| Next changeset 1:5f4fbba31b6a (2017-10-11) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e |
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added:
sRbowtie.xml test-data/297_reference.fa test-data/al.fa test-data/input.fa test-data/input.fastq test-data/output.bam test-data/output.tab test-data/output2.bam tool-data/bowtie_indices.loc.sample tool_data_table_conf.xml.sample |
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| 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 |
| [ |
| b'@@ -0,0 +1,283 @@\n+<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.0">\n+ <description>for small RNA short reads</description>\n+ <requirements>\n+ <requirement type="package" version="1.1.2=py27_2">bowtie</requirement>\n+ <requirement type="package" version="1.2">samtools</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #if $refGenomeSource.genomeSource == "history":\n+ bowtie-build -f $refGenomeSource.ownFile genome &&\n+ ln -s -f \'$refGenomeSource.ownFile\' genome.fa &&\n+ #set index_path = \'genome\'\n+ #else:\n+ #set index_path = $refGenomeSource.index.fields.path\n+ #end if\n+ #if $input.extension == "fasta":\n+ #set format = "-f"\n+ #elif $input.extension == "fastq":\n+ #set format = "-q"\n+ #end if\n+\n+ ## set the method_prefix\n+ #if $method == "RNA":\n+ #set method_prefix = "-v %s -M 1 --best --strata --norc" % str($v_mismatches)\n+ #elif $method == "unique":\n+ #set method_prefix = "-v %s -m 1" % str($v_mismatches)\n+ #elif $method == "multiple":\n+ #set method_prefix = "-v %s -M 1 --best --strata" % str($v_mismatches)\n+ #elif $method == "k_option":\n+ #set method_prefix = "-v %s -k 1 --best" % str($v_mismatches)\n+ #elif $method == "n_option":\n+ #set method_prefix = "-n %s -M 1 --best" % str($v_mismatches)\n+ #elif $method == "a_option":\n+ #set method_prefix = "-v %s -a --best" % str($v_mismatches)\n+ #end if\n+ \n+ ## set the extra_output\n+ #if $additional_fasta == "No":\n+ #set extra_output = ""\n+ #elif $additional_fasta == "al":\n+ #set extra_output = " --al %s " % str($aligned)\n+ #elif $additional_fasta == "unal":\n+ #set extra_output = " --un %s " % str($unaligned)\n+ #else:\n+ #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned))\n+ #end if\n+ \n+ #set $method_postfix = " %s %s " % ($method_prefix, $extra_output)\n+\n+ ## run the bowtie alignement\n+ #if $output_format == "tabular":\n+ bowtie -p \\${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format \'$input\' > $output\n+ #elif $output_format == "sam":\n+ bowtie -p \\${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format \'$input\' > \'$output\'\n+ #elif $output_format == "bam":\n+ bowtie -p \\${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format \'$input\' | samtools view -u - | samtools sort -@ "\\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output\n+ #end if\n+ ##### | samtools view -uS\n+ ]]></command>\n+ <inputs>\n+ <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq file: reads clipped from their adapter" name="input" type="data" />\n+ <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select">\n+ <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option>\n+ <option value="unique">Match unique mappers on DNA reference index</option>\n+ <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option>\n+ <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option>\n+ <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option>\n+ <option value="a_option">Match and report all valid alignments</option>\n+ </param>\n+ <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select">\n+ '..b'="v_mismatches" value="1" />\n+ <param name="additional_fasta" value="al" />\n+ <param name="output_format" value="tabular" />\n+ <output file="output.tab" ftype="tabular" name="output" />\n+ <output file="al.fa" ftype="fasta" name="aligned" />\n+ </test>\n+ </tests>\n+ <help>\n+\n+**What it does**\n+\n+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.\n+\n+.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml\n+\n+A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution.\n+\n+However, this Bowtie wrapper tool only takes FASTQ files as inputs.\n+\n+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.\n+\n+------\n+\n+**OPTIONS**\n+\n+.. class:: infomark\n+\n+This script uses Bowtie to match reads on a reference index.\n+\n+Depending on the type of matching, different bowtie options are used:\n+\n+**Match on sense strand RNA reference index, multiple mappers randomly matched at a single position**\n+\n+Align on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches:\n+\n+*-v [0,1,2,3] -M 1 --best --strata -p 12 --norc*\n+\n+**Match unique mappers on DNA reference index**\n+\n+Align ONLY unique mappers on DNA reference index\n+\n+*-v [0,1,2,3] -m 1 -p 12*\n+\n+Note that using this option with -v values other than 0 is questionnable...\n+\n+**Match on DNA, multiple mappers randomly matched at a single position**\n+\n+Align multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option:\n+\n+*-v [0,1,2,3] -M 1 --best --strata -p 12*\n+\n+**Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)**\n+\n+Align with highest speed, not guaranteeing best hit for speed gain:\n+\n+*-v [0,1,2,3] -k 1 --best -p 12*\n+\n+**Match on DNA - RNAseq mode (-n bowtie option)**\n+\n+Align reads in as for RNAseq data alignment\n+\n+*-n [0,1,2,3] -M 1 --best -p 12*\n+\n+**Match and report all valid alignments**\n+\n+Align reads and report all valid alignments\n+\n+*-v [0,1,2,3] -a --best -p 12*\n+\n+\n+\n+-----\n+\n+**Input formats**\n+\n+.. class:: warningmark\n+\n+*Lists of reads, in fasta or fastq format, clipped from their adapter sequence*\n+\n+-----\n+\n+**OUTPUTS**\n+\n+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::\n+\n+ Column Description\n+ -------- --------------------------------------------------------\n+ 1 FastaID fasta identifier\n+ 2 polarity + or - depending whether the match was reported on the forward or reverse strand\n+ 3 target name of the matched target\n+ 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence\n+ 5 Seq sequence of the matched Read\n+\n+If you choose SAM, you will get the output in unordered SAM format.\n+\n+.. class:: warningmark\n+\n+if you choose BAM, the output will be in sorted BAM format.\n+To be viewable in Trackster, several condition must be fulfilled:\n+\n+.. class:: infomark\n+\n+Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes\n+\n+.. class:: infomark\n+\n+the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index.\n+\n+Please contact the Galaxy instance administrator if your genome is not referenced\n+\n+**Matched and unmatched fasta reads can be retrieved, for further analyses**\n+\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1186/gb-2009-10-3-r25</citation>\n+ </citations>\n+</tool>\n' |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -0,0 +1,10 @@ +>1 +CATTCTGCGAAGAAGC +>2 +GGAGAGACGACGTCAATTACT +>3 +AATTTCGAAACTACACCTGGAAGGTAACCA +>4 +ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT +>5 +TAAGATACTGATAAGGAAACTACCAATA |
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| 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 |
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| @@ -0,0 +1,10 @@ +>1 +CATTCTGCGAAGAAGC +>2 +GGAGAGACGACGTCAATTACT +>3 +AATTTCGAAACTACACCTGGAAGGTAACCA +>4 +ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT +>5 +TAAGATACTGATAAGGAAACTACCAATA |
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| 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 |
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| @@ -0,0 +1,20 @@ +@HTW-1 +CATTCTGCGAAGAAGC ++ +HHHHHHHHHHHHHHHH +@HTW-2 +GGAGAGACGACGTCAATTACT ++ +HHHHHHHHHHHHHHHHHHHHH +@HTW-3 +AATTTCGAAACTACACCTGGAAGGTAACCA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH +@HTW-4 +ATCGGATTTTCTTATTTATATTCAGGGTATTAAAGAATCTAT ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH +@HTW-5 +TAAGATACTGATAAGGAAACTACCAATA ++ +HHHHHHHHHHHHHHHHHHHHHHHHHHHH |
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| diff -r 000000000000 -r de9cd3998571 test-data/output.bam |
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| Binary file test-data/output.bam has changed |
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| 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 |
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| @@ -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 |
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| diff -r 000000000000 -r de9cd3998571 test-data/output2.bam |
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| Binary file test-data/output2.bam has changed |
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| 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 |
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| @@ -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): +# +#<unique_build_id> <dbkey> <display_name> <file_base_path> +# +#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. +# |
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| 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 |
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| @@ -0,0 +1,8 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the Bowtie mapper format --> + <table name="bowtie_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bowtie_indices.loc" /> + </table> +</tables> |