| Next changeset 1:6d4d39720545 (2015-10-10) |
|
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/hisat2 commit 1e8d3feeb391aabcfff2338b57913138deea51ec-dirty |
|
added:
hisat2.xml hisat2_macros.xml test-data/hisat_input_1_forward.fastq test-data/hisat_input_1_reverse.fastq test-data/hisat_input_2_forward.fastq test-data/hisat_input_2_reverse.fastq test-data/hisat_output_1.bam test-data/hisat_output_2.bam test-data/hisat_output_3.bam test-data/phiX.fa tool-data/hisat2_indexes.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e hisat2.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hisat2.xml Sat Oct 10 14:54:39 2015 -0400 |
| [ |
| b'@@ -0,0 +1,404 @@\n+<?xml version="1.0"?>\n+<tool id="hisat2" name="HISAT2" version="1.0.0">\n+ <description>A fast and sensitive alignment program</description>\n+ <macros>\n+ <import>hisat2_macros.xml</import>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="2.0">hisat</requirement>\n+ <requirement type="package" version="1.2">samtools</requirement>\n+ </requirements>\n+ <stdio>\n+ <regex match="hisat2-align exited with value 1" source="both" level="fatal"/>\n+ <exit_code range="1:" />\n+ </stdio>\n+ <version_command>hisat2 --version</version_command>\n+ <command>\n+ <![CDATA[\n+ #if str($spliced_options.spliced_options_selector) == "advanced" and str($spliced_options.known_splice_gtf) != \'None\':\n+ ln -s "${spliced_options.known_splice_gtf}" splice_sites.gtf &&\n+ extract_splice_sites.py splice_sites.gtf > splice_sites.txt &&\n+ #end if\n+ #if $reference_genome.reference_genome_source == "history":\n+ ln -s "$reference_genome.history_item" genome.fa &&\n+ hisat2-build genome.fa genome && \n+ #set index_path = \'genome\'\n+ #else:\n+ #set index_path = $reference_genome.index.fields.path\n+ #end if\n+ hisat2 -p \\${GALAXY_SLOTS:-1} -x "${index_path}"\n+ #if str($input_format.paired.paired_selector) == \'paired\':\n+ -1 "${reads_f}" -2 "${reads_r}"\n+ @paired_end_options@\n+ #else if str($input_format.paired.paired_selector) == \'paired_collection\':\n+ -1 "${input_format.paired.reads.forward}" -2 "${input_format.paired.reads.reverse}"\n+ @paired_end_options@\n+ #else:\n+ -U "${input_format.paired.reads}"\n+ #end if\n+ #if $input_format.input_format_selector == \'fasta\':\n+ -f\n+ #end if\n+ #if $max_primary:\n+ -k ${max_primary}\n+ #end if\n+ #if str($input_options.input_options_selector) == "advanced":\n+ #if int( $input_options.skip ) > 0:\n+ -s ${input_options.skip}\n+ #end if\n+ #if int( $input_options.stop_after ) > 0:\n+ -u ${input_options.stop_after}\n+ #end if\n+ -5 ${input_options.trim_five} -3 ${input_options.trim_three}\n+ #end if\n+ #if str($scoring_options.scoring_options_selector) == "advanced":\n+ --ma ${scoring_options.match_bonus} --np ${scoring_options.ambiguous_penalty}\n+ --mp ${scoring_options.max_mismatch},${scoring_options.min_mismatch}\n+ --rdg ${scoring_options.read_open_penalty},${scoring_options.read_extend_penalty}\n+ --rfg ${scoring_options.ref_open_penalty},${scoring_options.ref_extend_penalty}\n+ --sp ${scoring_options.soft_clip_penalty_max},${scoring_options.soft_clip_penalty_min}\n+ --score-min ${scoring_options.function_type},${scoring_options.constant_term},${scoring_options.coefficient}\n+ #end if\n+ #if str($alignment_options.alignment_options_selector) == "advanced":\n+ --n-ceil ${alignment_options.function_type},${alignment_options.constant_term},${alignment_options.coefficient}\n+ ${alignment_options.skip_forward} ${alignment_options.skip_reverse}\n+ #end if\n+ #if str($spliced_options.spliced_options_selector) == "advanced":\n+ --pen-cansplice ${spliced_options.canonical_penalty} --pen-noncansplice ${spliced_options.noncanonical_penalty}\n+ --pen-canintronlen ${spliced_options.function_type},${spliced_options.constant_term},${spliced_options.coefficient}\n+ --pen-noncanintronlen ${spliced_options.nc_function_type},${spliced_options.nc_constant_term},${spliced_options.nc_coefficient}\n+ #if str($spliced_options.known_splice_gtf) != \'None\':\n+ --known-splicesite-infile splice_sites.txt\n+ #end if\n+ ${spliced_options.no_spliced_alignment}\n+ '..b'say that a read has an alignment, we mean that it\n+has a `valid\n+alignment <#valid-alignments-meet-or-exceed-the-minimum-score-threshold>`__.\n+When we say that a read has multiple alignments, we mean that it has\n+multiple alignments that are valid and distinct from one another.\n+\n+Distinct alignments map a read to different places\n+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n+\n+Two alignments for the same individual read are "distinct" if they map\n+the same read to different places. Specifically, we say that two\n+alignments are distinct if there are no alignment positions where a\n+particular read offset is aligned opposite a particular reference offset\n+in both alignments with the same orientation. E.g. if the first\n+alignment is in the forward orientation and aligns the read character at\n+read offset 10 to the reference character at chromosome 3, offset\n+3,445,245, and the second alignment is also in the forward orientation\n+and also aligns the read character at read offset 10 to the reference\n+character at chromosome 3, offset 3,445,245, they are not distinct\n+alignments.\n+\n+Two alignments for the same pair are distinct if either the mate 1s in\n+the two paired-end alignments are distinct or the mate 2s in the two\n+alignments are distinct or both.\n+\n+Default mode: search for one or more alignments, report each\n+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n+\n+HISAT searches for up to N distinct, primary alignments for each read,\n+where N equals the integer specified with the ``-k`` parameter. Primary\n+alignments mean alignments whose alignment score is equal or higher than\n+any other alignments. It is possible that multiple distinct alignments\n+whave the same score. That is, if ``-k 2`` is specified, HISAT will\n+search for at most 2 distinct alignments. The alignment score for a\n+paired-end alignment equals the sum of the alignment scores of the\n+individual mates. Each reported read or pair alignment beyond the first\n+has the SAM \'secondary\' bit (which equals 256) set in its FLAGS field.\n+See the `SAM specification <http://samtools.sourceforge.net/SAM1.pdf>`__\n+for details.\n+\n+HISAT does not "find" alignments in any specific order, so for reads\n+that have more than N distinct, valid alignments, HISAT does not\n+gaurantee that the N alignments reported are the best possible in terms\n+of alignment score. Still, this mode can be effective and fast in\n+situations where the user cares more about whether a read aligns (or\n+aligns a certain number of times) than where exactly it originated.\n+\n+Alignment summmary\n+------------------\n+\n+When HISAT finishes running, it prints messages summarizing what\n+happened. These messages are printed to the "standard error" ("stderr")\n+filehandle. For datasets consisting of unpaired reads, the summary might\n+look like this:\n+\n+::\n+\n+ 20000 reads; of these:\n+ 20000 (100.00%) were unpaired; of these:\n+ 1247 (6.24%) aligned 0 times\n+ 18739 (93.69%) aligned exactly 1 time\n+ 14 (0.07%) aligned >1 times\n+ 93.77% overall alignment rate\n+\n+For datasets consisting of pairs, the summary might look like this:\n+\n+::\n+\n+ 10000 reads; of these:\n+ 10000 (100.00%) were paired; of these:\n+ 650 (6.50%) aligned concordantly 0 times\n+ 8823 (88.23%) aligned concordantly exactly 1 time\n+ 527 (5.27%) aligned concordantly >1 times\n+ ----\n+ 650 pairs aligned concordantly 0 times; of these:\n+ 34 (5.23%) aligned discordantly 1 time\n+ ----\n+ 616 pairs aligned 0 times concordantly or discordantly; of these:\n+ 1232 mates make up the pairs; of these:\n+ 660 (53.57%) aligned 0 times\n+ 571 (46.35%) aligned exactly 1 time\n+ 1 (0.08%) aligned >1 times\n+ 96.70% overall alignment rate\n+\n+The indentation indicates how subtotals relate to totals.\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.1038/nmeth.3317</citation>\n+ </citations>\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e hisat2_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hisat2_macros.xml Sat Oct 10 14:54:39 2015 -0400 |
| [ |
| @@ -0,0 +1,66 @@ +<?xml version="1.0"?> +<macros> + <xml name="function" tokens="helptext"> + <param display="radio" help="@HELPTEXT@" label="Function type" name="function_type" type="select"> + <option value="C">Constant</option> + <option value="L">Linear [f(x) = y + z * x]</option> + <option value="S">Square root [f(x) = y + z * x²]</option> + <option value="G">Natural logarithm [f(x) = y + z * log(x)]</option> + </param> + <param help="@HELPTEXT@" label="Constant term (y)" name="constant_term" type="integer" value="0" /> + <param help="@HELPTEXT@" label="Coefficient (z)" name="coefficient" type="integer" value="0" /> + </xml> + <xml name="single_paired_selector"> + <param label="Single end or paired reads?" name="paired_selector" type="select"> + <option value="paired_collection">Collection of paired reads</option> + <option value="paired">Individual paired reads</option> + <option value="single">Individual unpaired reads</option> + </param> + </xml> + <xml name="paired_input_conditional" tokens="ftype"> + <conditional name="paired"> + <expand macro="single_paired_selector" /> + <when value="paired_collection"> + <param collection_type="paired" format="@FTYPE@" label="Paired reads" name="reads" type="data_collection" /> + <expand macro="paired_end_conditional" /> + </when> + <when value="paired"> + <param format="@FTYPE@" label="Forward reads" multiple="true" name="reads_f" type="data" /> + <param format="@FTYPE@" label="Reverse reads" multiple="true" name="reads_r" type="data" /> + <expand macro="paired_end_conditional" /> + </when> + <when value="single"> + <param format="@FTYPE@" label="Reads" multiple="true" name="reads" type="data" /> + </when> + </conditional> + </xml> + <xml name="paired_end_conditional"> + <conditional name="paired_end_options"> + <param label="Paired-end options" name="paired_end_options_selector" type="select"> + <option value="defaults">Use default values</option> + <option value="advanced">Specify paired-end parameters</option> + </param> + <when value="defaults" /> + <when value="advanced"> + <param name="no_mixed" label="Disable alignments of individual mates" type="boolean" truevalue="--no-mixed" falsevalue="" + help="By default, when hisat cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates. This option disables that behavior. (--no-mixed)" /> + <param name="no_discordant" label="Disable discordant alignments" type="boolean" truevalue="--no-discordant" falsevalue="" + help="By default, hisat looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (--fr/--rf/--ff, -I, -X). This option disables that behavior. (--no-discordant)" /> + <param name="skip_reverse" label="Skip reference strand of reference" type="boolean" truevalue="--norc" falsevalue="" help="(--norc) If --norc is specified, hisat 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 hisat to explore only those paired-end configurations corresponding to fragments from the reverse-complement (Crick) strand." /> + </when> + </conditional> + </xml> + <token name="@paired_end_options@"> + #if str($input_format.paired.paired_end_options.paired_end_options_selector) == 'advanced': + ${input_format.paired.paired_end_options.no_mixed} + ${input_format.paired.paired_end_options.no_discordant} + #end if + </token> + <token name="strandedness_parameters"> + #if str($spliced_options.spliced_options_selector) == "advanced": + #if str($spliced_options.rna_strandness).strip() != '': + --rna-strandness $spliced_options.rna_strandness + #end if + #end if + </token> +</macros> |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e test-data/hisat_input_1_forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat_input_1_forward.fastq Sat Oct 10 14:54:39 2015 -0400 |
| b |
| @@ -0,0 +1,40 @@ +@phiX174_1980_2501_0:1:0_3:0:0_0/1 +TTAGGTGTGTGTAAAACAGGTGCCGAAGAAGCTGGATTAACAGAATTGAGAACCAGCTTATCAGAAAAAA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1542_1965_0:0:0_0:0:0_1/1 +CTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGCA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2950_3377_0:0:0_2:0:0_2/1 +CTCAAATCCGGCGTCAACCATACCAGCATAGGAAGCATCAGCACCAGCACGCTCCCAAGCATTAATCTCA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2259_2739_1:0:0_1:0:0_3/1 +CTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAACGCCGAAGCGGTAAAAAAT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1141_1609_1:0:0_1:0:0_4/1 +TGGCGCTCTCCGTCTTTCTCCATTTCGTCGTGGCCTTGCTATTGACTCTACTGTAGACATTTTTACTTTT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_185_708_0:0:0_1:0:0_5/1 +CCTTTCGCCATCAACTAACGATTCTGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1363_1914_3:0:0_0:0:0_6/1 +GCGTTAAGGTACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGC ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_3199_3732_0:0:0_1:0:0_7/1 +CTGGCACTTCTGCCGTTTCTGATAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_36_572_1:0:0_0:0:0_8/1 +ACCATAAACGCAAGCCTCAACGCAGCGACGAGCACGAGAGCGGTCAGTAGCAATCCAAACTTTGTTACTC ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2128_2577_0:0:0_4:0:0_9/1 +TTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGATTATGACCAGTGTTTCCAGTCCGTTCAG ++ +2222222222222222222222222222222222222222222222222222222222222222222222 |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e test-data/hisat_input_1_reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat_input_1_reverse.fastq Sat Oct 10 14:54:39 2015 -0400 |
| b |
| @@ -0,0 +1,40 @@ +@phiX174_1980_2501_0:1:0_3:0:0_0/2 +GTGAAATTTCTAGGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGTTTAAGATTGCTGAGGGTCA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1542_1965_0:0:0_0:0:0_1/2 +CCATACAAAACAGGGTCGCCAGCAATATCGGTATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2950_3377_0:0:0_2:0:0_2/2 +GCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAAAGCCGCCTC ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2259_2739_1:0:0_1:0:0_3/2 +GCGACCATTCAAAGGATAAACATCATAGGCAGTCGGGAGGGTAGTCGGAACCGACGAAGACTCAAAGCGA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1141_1609_1:0:0_1:0:0_4/2 +CAAATTAGCATAAGCAGCTTGCAGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCTAGAA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_185_708_0:0:0_1:0:0_5/2 +TGTTTTCCGTAAATTCAGCGCCTTCCATGATGCGACAGGCCGTTTGAATGTTGACGGGATGAACATAATA ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_1363_1914_3:0:0_0:0:0_6/2 +TAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACAACTATTTTCAAGCGCCGAGGATGCGTGACCGT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_3199_3732_0:0:0_1:0:0_7/2 +TCTGCGTTTGCTGATGAACTAAGTCAACCTCAGCACTAACCTTGCGAGTCATTTCATTGATTTGGTCATT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_36_572_1:0:0_0:0:0_8/2 +TTTCGGATATTTCTGATGAGTCGAAAAATTATCTTGATAAAGCAGTAATTACTACTGCTTGTTTACGAAT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 +@phiX174_2128_2577_0:0:0_4:0:0_9/2 +CTGAATGGAATTAAGAAAACCACCAATACCAGCATTAACCTTCAAACTATCAAAATATAACGTTGACGAT ++ +2222222222222222222222222222222222222222222222222222222222222222222222 |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e test-data/hisat_input_2_forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat_input_2_forward.fastq Sat Oct 10 14:54:39 2015 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\n+@phiX174_4023_4544_0:0:0_0:0:0_0/1\n+TTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCATTTCTACTCTTTCTCAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_927_1458_2:0:0_2:0:0_1/1\n+TTAAGCTCATTAGGGTTAGCCTCGGTACGGTCAGGCATCCACGGCTCATTAAAATAGTTGTTATAGATAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2195_2674_0:0:0_4:0:0_2/1\n+AGCGAACCAAACAGGCAAAAACTTTAGGGTCGGCATCAAAAGCAATATCAGCACCCACAGAACCAACCAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4438_4887_3:0:0_0:0:0_3/1\n+ATTACCCCAACCAGAAAGGTATTAAGGATGAGTGTTCAAGATTGCTGGAGGCCACCACTATGAAATCGCG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4418_4896_1:0:0_1:0:0_4/1\n+GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGAGTTCAAGATTGCTGGAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1459_1934_0:0:0_1:0:0_5/1\n+TCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2580_3121_1:0:0_1:0:0_6/1\n+GGATACATCTGTCAACGCCGCTAATCAGGTTGTTACTGTTGGTGCTGATATTGCTTTTGATGCCGACCCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_268_822_1:0:0_2:0:0_7/1\n+TTTGACGCACGTTTTCTTCTGCGTCAGTCAGAACGTCAGTGTTTCCTGGGCGTACACGCAAGGTAAACGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4373_4951_0:0:0_2:0:0_8/1\n+GGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTAC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4817_5237_1:0:0_1:0:0_9/1\n+GTTGAACGGCGTCGCGTCGTAACCCAGCTTGGTAAGTTGGATTAATCACTCCGTGGACAGATTTGTCATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_498_1078_5:0:0_0:0:0_a/1\n+CTGAGGAGTAACAAAGTTTGGATTGCTACTGACCGCTCACGTGCTCGTGGCAGCGTTGAGTCTTGCGTTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4746_5200_3:0:0_0:0:0_b/1\n+TGGATTAAGCACTCCGTGGACAGATTTGTCATTGTGAGCATTTTCATCCCGAAGTTGCGGCTCATTCTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4746_5155_3:0:0_0:0:0_c/1\n+ATCCCGAAGTTGCGGCTCATTCTGATTCTGAACAGCTTCTTGGGAAGTAGCGACAGCTTGGTTTTTAGTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2025_2501_0:0:0_0:1:0_d/1\n+AGAAGTTTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2574_3097_1:0:0_2:0:0_e/1\n+ATGGCAGATTTAATACCAGCATCCCCCATGCCTACAGTATTGTTCTCGGTAGCAAGCACATCACCTTGAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1432_1904_0:0:0_0:0:0_f/1\n+TACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGCTCGTTATGGTTTCCGTTGCTGCCATCTCAAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_79_485_2:0:0_2:0:0_10/1\n+ATCTTCGTTTAAATCCAAAACGGCAGAAGCCTGAATGAGCTTAATAGAGGCCACAGCGGTCTGGAAACGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_696_1131_1:0:0_0:0:0_11/1\n+ATCTCGAAGGAGTCGCCAGCGATAACCGGAGTAGTTGAAATGGTAATAAGACGACCAATCTGACCAGCAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1085_1572_3:0:0_1:0:0_12/1\n+ATTACCATTTCACCTACTCCGGTTATCGCTGGCGCCTCCTTCGATATGGACGCCGTTGGCGCTCTCCGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2384_2869_1:0:0_2:0:0_13/1\n+GGAGTTTAATCATTTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGTTCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_794_1377_1:1:0_1:0:0_14/1\n+TGAAACAACTGCTTAGGGATTTTATTGGTATCAGGGTTAATCGTGCCAAGAAAAGCGGCATGGTCAATAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1015_1593_1:0:0_2:0:0_15/1\n+AACTGGCTCCGAGCGTATGCCGCATGACCTTTCCCATCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTT\n++\n+2222222222222222222222222222'..b'ACCGATAACAATACTGTAGGCAAGGGTGATGCTGGTATTAAATCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3247_3815_1:0:0_2:0:0_1df/1\n+AACCACACCAGAAGCAGCATCAGTGACGACATTAGAAATATCCTTTGCAGAAGCGCCAATAAGAGAAGAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3223_3567_2:0:0_3:0:0_1e0/1\n+AGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCAGATAAAGTAAAGGATACTCGTGATTATCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1692_2163_3:0:0_1:0:0_1e1/1\n+CTGACAACCGTCCTTTACTTTTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTTTATTGAACTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2788_3310_1:0:0_5:0:0_1e2/1\n+TCATGAAATGCCTCAGCAAGATAATCACGAGTATCCTTTCCTTTATGAGCGGCAGACATGCCACCAAGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3894_4392_0:0:0_0:0:0_1e3/1\n+TGCGGCAAAACTGCGTAACCGTCTTCTCGTTCTCTAAAAACCATTTTTCGTCCCCTTCGGGGCGGTGGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4515_5044_3:0:0_0:0:0_1e4/1\n+TCCATATCTGACTTTTTGTTAACGTATTTAGCCACATAGAAACCAACAGCCATATAACTGGTAGCTTTAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4404_4767_2:0:0_4:0:0_1e5/1\n+GAATACGGCCATTAGCTGTACCATACTCAGGGACACAAAAATACTGATCGCAGTCTGCGTGTGAATCATT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_225_637_0:0:0_1:0:0_1e6/1\n+GCAATGACGGCAGCAATAAACTCAACAGGAGCAGGAAAGCGAGGGTATCCCAGAAAGTCCAGCGTACCAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_543_956_2:0:0_3:0:0_1e7/1\n+CGTCGCTGCGTTGAGGCTTTCGATTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1929_2438_3:0:0_0:0:0_1e8/1\n+CTTATACCTATATTGCTGGCGACCCTGTTTTGTATGGCAACTTGCCGCCGCGTTAAAATTCTATGAAGGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_492_987_1:0:0_1:0:0_1e9/1\n+GATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACGGCTCTCGTGCTCGTCGCTGCGTTGAGGCTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3808_4333_2:0:0_1:0:0_1ea/1\n+GGGCGGTGGTCTATAGTGTTATTAATATCACGTTGGGGGAGCACATTGTAGCATTGTGCCAATTCATCCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2304_2701_0:0:0_1:0:0_1eb/1\n+TTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2008_2481_4:0:0_1:0:0_1ec/1\n+TTCTGGTGATTCGTCTAAGAAGTTTCAGATTGCTGAGGGTCAGAGGTATCGTTATGCGCCTTGGTATGAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3419_3973_2:0:0_0:0:0_1ed/1\n+AGAGATTGCCGAGATTCAAAATGAGAGTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_383_987_3:0:0_1:0:0_1ee/1\n+GTAAGGGGCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTACAAACCAAAGACGAGCGCCTTTACGCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1054_1487_0:0:0_2:0:0_1ef/1\n+AACGGAAACGATAACGAGCATCATCTTGATTAAGCTCATTAGGGTTAGCCTCGGTACGTTCAGGCATCCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4040_4592_2:0:0_0:0:0_1f0/1\n+CGAGGCTCTTAAACCTGCTATTGAGGCTTGTGGCAATTCTACTCTTTCTCACTCCCCAATGCTTGGCTTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2907_3500_0:0:0_0:0:0_1f1/1\n+GTCTTTCGTATTCTGGCGTGAAGTCGCCGACTGAATGCCAGCAATCTCTTTTTGAGTCTCATTTTGCATC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2716_3207_1:0:0_1:0:0_1f2/1\n+AAGTGCCAGCCTGCAACGTACCTTCAAGAAGTCCTTTACCAGCTTTAGCCATAGCACCAGAAACAAAACA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3328_3788_1:0:0_1:0:0_1f3/1\n+GTGCTGGTGCTGATGCTTCCTCTGCTGGTATGGTTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTCA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e test-data/hisat_input_2_reverse.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat_input_2_reverse.fastq Sat Oct 10 14:54:39 2015 -0400 |
| b |
| b'@@ -0,0 +1,2000 @@\n+@phiX174_4023_4544_0:0:0_0:0:0_0/2\n+CATTGCATTCATCAAACGCTGAATAGTAAAGCCTCTACGCGATTTCATAGTGGAGGCCTCCAGCAATCTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_927_1458_2:0:0_2:0:0_1/2\n+GCGCTCGTCTTTGGTATGTATGTGGTCCACAATTTTAATTGCAGGGGCTTCGGCCCCTTACTTGAGGATA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2195_2674_0:0:0_4:0:0_2/2\n+CAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCTGCCGACCACTCGCG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4438_4887_3:0:0_0:0:0_3/2\n+AACCATAAGGCCACGTATTTTGCAAGCTATTTAACTGGCGGCGATTGCGTACCCGACGACCAAAATTAGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4418_4896_1:0:0_1:0:0_4/2\n+GCATACTGTAACCATCAGGCCACGTATTTTGCAAGCTATTTAACTGGCGGCGATTGCGTACCCGACGACC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1459_1934_0:0:0_1:0:0_5/2\n+TATAAGTCAAAGCACCTTTAGCGTTAAGGTACTGAATCTCTTTATTCGCAGTAGGCGGAAAACGAACAAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2580_3121_1:0:0_1:0:0_6/2\n+GGGTTAGGAACATTAGAGCCTTGAATGGCAGATTTAATCCCAGCATCACCCATGCCTACAGTATTGTTAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_268_822_1:0:0_2:0:0_7/2\n+AAGGACTGGTTTAGATATGAGTCACATTTAGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4373_4951_0:0:0_2:0:0_8/2\n+GGCCACAACCAACCAGAACGTGAAAAAGCGTCCTGCGTGTATCTAACTGCGATGGGCATACTGTAACCAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4817_5237_1:0:0_1:0:0_9/2\n+CCCTAATTTTGGTCGTCGGGTACGCAATCGCCGCCAGTTAAATAGCATGCAAAATACGTGGCCTTATGGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_498_1078_5:0:0_0:0:0_a/2\n+ACCAATCTGACCAGCAAGGAAGCCAAGATGGGAAAGGTCATGCGGCATACGCTCGGCGCCAGTTTGAATA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4746_5200_3:0:0_0:0:0_b/2\n+TGTACAGCTAATGGCCGTCTTCATTTCCATGCGGTGCATTTTATGCGGACAGTTCCTACAGGTAGCGTAG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4746_5155_3:0:0_0:0:0_c/2\n+GGTACCGCTAATGGCCGTCTTCATTTCCATGGTGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2025_2501_0:0:0_0:1:0_d/2\n+TTAGGTGTCTGTAAAACAGGTGCCGAAGAAGCTGGAGTTACAGAAGTGAGAACCAGCTTATCAGAAAAAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2574_3097_1:0:0_2:0:0_e/2\n+TCAGATGGATACATCAGTCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1432_1904_0:0:0_0:0:0_f/2\n+ACTGAATCTCTTTAGTCGCAGTAGGCGGAAAACGAACAAGCGCAAGAGTAAACATAGTGCCATGCTCAGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_79_485_2:0:0_2:0:0_10/2\n+AGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCAGGCGGACAATGAGAAAATTCGACC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_696_1131_1:0:0_0:0:0_11/2\n+TTTACGGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGACTTGTTCGCGTTTACCTTGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1085_1572_3:0:0_1:0:0_12/2\n+ATAGATGTGGTAGAAGTGGTCATTTGGCGAGAAAGCTCAGTCTCAGGAGGAAGCGGAGCAGTCCAAATGT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2384_2869_1:0:0_2:0:0_13/2\n+CCAATGCGCGGCATTTAGTAGCGGTCAAGTTAGACCAAACCATGAAACCAACATAAACATTATTGCCCGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_794_1377_1:1:0_1:0:0_14/2\n+TACTGACGCAGAAGAAAACGTGCGTCAAACTTTACGTGCAGAAGGAGTGATGTAATGTCTAAAGGTAAAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1015_1593_1:0:0_2:0:0_15/2\n+GCTTGCCGACCCATAATGTCAATAGATGTGGTAGAAGTCGTCATTTGGCGAGAAAGCTCCGTCTCAGGAG\n++\n+2222222222222222222222222222'..b'CTTCTGTTGATAAGCAAGCATCTCATTTTTTGCATATACCTGGTCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3247_3815_1:0:0_2:0:0_1df/2\n+GTGGCAAGTGTGCCGCTGATAAAGGAAAGGATACTCGTGATTATCTTGCTGCTGCATTTCCTGAGCTTAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3223_3567_2:0:0_3:0:0_1e0/2\n+TAGACGCAACGCGAGCAGTCGACTCCTTCTGTTGAAAAGCAAGCATCTCATTATGTGCATATACCTGGTC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1692_2163_3:0:0_1:0:0_1e1/2\n+TGGCGAATAAGTACGCGTTCTTGCAAATCACCAGAAGGCGGTTCCTGAATGAATGGGACGCCTTCAAGAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2788_3310_1:0:0_5:0:0_1e2/2\n+CTTCCCCGTACGCCGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACATTACCGCTACTAAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3894_4392_0:0:0_0:0:0_1e3/2\n+GGCTCTAATTTGTCTAGGAAATAACCGTCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4515_5044_3:0:0_0:0:0_1e4/2\n+TTTACTATTCAGCGATTGATTCATGCAATGCGACAGGCTCATGCTGATGGTTGGTTTATCGTTTTTGACA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4404_4767_2:0:0_4:0:0_1e5/2\n+GAACGCCCTCTTAAGGATATTCGCGATGAGTATAATTACCCCAACCAGAAAGGTATTAAGGATGAGTGTT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_225_637_0:0:0_1:0:0_1e6/2\n+GTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTAGATATGAGTCACAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_543_956_2:0:0_3:0:0_1e7/2\n+GTTGACCACCTACATACCAAAGACGAGCGCCTTTAGGCTTGCCTTAAGTACGTCGCAACGGCTGCGGACG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1929_2438_3:0:0_0:0:0_1e8/2\n+GAAAAAAAGTTTGAATTATGGCGAGAAATAAAAGTCTGAAACATGATTAAACTCCTAAGCAGAAAACCTA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_492_987_1:0:0_1:0:0_1e9/2\n+GTAAGGGGCCGAAGCCCCTGCAATTAAAATTGTTGACCACCTACCTACCAAAGACGAGCGCCTTTACGCT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3808_4333_2:0:0_1:0:0_1ea/2\n+GTGTGGTTGATATTTTTGATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCTGGAAATACGG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2304_2701_0:0:0_1:0:0_1eb/2\n+GGGTAGTCGGAACCGAAGAAGACTCAAAGCGAACCAAACAGGCAAAAAATTTAGGGTCGGCATGAAAAGC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2008_2481_4:0:0_1:0:0_1ec/2\n+TGCCGAAGAAGCTGGAGTAACAGAAGTGAGAACCAGCTTATCAGAAAAAAAGATTGAATTATGGCGAGAA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3419_3973_2:0:0_0:0:0_1ed/2\n+CCTCCAAGATTTGGAGGCATGAAAACATACAATTGGGAGGGTGTCAATCCTGACGGTTATTTCCTAGACA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_383_987_3:0:0_1:0:0_1ee/2\n+AGAAATGATGAGTCAAGTTACTGAACAATCCGTACGTATCCAGACCGCTTTGGCCTCTATTAAGCTCAAT\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_1054_1487_0:0:0_2:0:0_1ef/2\n+TGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGACTCC\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_4040_4592_2:0:0_0:0:0_1f0/2\n+CGTGAGAGTGTCAAAAACGATAAACCAACCATCAGCATGAGCCTGTCGCATTGCATTCATCAAACGCTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2907_3500_0:0:0_0:0:0_1f1/2\n+CCAGCCACTTAAGTGAGGTGATTTATGTTTGGTGCTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_2716_3207_1:0:0_1:0:0_1f2/2\n+GATGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACAATTGACG\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n+@phiX174_3328_3788_1:0:0_1:0:0_1f3/2\n+GACATTAGAAATATGCTTTGCAGTAGCGCCAATATGAGAAGAGCCATACCGCTGATTCTGCGTTTGCTGA\n++\n+2222222222222222222222222222222222222222222222222222222222222222222222\n' |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e test-data/hisat_output_1.bam |
| b |
| Binary file test-data/hisat_output_1.bam has changed |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e test-data/hisat_output_2.bam |
| b |
| Binary file test-data/hisat_output_2.bam has changed |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e test-data/hisat_output_3.bam |
| b |
| Binary file test-data/hisat_output_3.bam has changed |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e test-data/phiX.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fa Sat Oct 10 14:54:39 2015 -0400 |
| b |
| @@ -0,0 +1,79 @@ +>phiX174 +GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT +GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG +TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA +GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC +TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT +TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT +CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT +TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG +TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC +GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA +CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG +TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT +AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC +CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA +TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC +TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA +CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA +GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT +GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA +ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC +TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT +TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC +ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC +CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT +GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC +CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC +TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG +TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT +TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA +AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT +TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT +ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC +GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC +TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT +TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA +TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG +TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC +CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG +AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC +CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT +TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG +CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA +AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT +GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG +GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA +TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT +CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG +TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA +GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC +CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA +TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA +AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC +TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT +CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA +TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG +TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT +CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT +TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC +ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG +TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA +ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG +GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC +CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT +GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG +GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT +ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG +CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC +CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC +GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT +CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG +CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA +TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT +TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG +TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC +AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC +TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA + |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e tool-data/hisat2_indexes.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/hisat2_indexes.loc.sample Sat Oct 10 14:54:39 2015 -0400 |
| b |
| @@ -0,0 +1,39 @@ +# hisat2_indexes.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 HISAT2. +# 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 hisat2_indexes.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. +# +# <unique_build_id> <dbkey> <display_name> <file_base_path> +# +# So, for example, if you had sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/hisat2_indexes/ +# +# containing sacCer3 genome and sacCer3.*.ht2 files, such as: +# +# -rw-rw-r-- 1 dave dave 12M Sep 23 13:57 sacCer3.1.ht2 +# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.2.ht2 +# -rw-rw-r-- 1 dave dave 161 Sep 23 13:57 sacCer3.3.ht2 +# -rw-rw-r-- 1 dave dave 2.9M Sep 23 13:57 sacCer3.4.ht2 +# -rw-rw-r-- 1 dave dave 7.3M Sep 23 13:57 sacCer3.5.ht2 +# -rw-rw-r-- 1 dave dave 3.0M Sep 23 13:57 sacCer3.6.ht2 +# -rw-rw-r-- 1 dave dave 128K Sep 23 13:57 sacCer3.7.ht2 +# -rw-rw-r-- 1 dave dave 32K Sep 23 13:57 sacCer3.8.ht2 +# +# then the hisat2_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/hisat2_indexes/sacCer3 +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/hisat2_indexes/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/hisat2_indexes/dm3 +# +# |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Sat Oct 10 14:54:39 2015 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of indexes in the HISAT mapper format --> + <table name="hisat2_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/hisat2_indexes.loc" /> + </table> +</tables> |
| b |
| diff -r 000000000000 -r 5bafe7d7a55e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sat Oct 10 14:54:39 2015 -0400 |
| b |
| @@ -0,0 +1,9 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="hisat" version="2.0"> + <repository changeset_revision="c65f00072e57" name="package_hisat_2_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |