+AGCCCAATTTCCCCAAACAACGCATTTTAGAGGAAATACATACCCTCGACTACAACAACC
+CTCTACATATAAAAATACTAACTTCCCGATTACTAAACGACTAAGACCATCGGACAGTGA
+ACAAACTAAAATGTCTATTGACGAAATTAGATTCCAAGACGCGCATGAATTCGAACAAGT
+CCAACCTAATTATTACGAGCAACAGTATTTTAACCAAAATCAATACAATCCGTATCAAAA
+TCATAGCTTCATTAATGAAGGGCAACAACAAGTTCAATTTGTACAAATTAATAACAAACA
+AAACCAAAATAATTCTGAACTAAACGAAAATTTTCGGTTAACAGTTCCGGAAAATACGAA
+TACATAAAAATAGTATACAAAGGGCGTTCATACAAATGCCTTCTAGACACAGGATCAACA
+ATTAATATGATCAATGAAAATATATTTTGTCTTCCCATTCAAAATAGTAGATGTGAAGTT
+TTAACATCAAATGGCCCTATTACCTTGAACGACTTGATTATGTTACCCAGAAATAGTATT
+TTCAAAAAAACCGAACCATTTTATGTGCACAGATTTTCTAATAATTACGATATGCTAATT
+GGCAGAAAATTGTTGAAAAATGCTCAATCAGTTATTAATTACAAAAATGATACAGTTACC
+CTTTTTGATCAAACATACAAATTAATTACTTCAGAATCCGAAAGAAACCAAAATTTGTAT
+ATCCAAAGGACACCAGAATCAATTGCAAGCTCAGATCAGGAATCAATAAAAAAATTAGAT
+TTTTCACAGTTTCGATTAGATCACCTAAATCAGGAGGAAACTTTTAAGTTAAAAGGCTTG
+TTAAATAAATTTAGAAATCTTGAATATAAGGAGGGAGAGAAATTAACATTTACAAATACA
+ATTAAACACGTACTAAATACAACACATAACTCCCCAATTTATTCGAAACAATACCCACTT
+GCGCAAACACACGAAATCGAAGTAGAAAACCAAGTACAGGAAATGCTGAATCAGGGATTA
+ATTAGGGAAAGTAATTCTCCATACAATAGTCCTACTTGGGTCGTACCAAAGAAACCGGAT
+GCTTCTGGTGCAAATAAGTACAGGGTAGTAATTGATTATAGAAAGCTAAATGAAATAACC
+ATACCTGACAGATATCCAATTCCAAATATGGACGAAATTCTTGGCAAACTGGGTAAATGC
+CAATATTTTACAACGATCGATCTGGCAAAGGGATTTCATCAAATAGAAATGGACGAAGAA
+TCAATTTCTAAAACTGCATTCTCCACAAAAAGCGGTCATTACGAATACCTTCGAATGCCA
+TTTGGCCTTAGGAATGCACCCGCTACTTTTCAAAGGTGCATGAATAATATCCTTCGACCG
+TTGCTTAACAAACACTGTTTGGTGTATCTGGATGATATTATAATTTTTTCAACATCCCTT
+ACAGAACATTTAAATTCAATACAATTAGTTTTTACAAAGCTTGCAGATGCAAATTTAAAA
+TTGCAACTAGACAAATGTGAGTTCTTAAAAAAGGAAGCTAACTTTCTTGGTCACATAGTT
+ACCCCTGATGGTATTAAACCAAATCCTATTAAAGTTAAAGCCATAGTTTCATACCCAATT
+CCGACAAAAGATAAAGAGATAAGAGCTTTCCTTGGATTAACAGGTTATTATCGCAAATTT
+ATTCCAAATTACGCAGACATAGCAAAACCCATGACCAGCTGCTTAAAAAAAAGGACAAAG
+ATAGATACACAAAAACTTGAGTACATAGAGGCATTCGAAAAACTTAAGGCTTTGATAATT
+CGTGACCCAATTTTACAATTACCTGATTTTGAAAAGAAATTTGTTTTAACCACAGATGCA
+AGTAACTTGGCCCTCGGGGCTGTCCTTTCTCAAAACGGTCATCCTATATCTTTTATTAGT
+AGAACACTTAACGATCACGAATTAAATTACAGTGCTATCGAAAAAGAATTACTTGCCATA
+GTTTGGGCCACAAAAACTTTTCGACATTATTTACTAGGACGACAATTTCTCATTGCCAGT
+GACCATCAACCTCTTAGATGGCTTCATAACTTAAAGGAACCAGGTGCTAAGTTAGAAAGA
+TGGAGAGTTAGATTAAGCGAATACCAATTTAAAATAGATTATATTAAAGGGAAAGAAAAT
+TCAGTTGCCGATGCATTATCAAGAATTAAAATTGAAGAAAATCATCATAGTGAAGCTACT
+CAACATAGTGCAGAAGAGGACAATAGCAACCTTATTCATTTAACAGAAAAACCAATAAAT
+TATTTCAAAAAACAAATAATCTTTATTAAATCCGATAAAAATAAAGTAGAGCATTCAAAA
+ATATTCGGTAACTCCATTACCACAATTCAATATGACGTAATGACACTTGAAAAGGCCAAA
+CAAATTTTACTCGATCACTTTATCCATAGAAACATTACCATTTATATTGAGAGCGATGTA
+GATTTTGAAATCGTTCAAAGAGCACACATAGAAATTGTTAATACCACCTACACAAAAGTA
+ATTCGCAGTCTTTTCCTATTAAAGAACGTTGGTTCATACGCCGAATTCAAAGAAATCATA
+CTTCAATCACATGAAAAACTTTTACACCCTGGTATACAGAAAATGACAAAATTATTTAAA
+GAAAATCACTTCTTTCCAAATAGCCAACTATTAATTCAGAATATAATAAACGAATGCAAC
+ATATGCAATTTGGCCAAAACAGAACATAGAAACACCAAAATGCCTTTAAAAATCACACCC
+AACCCGGAACATTGCCGAGAAAAATTTGTAGTAGATATTTATTCATCTGAGGGAAAACAT
+TACATCAGTTGCATTGATATTTATTCTAAATTCGCTACACTTGAGCAAATTAAAACTAAG
+GATTGGATAGAATGCAGAAACGCATTAATGCGCATTTTTAATCAACTAGGAAAACCCAAA
+TTATTAAAGGCAGACAGAGACGGAGCTTTCTCCAGTTTAGCTTTAAAGCGATGGCTTGAA
+GAAGAAGAAGTCGAATTACAGCTCAATACAGCAAAAAACGGAGTAGCAGACGTCGAAAGA
+TTACACAAAACAATAAATGAAAAAATTCGTATAATCAATTCATCTGATGATGAAGAAGTA
+AAATTAAGCAAGATAGAAACAATCCTCTACACATACAACCAAAAAATTAAACATGACACT
+ACTGGACAGAGACCTGCTCAAATTTTCTTATACGCTGGGCATCCCATATTAGACACTCAA
+AAAATTAAAGAGAAGAAAATAGAGAAAATAAATGAAGACAGACGGGAATTTAATATTGAC
+ACTAATTACAGAAAAGGTCCACTACAGAAAGGCAAATTAGAAAACCCATTTAAACCAACC
+AAAAATGTAGAACAGACAGACCCTGACCATTACAAAATCACTAATAGAAATAGAGTTACG
+CACTACTACAAAACACAATTCAAAAAACAAAAGAAAAATAATAAACTCTCAATTTCACAG
+GCACCTGGTACCCGATAACACTATTGTTTATACTGATCACAGCTGTTCATGGACAACAAA
+TTCAAATTAATAATATTGACACCAACCACGGATATCTCCTTTTTTCTGATAAGCCAGTAC
+AGATACCATCCTCCTTTGAACATCACTCCTTAAAAATCAATTTAACTGAAATAGACATCG
+TGGTTGACTATTTTGAGCAAAGACTACGAACCGATTACCATGCACCCCAGATCAATTTTT
+TATACAATAAAATAAAAAGAGAACTAGCCAGAATAACCCTGAAACATAGAAACAAACGGG
+GTTTTATTAACATTGTGGGTTCAGGTTTTAAATACCTATTTGGAACACTAGATGAAAATG
+ATCGAGTCGAAATACAGAAAAAACTTGAAATCAACGTCCATAACTCAGTAAAATTACATG
+AACTCAACGACGCCATACGATTGATAAATGACGGAATGCAAAAAATACAGAATTATGAAA
+ATAACCACACCATCATTGACAGTCTTTTGTTCGAACTAATGCAGTTTACGGAATACATAG
+AAGATTTGGAAATGGCTATGCAGCTTTCCAGACTTGGACTGTTTAACCCCAAATTACTAA
+ACTACGACAAACTTGAAAATGTGAACAGCCAAAACATTTTGAACATTAAAACATCCACTT
+GGATTAACTACAATGATAACCAAGTATTAATCATATCCCACATACCCATTTACCTTTCAC
+TAATAAGCACAATTAAAATAATTCCTTACCCAGACTCCAACGGCTATCAGCTAGATTACA
+CAGACACACAATCATATTTTGAAAAAGAAAATAAAGTTTATAATACCGAAAATAAAGAAG
+TAAAAAATGAATGTGTCACCAATATTATTAAACACTTAAATCCAATTTGTAATTTTAAGC
+CAGTACACACGAACGAAATAATAAAATACATAGAACCAAACACAATTGTAACTTGGAACT
+TAACCCAAACAATTCTTAACCAAAATTGCCAAAATTCAATTAATAAAATAAAAATAGAAG
+GAAACAAAATGATAAGAGTAACGCAATGCAAAATAGAAATCAATAATATAAATTTTAGTG
+AAACTCTGTTAGAACCAGAAATAGATTTGACACCACTATACACACCACTTAATATAACAA
+AAATAAAAATTGTAAAACACAACGACATTATTGAGATGATTTCAGAGAACAATATTACAC
+TTTACATACAAATGATCATTGTAATAATCGCACTAATTTTGTTGTACTCATATTTAAGAT
+ATGTATCATTTAAACCATTTATGATGTTGTATGCAAAACTTAAAATAAGAAAAAATCAAA
+ATCAAAACACACCACAACAAACAGAAATAGAAGAAATTCCATTTCCCACACTATATCCAT
+CAATCCCAGCCCAAGTATAGGCTTCTCTTTAAGGGAAGGGGAGTGACGTATTTGGGTGGT
+CCAAACCAGCCACTTCCATTATTTCAAAGAAATCAGTAATGCACTCTAGTAATTTTCCAT
+AACTGTATCCCAGCTGCGCAGACTCGTTTATCTTTTGCAGCGCAGCGTTCTTTGTAAACA
+TCCTAAAGACCTGCCTAAGCAGATTTGACTGCCCTCTTTCAACGCTACCTAATCTTAAGA
+ACCCAAGAGCGAGGCTCTCCCGAAATACAAATATTGTTCAAATACTGAGGCTTCTCCTCA
+ATCCAATTTGCATTTGATTTTTAGTCTTAAGCTGAGATCCAAAGAATAAAGTCGTGAAAC
+TATTTCTCCTAAAAACTATTTTTTATTTCTTGGCGTTGTCCTTAGTCAACTGACGGGACA
+TTAGTTCGACTCATAAATAAAACAACAATTTTACT
diff -r 000000000000 -r de9cd3998571 test-data/al.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/al.fa Sat Sep 02 10:52:05 2017 -0400
@@ -0,0 +1,10 @@
+>1
+CATTCTGCGAAGAAGC
+>2
+GGAGAGACGACGTCAATTACT
+>3
+AATTTCGAAACTACACCTGGAAGGTAACCA
+>4
+ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT
+>5
+TAAGATACTGATAAGGAAACTACCAATA
diff -r 000000000000 -r de9cd3998571 test-data/input.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fa Sat Sep 02 10:52:05 2017 -0400
@@ -0,0 +1,10 @@
+>1
+CATTCTGCGAAGAAGC
+>2
+GGAGAGACGACGTCAATTACT
+>3
+AATTTCGAAACTACACCTGGAAGGTAACCA
+>4
+ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT
+>5
+TAAGATACTGATAAGGAAACTACCAATA
diff -r 000000000000 -r de9cd3998571 test-data/input.fastq
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/input.fastq Sat Sep 02 10:52:05 2017 -0400
@@ -0,0 +1,20 @@
+@HTW-1
+CATTCTGCGAAGAAGC
++
+HHHHHHHHHHHHHHHH
+@HTW-2
+GGAGAGACGACGTCAATTACT
++
+HHHHHHHHHHHHHHHHHHHHH
+@HTW-3
+AATTTCGAAACTACACCTGGAAGGTAACCA
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+@HTW-4
+ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
+@HTW-5
+TAAGATACTGATAAGGAAACTACCAATA
++
+HHHHHHHHHHHHHHHHHHHHHHHHHHHH
diff -r 000000000000 -r de9cd3998571 test-data/output.bam
Binary file test-data/output.bam has changed
diff -r 000000000000 -r de9cd3998571 test-data/output.tab
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output.tab Sat Sep 02 10:52:05 2017 -0400
@@ -0,0 +1,5 @@
+1 + FBgn0000005_297 1151 CATTCTGCGAAGAAGC
+2 + FBgn0000005_297 1167 GGAGAGACGACGTCAATTACT
+3 + FBgn0000005_297 1188 AATTTCGAAACTACACCTGGAAGGTAACCA
+4 + FBgn0000005_297 1218 ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT
+5 + FBgn0000005_297 1260 TAAGATACTGATAAGGAAACTACCAATA
diff -r 000000000000 -r de9cd3998571 test-data/output2.bam
Binary file test-data/output2.bam has changed
diff -r 000000000000 -r de9cd3998571 tool-data/bowtie_indices.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/bowtie_indices.loc.sample Sat Sep 02 10:52:05 2017 -0400
@@ -0,0 +1,37 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#
+#
+#So, for example, if you had hg18 indexed stored in
+#/depot/data2/galaxy/bowtie/hg18/,
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18 hg18 hg18 /depot/data2/galaxy/bowtie/hg18/hg18
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#
diff -r 000000000000 -r de9cd3998571 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Sat Sep 02 10:52:05 2017 -0400
@@ -0,0 +1,8 @@
+
+
+
+