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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty" |
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modified:
macros.xml test-data/cached_locally/salmon_indexes_versioned.loc |
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added:
old/README.rst old/salmon.xml old/static/images/ReadLibraryIllustration.png old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv old/test-data/cached_locally/prebuilt_index/hash.bin old/test-data/cached_locally/prebuilt_index/header.json old/test-data/cached_locally/prebuilt_index/indexing.log old/test-data/cached_locally/prebuilt_index/quasi_index.log old/test-data/cached_locally/prebuilt_index/refInfo.json old/test-data/cached_locally/prebuilt_index/rsd.bin old/test-data/cached_locally/prebuilt_index/sa.bin old/test-data/cached_locally/prebuilt_index/txpInfo.bin old/test-data/cached_locally/prebuilt_index/versionInfo.json old/test-data/cached_locally/salmon_indexes_versioned.loc old/test-data/gene_map.tab old/test-data/reads_1.fastq old/test-data/reads_1.fastq.bz2 old/test-data/reads_1.fastq.gz old/test-data/reads_2.fastq old/test-data/reads_2.fastq.bz2 old/test-data/reads_2.fastq.gz old/test-data/reads_both.fastq old/test-data/reads_both.fastq.bz2 old/test-data/reads_both.fastq.gz old/test-data/salmon_genMap_result1.tab old/test-data/salmon_quant_result1.tab old/test-data/transcripts.fasta old/tool-data/salmon_indexes_versioned.loc.sample old/tool_data_table_conf.xml.sample old/tool_data_table_conf.xml.test |
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removed:
salmonquant.xml |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 macros.xml --- a/macros.xml Mon Sep 09 11:11:22 2019 -0400 +++ b/macros.xml Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -1,7 +1,7 @@ <macros> <token name="@VERSION@">0.14.1</token> <token name="@GALAXY_VERSION@">galaxy0</token> - <token name="@IDX_VERSION@">q5</token> + <token name="@IDX_VERSION@">q6</token> <xml name="requirements"> <requirements> <requirement type="package" version="1.0.6">bzip2</requirement> |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/README.rst Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -0,0 +1,62 @@ +Galaxy wrappers for salmon +===================================== + +These wrappers are copyright 2014, updated 2018 by Björn Grüning, Mhd Ramez Alrawas and additional contributors. +All rights reserved. See the licence text below. + +Currently tested with salmon 0.11.2. + + +Automated Installation +====================== + +Galaxy should be able to automatically install the salmon for you if you have Conda dependency management enabled in Galaxy. +For more information please read the documentation at: https://github.com/galaxyproject/galaxy/blob/dev/doc/source/admin/conda_faq.rst + + +History +======= + +======== ====================================================================== +Version Changes +-------- ---------------------------------------------------------------------- +v0.6.3.0 - First release +-------- ---------------------------------------------------------------------- +v0.7.2 - Second release +-------- ---------------------------------------------------------------------- +v0.8.2 - Third release +-------- ---------------------------------------------------------------------- +v0.9.1 - Fourth release +-------- ---------------------------------------------------------------------- +v0.11.2 - Fifth release + +======== ====================================================================== + + +Bug Reports +=========== + +You can file an issue here https://github.com/bgruening/galaxytools/issues or ask +us on the Galaxy development list http://lists.bx.psu.edu/listinfo/galaxy-dev + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/salmon.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/salmon.xml Wed Oct 02 04:31:53 2019 -0400 |
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| b'@@ -0,0 +1,885 @@\n+<tool id="salmon" name="Salmon" version="@VERSION@">\n+\n+ <description>Transcript Quantification from RNA-seq data</description>\n+\n+ <macros>\n+ <xml name="strandedness">\n+ <param name="strandedness" type="select" label="Specify the strandedness of the reads">\n+ <option value="U" selected="True">Not stranded (U)</option>\n+ <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>\n+ <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>\n+ </param>\n+ </xml>\n+ <xml name="orientation">\n+ <param name="orientation" type="select" label="Relative orientation of reads within a pair">\n+ <option value="M">Mates are oriented in the same direction (M = matching)</option>\n+ <option value="O">Mates are oriented away from each other (O = outward)</option>\n+ <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>\n+ </param>\n+ </xml>\n+ <token name="@VERSION@">0.11.2</token>\n+ <token name="@IDX_VERSION@">q5</token>\n+ </macros>\n+\n+ <requirements>\n+ <requirement type="package" version="1.0.6">bzip2</requirement>\n+ <requirement type="package" version="@VERSION@">salmon</requirement>\n+ <requirement type="package" version="1.2">seqtk</requirement>\n+ </requirements>\n+\n+ <stdio>\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ <regex match="Exception :" />\n+ </stdio>\n+ <version_command>salmon -version</version_command>\n+ <command><![CDATA[\n+ mkdir ./index\n+ &&\n+ mkdir ./output\n+ #if $refTranscriptSource.TranscriptSource == "history":\n+ &&\n+ salmon index\n+ --transcripts $refTranscriptSource.ownFile\n+ --kmerLen $refTranscriptSource.kmerLen\n+ --threads "\\${GALAXY_SLOTS:-4}"\n+ --index \'./index\'\n+ --type \'$quasi_orphans.type\'\n+ $perfectHash\n+ #set $index_path = \'./index\'\n+ #else:\n+ #set $index_path = $refTranscriptSource.index.fields.path\n+ #end if\n+ &&\n+ #set compressed = \'no\'\n+ #if $single_or_paired.single_or_paired_opts == \'single\':\n+ #if $single_or_paired.input_singles.ext == \'fasta\':\n+ #set $ext = \'fasta\'\n+ #else:\n+ #if $single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set compressed = \'GZ\'\n+ #else if $single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set compressed = \'BZ2\'\n+ #end if\n+ #set $ext = \'fastq\'\n+ #end if\n+ ln -s $single_or_paired.input_singles ./single.$ext &&\n+ #else if $single_or_paired.single_or_paired_opts == \'paired\':\n+ #if $single_or_paired.input_mate1.ext == \'fasta\':\n+ #set $ext = \'fasta\'\n+ #else:\n+ #if $single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):\n+ #set compressed = \'GZ\'\n+ #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):\n+ #set compressed = \'BZ2\'\n+ #end if\n+ #set $ext = \'fastq\'\n+ #end if\n+ ln -s $single_or_paired.input_mate1 ./mate1.$ext &&\n+ ln -s $single_or_paired.input_mate2 ./mate2.$ext &&\n+ #else if $single_or_paired.single_or_paired_opts == \'paired_collection\':\n+ #if $single_or_paired.input_1.forward.ext == \'fasta\':\n+ #set $ext = \'fasta\'\n+ #else:\n+ #if $single_or_paired.input_1.forward.is_of_type('..b'may be unstraned or strand-specific. Finally, paired-end\n+protocols will have a specified relative orientation. To characterize the\n+various different typs of sequencing libraries, we\'ve created a miniature\n+"language" that allows for the succinct description of the many different types\n+of possible fragment libraries. For paired-end reads, the possible\n+orientations, along with a graphical description of what they mean, are\n+illustrated below:\n+.. image:: ReadLibraryIllustration.png\n+The library type string consists of three parts: the relative orientation of\n+the reads, the strandedness of the library, and the directionality of the\n+reads.\n+The first part of the library string (relative orientation) is only provided if\n+the library is paired-end. The possible options are:\n+::\n+\n+ I = inward\n+ O = outward\n+ M = matching\n+\n+The second part of the read library string specifies whether the protocol is\n+stranded or unstranded; the options are:\n+::\n+\n+ S = stranded\n+ U = unstranded\n+\n+If the protocol is unstranded, then we\'re done. The final part of the library\n+string specifies the strand from which the read originates in a strand-specific\n+protocol \xe2\x80\x94 it is only provided if the library is stranded (i.e. if the\n+library format string is of the form S). The possible values are:\n+::\n+\n+ F = read 1 (or single-end read) comes from the forward strand\n+ R = read 1 (or single-end read) comes from the reverse strand\n+\n+So, for example, if you wanted to specify a fragment library of strand-specific\n+paired-end reads, oriented toward each other, where read 1 comes from the\n+forward strand and read 2 comes from the reverse strand, you would specify ``-l\n+ISF`` on the command line. This designates that the library being processed has\n+the type "ISF" meaning, **I**\\ nward (the relative orientation), **S**\\ tranded\n+(the protocol is strand-specific), **F**\\ orward (read 1 comes from the forward\n+strand).\n+The single end library strings are a bit simpler than their pair-end counter\n+parts, since there is no relative orientation of which to speak. Thus, the\n+only possible library format types for single-end reads are ``U`` (for\n+unstranded), ``SF`` (for strand-specific reads coming from the forward strand)\n+and ``SR`` (for strand-specific reads coming from the reverse strand).\n+A few more examples of some library format strings and their interpretations are:\n+::\n+\n+ IU (an unstranded paired-end library where the reads face each other)\n+\n+::\n+\n+ SF (a stranded single-end protocol where the reads come from the forward strand)\n+\n+::\n+\n+ OSR (a stranded paired-end protocol where the reads face away from each other,\n+ read1 comes from reverse strand and read2 comes from the forward strand)\n+\n+.. note:: Correspondence to TopHat library types\n+\n+ The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq\n+ read aligner has a different convention for specifying the format of the library.\n+ Below is a table that provides the corresponding Salmon/salmon library format\n+ string for each of the potential TopHat library types:\n+\n+ +---------------------+-------------------------+\n+ | TopHat | Salmon (and Sailfish) |\n+ +=====================+============+============+\n+ | | Paired-end | Single-end |\n+ +---------------------+------------+------------+\n+ |``-fr-unstranded`` |``-l IU`` |``-l U`` |\n+ +---------------------+------------+------------+\n+ |``-fr-firststrand`` |``-l ISR`` |``-l SR`` |\n+ +---------------------+------------+------------+\n+ |``-fr-secondstrand`` |``-l ISF`` |``-l SF`` |\n+ +---------------------+------------+------------+\n+\n+ The remaining salmon library format strings are not directly expressible in terms\n+ of the TopHat library types, and so there is no direct mapping for them.\n+]]> </help>\n+ <citations>\n+ <citation type="doi">10.1101/021592</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/static/images/ReadLibraryIllustration.png |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -0,0 +1,1 @@ +RetainedTxp DuplicateTxp |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/cached_locally/prebuilt_index/hash.bin |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/cached_locally/prebuilt_index/header.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/cached_locally/prebuilt_index/header.json Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -0,0 +1,14 @@ +{ + "value0": { + "IndexType": 1, + "IndexVersion": "q5", + "UsesKmers": true, + "KmerLen": 31, + "BigSA": false, + "PerfectHash": false, + "SeqHash": "238a71484cdcf251805629c612f7edd515eb1a23d9be2e2014b62fd5931eb4ac", + "NameHash": "2fc64c34c65a78d18fec933772e1aa454cfed52b2b48d43eb75d2933a22feb04", + "SeqHash512": "a45ea3d0c5f11c16a45b8b75f902f908996117d7486d72b3d19a8ae619b07b22f3ca0888f5ee6e9dbabf639ae51f7fc74b8eea8808435bbb2ec70b96162849aa", + "NameHash512": "6123f1c58bf2153fca204e97fa72a2d25460242f14b886e421316ff251cc57293e77c02d536122e97f46d2508c626e42a35a1798209766359904ddf49fb7bf33" + } +} \ No newline at end of file |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/cached_locally/prebuilt_index/indexing.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/cached_locally/prebuilt_index/indexing.log Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -0,0 +1,2 @@ +[2019-07-25 13:45:20.599] [jLog] [info] building index +[2019-07-25 13:45:20.654] [jLog] [info] done building index |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/cached_locally/prebuilt_index/refInfo.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/cached_locally/prebuilt_index/refInfo.json Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -0,0 +1,5 @@ +{ + "ReferenceFiles": [ + "tools/salmon/test-data/transcripts.fasta" + ] +} \ No newline at end of file |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/cached_locally/prebuilt_index/versionInfo.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/cached_locally/prebuilt_index/versionInfo.json Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -0,0 +1,6 @@ +{ + "indexVersion": 2, + "hasAuxIndex": false, + "auxKmerLength": 31, + "indexType": 1 +} \ No newline at end of file |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/cached_locally/salmon_indexes_versioned.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/cached_locally/salmon_indexes_versioned.loc Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -0,0 +1,33 @@ +# salmon_indexes_versioned.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 Salmon. +# 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 salmon_indexes_versioned.loc.sample 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> <version> +# +# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" + + + +# So, for example, if you had sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/salmon_indexes/ +# +# then the salmon_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 +# +# +hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q5 |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/gene_map.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/gene_map.tab Wed Oct 02 04:31:53 2019 -0400 |
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| @@ -0,0 +1,4 @@ +NM_174914 foo +NM_001168316 bar +NR_003084 baz +NR_031764 foo |
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| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/reads_1.fastq Wed Oct 02 04:31:53 2019 -0400 |
| b |
| b'@@ -0,0 +1,40000 @@\n+@1:NM_014620:16:182\n+GTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+TGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GGAAGGACTCAGAAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+CTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+AAGGGACTGTCTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+ATAACATCCAAGAAAGACACCTTGCATATTCTTTCAGTTTCTGTTTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+CCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+AAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CAACGAGGGCAACAAGGGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+CCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+CACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@16:NM_022658:1052:179\n+CAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGGGCAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@17:NM_022658:1351:186\n+TCCATCAGGTTCCTAGAGAAAGTCAAGGGGGTTTTTCTAAGCAGGGAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@18:NM_022658:1777:222\n+TAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTTTAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@19:NM_018953:838:165\n+GCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCACAGACAAAAGCGCTTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@20:NM_022658:997:196\n+GGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGAGTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@21:NM_022658:1639:210\n+TCGGGCCCATGCCTTCCTCTCCTTCGCTGTTTGATTTCTATTCTGTTGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@22:NM_174914:42:131\n+TCAGGAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@23:NM_022658:782:137\n+TTCTTTTTTGCTTAGTCCTTGTTTTCTTCCTTTTCCTCCTCTTCTTTCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@24:NM_022658:623:187\n+AGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAACTAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@25:NM_022658:1061:175\n+GGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@26:NM_174914:1681:185\n+AGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@27:NM_022658:619:223\n+GGGGAGGCGCAGTGGACGGCAAACTTACAGCCGGTATCAGACCTTGGAAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@28:NM_022658:1432:199\n+GAAATAAGGAAAAAAGCAAGGAATATCCCCTCCCCCTCCCCCTCCCCCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@29:NM_173860:122:191\n+CGCCGCCACCCTCGGCGCACGGCTCGCGGTAGTAACCCTTGCCGTCCTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@30:NM_022658:1594:160\n+GCCTGCAGTCGCCTCTAAAATCCTACCTAACCATCCCATGGTCACTCGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@31:NM_153633:1041:170\n+ATTTCCCCTGAAATTCACCCAAGCCAGACCATCACACCTTGCAATATATA\n+'..b'IIIIIIIIIIIIIIIIIIIIIIII\n+@9971:NM_022658:1616:193\n+TTCTTTTTCAAGATTATTGCAGGTTCCCTTTAGGTAGTATGTTAAAGATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9972:NM_006897:924:149\n+ATATCTCAACACTGAACCCTCCCAAATCGCAAGAGTTTTCTTTTCCCCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9973:NM_174914:1854:200\n+GGAATCCATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9974:NM_022658:453:180\n+AGGCGCTCCCCAGACAGTCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9975:NM_022658:963:167\n+GTTTCTCCGTCTCCCCCCTCCAGCCCCCAAACAAATAAAGAGTGGGGGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9976:NM_014620:1302:181\n+GTTATGTTTTATAACCTGGTAATGTCCTCTGCCCGTTGCTGCTCCGGCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9977:NM_022658:175:88\n+CAGCATGAGCTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9978:NM_022658:57:146\n+GCCCAGTCCCGGGGAGCCAGCTGGCCTGGGGTTCGGTCCCGGGGGGAGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9979:NM_174914:1282:193\n+GGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGATTTCCGGATTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9980:NM_014620:772:176\n+GGTGGTGGCCCGCCTGGGCCGGCCCGTGGCCTCGCGAATTGCCGGGCCCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9981:NM_022658:184:203\n+CTCCTACTTCGTCAACCCCCTGTTCTCCAAATACAAAGCCGGCGAGTCCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9982:NM_022658:1973:206\n+ATGACAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9983:NM_174914:435:160\n+CTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGCTAGCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9984:NM_022658:470:179\n+TCCCTTTATGGGGCTCAGCAAGAGGCGAGCGTGGTGCAATATCCCGACTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9985:NM_014620:1158:203\n+GGACAGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+TTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+GTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+GAGAGCATGTCTTTCTCCTGGTAAAAGGAATTAGATCCATAGTCATACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+CTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+TTTGTGCTTGCTGCCGGCGAGCGCGTCCGCCTCGGGCGAGGGCAGTGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+ACGGCTCCAGCGGGAGCAGCGCTGCCCCGGGCCCGGCTCCCGGGTCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+TAAACTTCTCAATTTATCTGCTACCATAAAACGAAACTTCAAGGGAGTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+AGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+AGGGAGTTGCTAAGGGGGGGGGGGTCTTTCTTTTTTGCTTAGTCCTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+AGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+ATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+GAGCCAAGTCCGCATGTAGCGCGTGTCGGCGCCGAGGTGGGGCTGGGGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+ACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+GCATTACAAATACTCTCAAAGCAGGATTTCTTTCTATAGGTAGTGATAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGAAGGAGGAGGAGGAGAAGGATGAGAATTGGCTTTAAAATTTCTTTCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_1.fastq.bz2 |
| b |
| Binary file old/test-data/reads_1.fastq.bz2 has changed |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_1.fastq.gz |
| b |
| Binary file old/test-data/reads_1.fastq.gz has changed |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/reads_2.fastq Wed Oct 02 04:31:53 2019 -0400 |
| b |
| b'@@ -0,0 +1,40000 @@\n+@1:NM_014620:16:182\n+CCCCAGCTGCCCCCAGCTTCGGCAACTCCACCTGGGAGGAAAAAAAATTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+AGAGGCACAGCGAGTGGGCGATCTCGATCCTTCTCCTTCGGGTCAGGTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+CTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTCCGTGGCAGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACCCACATCTCCTTCAGGTTTCCATCAGGTTCCTAGAGAAAGTCAAGGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GATTCCAGCGACTGGCAGGAGGGCGGGTCGTGCGGAGGTCCTGCGCCGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+GTTAACTATACATTCAGTGCAATTTAGTTCTACTCTACTGGGGTTAGAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+CGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+GAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+GAGAACAGGGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+TCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CGAGGAGCACGGAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CCAGGGCGCGCCGCTGGCCGAGAGCCCGCCGCCGGGGTTCAACGGCGATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+AGGCATGGGCCCGAGTGACCATGGGATGGTTAGGTAGGATTTTAGAGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+ACATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@16:NM_022658:1052:179\n+TGCAGCTCTGGTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@17:NM_022658:1351:186\n+AAGGCTAGTGTACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@18:NM_022658:1777:222\n+GGGTTTTCTTAGTGAAATAAGCAGCAACAAACGACAACAAAACCGCATTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@19:NM_018953:838:165\n+CCTGCGGAGCTTGCCCTGGGCCCCGGGTACCGAGCTGAGCCGAGCTGAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@20:NM_022658:997:196\n+TTGCTTTTATAGAGAATAGAATGACACTCACAACTCTAACTACCTGTCAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@21:NM_022658:1639:210\n+TTTTTTTCTCCTATAGCAGGATTTTAAAATTTTTCTCTTTTTCTTTTTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@22:NM_174914:42:131\n+CCCTGTGCTTGAGAGTTCAGGGCCGGACACAGGCTCACAGGTCTCCACAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@23:NM_022658:782:137\n+ATGAAGTGGAAAAAGGAGAACAACAAGGATAAACTGCCGGGAGCCCGAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@24:NM_022658:623:187\n+CCTTGTTGTTCTCCTTTTTCCACTTCATCCTTCGGTTCTGGAACCAGATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@25:NM_022658:1061:175\n+GAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@26:NM_174914:1681:185\n+ATCATGGATTCCTTAAAGAATGAGAACTTCGACATGGTGATAGTTGAAAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@27:NM_022658:619:223\n+CTTCTCCTCATCTCGGGCTCCCGGCAGTTTATCCTTGTTGTTCTCCTTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@28:NM_022658:1432:199\n+GGGATGGTTAGGTAGGATTTTAGAGGCGACTGCAGGCTCCTATCTACCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@29:NM_173860:122:191\n+GCTGTCCTACCCACGCCGCGACAACGTGTGCTCCCTGTCCTGGCCGTCGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@30:NM_022658:1594:160\n+TTATTATTTTCGTGATTATGGTGATTTCTGAGCACTAACACTAATGCAGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@31:NM_153633:1041:170\n+CACTGTTAAGGACCCTTTTAAGCATGTGATGTTGTCTTAGCATGGTACCT\n+'..b'IIIIIIIIIIIIIIIIIIIIIIII\n+@9971:NM_022658:1616:193\n+CTACCTAACCATCCCATGGTCACTCGGGCCCATGCCTTCCTCTCCTTCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9972:NM_006897:924:149\n+AACCCCACAAAATACCCCAACACAGGCGGGGGAGAGACGAAAAAGAAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9973:NM_174914:1854:200\n+TTAAAAAGGAAGAAAAATCATATCAAGTTATCAGTTGGCTTGCACCTGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9974:NM_022658:453:180\n+CACTGCGCCTCCCCGGAGCGTGGGGTCTCATCCATGGAAACATGAGGCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9975:NM_022658:963:167\n+GTAGCAGATAAATTGAGAAGTTTACGACTGTCATTTGCTTTTATAGAGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9976:NM_014620:1302:181\n+GCATGAAATGGAAGAAGGACCACCGACTCCCCAACACCAAAGTCAGGTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9977:NM_022658:175:88\n+GAACCGGCAGTCGTAATAGGCCGGTTCCAGGGACTCGCCGGCTTTGTATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9978:NM_022658:57:146\n+GGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACCCGCGGCCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9979:NM_174914:1282:193\n+CTCTGCTTCCCAACACTGTTTATGTTGGAGGCTTGATGGAAAAACCTATT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9980:NM_014620:772:176\n+ACACAGTCCGGAATATTACGGCCGGACCAGGGAATCGGGATTCCAGCATC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9981:NM_022658:184:203\n+AGTTGGAGATGCCGGAGGTGCCGTGGTGGAAGAAGTCTTGAACGTGGTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9982:NM_022658:1973:206\n+TGCTGCTTATTTCACTAAGAAAACCCAACAACTGAGACTGCCTAGCCCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9983:NM_174914:435:160\n+TCTAGTCCTTCTAGTTATCTCCTGTTTTCTTGAAGAACAGGAAAAATGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9984:NM_022658:470:179\n+CTGTAAGTTTGCCGTCCACTGCGCCTCCCCGGAGCGTGGGGTCTCATCCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9985:NM_014620:1158:203\n+CGGGGGTGCTGACCTGACTTTGGTGTTGGGGAGTCGGTGGTCCTTCTTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+GTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTGCATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+CTTTAGTTTCTGCAGGAGGCAACAGCACATGCAGTCTACATTTGACAACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+ACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+ATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+GGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+CTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+CCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+CTTCTTCCATTTCATGCGACGGTTTTGGAACCAGATTTTGATCTGCCTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+CAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+TGCAATTTAGTTCTACTCTACTGGGGTTAGAAGCACAATAAAAGCGCACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+GGCCTTTTAAAAAAAAACACCCAGCAGGTACCATGCTAAGACAACATCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+TGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+CAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCGAGCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+TACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_2.fastq.bz2 |
| b |
| Binary file old/test-data/reads_2.fastq.bz2 has changed |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_2.fastq.gz |
| b |
| Binary file old/test-data/reads_2.fastq.gz has changed |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_both.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/reads_both.fastq Wed Oct 02 04:31:53 2019 -0400 |
| b |
| b'@@ -0,0 +1,80000 @@\n+@1:NM_014620:16:182\n+GTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAACCATTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@1:NM_014620:16:182\n+CCCCAGCTGCCCCCAGCTTCGGCAACTCCACCTGGGAGGAAAAAAAATTA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+ATGAAAAAAATTCACGTTAGCACGGTGAACCCCAATTATAACGGAGGGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@2:NM_014620:1094:172\n+AGAGGCACAGCGAGTGGGCGATCTCGATCCTTCTCCTTCGGGTCAGGTAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+TGTACGGGCCCGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@3:NM_022658:294:172\n+CTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTCCGTGGCAGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACTAGATGTACTTTTTCTAAAAAGGAAAGGACAGAAAAAAATGAAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@4:NM_022658:1362:195\n+ACCCACATCTCCTTCAGGTTTCCATCAGGTTCCTAGAGAAAGTCAAGGGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCCGGGGCAGCGCTGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@5:NM_173860:323:180\n+GATTCCAGCGACTGGCAGGAGGGCGGGTCGTGCGGAGGTCCTGCGCCGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GGAAGGACTCAGAAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@6:NM_022658:1062:146\n+GTTTTATTACCTTTGGACTTCCCCCACTCTTTATTTGTTTGGGGGCTGGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+CTACCTATAGAAAGAAATCCTGCTTTGAGAGTATTTGTAATGCGGTTTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@7:NM_022658:1912:184\n+GTTAACTATACATTCAGTGCAATTTAGTTCTACTCTACTGGGGTTAGAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+AAGGGACTGTCTGGGGAGCGCCTCGTAGCCATAGAATTTGGAGGCGTCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@8:NM_022658:304:172\n+CGGCGGCTCGGCGCCCGGCTTCCAGCACGCTTCGCACCACGTTCAAGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+ATAACATCCAAGAAAGACACCTTGCATATTCTTTCAGTTTCTGTTTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9:NM_174914:46:212\n+GAAATCTGGAAACCTACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+CCAACCTGCCCAGCCCCCAGCCCACCAGCCCAGCCCAGTCCCGGGGAGCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10:NM_022658:25:186\n+GAGAACAGGGGGTTGACGAAGTAGGAGCTCATGCTGGGTACATGAAAACC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+AAGGGTGGGGGCAGGGACAAGTGTGTGTGGGGCAAGGAGTGAGACAGAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@11:NM_022658:1031:165\n+TCTAACTACCTGTCAGATACTTGCAGCTCTGGTTTTATTACCTTTGGACT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CTTTATTTGTTTGGGGGCTGGAGGGGGGAGACGGAGAAACAGTGAAAAGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@12:NM_022658:1090:157\n+CGAGGAGCACGGAGGCCAGGTCTCAGACCTTAAAATCCAGGAAGGACTCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CAACGAGGGCAACAAGGGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTAT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@13:NM_173860:524:97\n+CCAGGGCGCGCCGCTGGCCGAGAGCCCGCCGCCGGGGTTCAACGGCGATA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+CCCTCCCCCTCCCCAGGGCTCCCTGCTTAGAAAAACCCCCTTGACTTTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@14:NM_022658:1471:182\n+AGGCATGGGCCCGAGTGACCATGGGATGGTTAGGTAGGATTTTAGAGGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+CACTTGTCCCTGCCCCCACCCTTCTGAGTCCTTCCTGGATTTTAAGGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@15:NM_022658:1173:198\n+ACATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@16:NM_022658:1052:179\n+CAGGTCTCAGACCTTAAAATCCAGGAAGGACTCAGAAGGGTGGGGGCAGG\n++\n+IIIIIIIII'..b'IIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+TTCTGAGTCCTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9986:NM_022658:1194:170\n+GTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTGCATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+GTCGAGCAAAATCAAAGGCAAAGTCAGAGTTAATGAACCACAACTCTGCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9987:NM_174914:1475:158\n+CTTTAGTTTCTGCAGGAGGCAACAGCACATGCAGTCTACATTTGACAACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+GAGAGCATGTCTTTCTCCTGGTAAAAGGAATTAGATCCATAGTCATACGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9988:NM_004503:167:199\n+ACGTCCTCCCCAACGTCGCCCTCAATTCCACCGCCTATGATCCAGTGAGG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+CTTCCTGGATTTTAAGGTCTGAGACCTGGCCTCCGTGCTCCTCGGTCTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9989:NM_022658:1203:166\n+ATCTAGTACACTAGCCTTAGCATAAAAACAAAACCACAAGTCCTTTTCTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+TTTGTGCTTGCTGCCGGCGAGCGCGTCCGCCTCGGGCGAGGGCAGTGTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9990:NM_006897:430:179\n+GGGGCCGTCACTACGCCCTCAAGCCGGACGCCTACCCCGGGCGCCGCGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+ACGGCTCCAGCGGGAGCAGCGCTGCCCCGGGCCCGGCTCCCGGGTCGCGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9991:NM_173860:200:188\n+CTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGCCGCACGTGCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+TAAACTTCTCAATTTATCTGCTACCATAAAACGAAACTTCAAGGGAGTTG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9992:NM_022658:826:161\n+CCGAGATGAGGAGAAGGTGGAGGAAGAAGGAAATGAGGAAGAGGAGAAAG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+AGCCTATACCCGGCAGCAAGTCCTGGAATTAGAGAAAGAGTTTCATTACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9993:NM_014620:1162:157\n+CTTCTTCCATTTCATGCGACGGTTTTGGAACCAGATTTTGATCTGCCTCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+AGGGAGTTGCTAAGGGGGGGGGGGTCTTTCTTTTTTGCTTAGTCCTTGTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9994:NM_022658:752:194\n+CAAGTGAAGATCTGGTTCCAGAACCGAAGGATGAAGTGGAAAAAGGAGAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+AGAAACCTCCAGCGTATTTTATCACTACCTATAGAAAGAAATCCTGCTTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9995:NM_022658:1888:191\n+TGCAATTTAGTTCTACTCTACTGGGGTTAGAAGCACAATAAAAGCGCACA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+ATATATATATATATATATATATAGGTTCTTTTCTCTCTTCCTCTCACCTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9996:NM_014620:1559:191\n+GGCCTTTTAAAAAAAAACACCCAGCAGGTACCATGCTAAGACAACATCAC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+GAGCCAAGTCCGCATGTAGCGCGTGTCGGCGCCGAGGTGGGGCTGGGGGC\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9997:NM_006897:223:164\n+TGGTGCCGGACTGTAGCGATTTTCCGTCCTGTAGCTTCGCGCCCAAGCCG\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+ACCCAACAACTGAGACTGCCTAGCCCGCCGGTCCTGTGCGCTTTTATTGT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9998:NM_022658:1995:180\n+CAAAAAATTATTATTATAGATATATTTTTAACATTTTTTTCTTTCGAGCA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+GCATTACAAATACTCTCAAAGCAGGATTTCTTTCTATAGGTAGTGATAAA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@9999:NM_022658:1773:182\n+TACCTAAAGGGAACCTGCAATAATCTTGAAAAAGAAAAAGAGAAAAATTT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGAAGGAGGAGGAGGAGAAGGATGAGAATTGGCTTTAAAATTTCTTTCCT\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n+@10000:NM_014620:1728:181\n+GGGTGTTTTTTTTTAAAAGGCCATTTTGGGGGGTTATTTATTTTTTAAGA\n++\n+IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII\n' |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_both.fastq.bz2 |
| b |
| Binary file old/test-data/reads_both.fastq.bz2 has changed |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/reads_both.fastq.gz |
| b |
| Binary file old/test-data/reads_both.fastq.gz has changed |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/salmon_genMap_result1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/salmon_genMap_result1.tab Wed Oct 02 04:31:53 2019 -0400 |
| b |
| @@ -0,0 +1,5 @@ +Name Length EffectiveLength TPM NumReads +baz 1640 1052.77 1.09566 0.00943897 +NR_031764 1853 1214.33 10407.1 103.415 +foo 348.949 235.269 976889 9737.65 +bar 2283 1528.95 12702.4 158.926 |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/salmon_quant_result1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/salmon_quant_result1.tab Wed Oct 02 04:31:53 2019 -0400 |
| b |
| @@ -0,0 +1,16 @@ +Name Length EffectiveLength TPM NumReads +NM_001168316 2283 2106.09 12428 158.641 +NM_174914 2385 2208.09 112348 1503.55 +NR_031764 1853 1676.09 10021.5 101.805 +NM_004503 1681 1504.09 36259.8 330.551 +NM_006897 1541 1364.09 80313.1 664 +NM_014212 2037 1860.09 4878.54 55 +NM_014620 2300 2123.09 45879.2 590.368 +NM_017409 1959 1782.09 4351.4 47 +NM_017410 2396 2219.09 3122.74 42 +NM_018953 1612 1435.09 26213 228 +NM_022658 2288 2111.09 381473 4881 +NM_153633 1666 1489.09 40073.1 361.67 +NM_153693 2072 1895.09 6478.45 74.4115 +NM_173860 849 672.091 236161 962 +NR_003084 1640 1463.09 0.00490872 4.3529e-05 |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/test-data/transcripts.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/test-data/transcripts.fasta Wed Oct 02 04:31:53 2019 -0400 |
| b |
| b'@@ -0,0 +1,498 @@\n+>NM_001168316\n+TTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\n+TACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGAC\n+CCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTT\n+CCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGT\n+GTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTA\n+GGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAA\n+GGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATC\n+ACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGC\n+TAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGAT\n+TTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATG\n+GGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACC\n+CCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCA\n+GACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAG\n+AAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTT\n+GAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGT\n+GGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCT\n+CTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAA\n+CTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCC\n+AAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTG\n+CCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAG\n+CCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTG\n+ACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGAT\n+TTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTC\n+CCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCAT\n+CAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTC\n+AGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGACAAAACTGGCCTAGAGCC\n+TTCTGTGAAATGTTCCTTGATGGTGTTGTCAAATGTAGACTGCATGTGCTGTTGCCTCCT\n+GCAGAAACTAAAGAACATCAGAAAATTCTTCACTCGGCCCCAGAAGTCCATGTGATCAGT\n+CAGCAAGGAACGGAATACTGGAACATAAGACAAGGGGATTGGTAGCCCAAATTCCAAAGA\n+GCCGAATGAAGTGGAAAGAATGGCCACAAATGGCTTCCCAAGCTTCTCAGCAATCAGGAA\n+AGGACAGTAGTCAAAAGTTTCAACTATCACCATGTCGAAGTTCTCATTCTTTAAGGAATC\n+CATGATATCCTTTCTATTTAAAAAATGACTGCACTGCAACGCCAAGTATTCTAGAACATT\n+TAATAAGTTTTCAAATTTTCCTCTGCCACCTAAAGTTTCTTCCAGAAAGAAATCAAAACT\n+CTTTTTAAATTCTCTTTGATGATCTTCAGGTGCAAGCCAACTGATAACTTGATATGATTT\n+TTCTTCCTTTTTAAAATCTACTGTAGATATTGTCAGGATTTTGGCAGCCTCTGAGAGCAG\n+GACCCCAGGGAGAAGGAAGCCCACTAGAAGAAGCACTCGCTGCCCAGCCATGCTCACTTC\n+TACGGAAGCCGCGGATCTCAGCCTGGGCTGCGCGCCCTGCGCCCGGCTAAGGGACCCTGT\n+GCACCTCAGTGCGCCAAAGGCACTGGCTGTGGGTAGAGGTAGGAGTAAGGATCCTGCCAG\n+TCT\n+>NM_174914\n+TTAGTGAGGTTGGGGAGAGATAACGCTGTAAACTTTTATTTTTCAGGAAATCTGGAAACC\n+TACAGTCTCCAAGCCTGCTCAGCCAAGAAGGAGCTCACTGTGGGCACCAGAGACAGGGAC\n+CCAATGTGGAGACCTGTGAGCCTGTGTCCGGCCCTGAACTCTCAAGCACAGGGCAGGCTT\n+CCTGAGCATTGAAGAGAATATGTGGGAGAACAAAACAGAAACTGAAAGAATATGCAAGGT\n+GTCTTTCTTGGATGTTATTCCATGATAGATAGTAGGGGCAGGAGTGAGAGAGGCTGACTA\n+GGTCTGGACATGGAGGCTGGAAGAGTCAGGGTGTGATTCGGAGAGGCGCATGAGAAGGAA\n+GGTGGATTTTAAGGCTGGAAATCTGAGGGTCAGTGGTCCAAGTCACTCAGAGACAGAATC\n+ACAGCATAGCCCTTGCTGATGGCAAACAAAGGAGGACAAGAGGACTGGAAAGAATTCTGC\n+TAGCAGGCAGGAGCTAGTAAGGATGAATTTGTAGCAAAATTAGCAAGTGGAAAGGATGAT\n+TTTTGGCCATTTTTCCTGTTCTTCAAGAAAACAGGAGATAACTAGAAGGACTAGAGAATG\n+GGGCTGCCAGAACTAGTGGGAAGCTCCCTAGAAATGGTGACATCGCCCACCAAACAGACC\n+CCGCCAAGGCTGCACCTGGCCTTATGTCTCCTTCACCTTTCTGGCCCCACGCAGCCACCA\n+GACAGCCATGCCCAGCAGCTTCCCACAAAGCCATAGAGTCCCCAGAGTGAGCCCCAGCAG\n+AAACACAAAAACGTCGAGCAGGTACTGCTCATGCCAGGGCTGCTGAAAGACATAGGGCTT\n+GAGGTGCGTCGCGCCCCCTGTCTGGAGGACGTGGTCAATCCAGCCCACCAGCCGCTGTGT\n+GGGGCTGAGCGGGTGGGAGCGCAGGATGACACTGGCAGCCACTGCCGCGGACTTGTATCT\n+CTTGTCTTCCATGATTTGTTTCATCTTAAGAGCCAATGTCTCTGCCTTGAGCTTCTTTAA\n+CTGAATAGAAACACCAAACTTTTTGGCTTCTACTCGGACCATGTTTTCAGGCTGGTCTCC\n+AAAGAGAGGGATCCCCACCATGGGCACACCATGCTGGATGGCCTCCATTATGCTATTCTG\n+CCCGCCGTGGGTGACAAACAGACGGATGCTTGGGTGAGCCAGGAGGTCACTCTGAGGAAG\n+CCAGTCCACAATTTTCACATTTGCAGCCAGGTGGACATCTTTGGGCCAATGAGAACACTG\n+ACACTTCCATATCACCCCTTGGGGTAGGTGAGCAAAGGCATTGTTCATCTCCTTGAAGAT\n+TTCCGGATTCTGACAGGTGTTCACCATGGAGCCCAAGGTCACAAGGACAAAACCAGAGTC\n+CCCAAACTTGGCAATGAAGTTCTCCAAGTCTTGTGGTACTGGTTTAATAGGTTTTTCCAT\n+CAAGCCTCCAACATAAACAGTGTTGGGAAGCAGAGGTCGAGCAAAATCAAAGGCAAAGTC\n+AGAGTTAATGAACCACAACTCTGCTTTCAGTAGAAGATGAGA'..b'G\n+GATCTAATTCCTTTTACCAGGAGAAAGACATGCTCTCAAACTGCAGACAAAACACCTTAG\n+GACATAACACACAGACCTCAATCGCTCAGGATTTTAGTTCTGAGCAGGGCAGGACTGCGC\n+CCCAGGACCAGAAAGCCAGTATCCAGATTTACCCCTGGATGCAGCGAATGAATTCGCACA\n+GTGGGGTCGGCTACGGAGCGGACCGGAGGCGCGGCCGCCAGATCTACTCGCGGTACCAGA\n+CCCTGGAACTGGAGAAGGAATTTCACTTCAATCGCTACCTAACGCGGCGCCGGCGCATCG\n+AGATCGCCAACGCGCTTTGCCTGACCGAGCGACAGATCAAAATCTGGTTCCAGAACCGCC\n+GGATGAAGTGGAAAAAAGAATCTAATCTCACATCCACTCTCTCGGGGGGCGGCGGAGGGG\n+CCACCGCCGACAGCCTGGGCGGAAAAGAGGAAAAGCGGGAAGAGACAGAAGAGGAGAAGC\n+AGAAAGAGTGACCAGGACTGTCCCTGCCACCCCTCTCTCCCTTTCTCCCTCGCTCCCCAC\n+CAACTCTCCCCTAATCACACACTCTGTATTTATCACTGGCACAATTGATGTGTTTTGATT\n+CCCTAAAACAAAATTAGGGAGTCAAACGTGGACCTGAAAGTCAGCTCTGGACCCCCTCCC\n+TCACCGCACAACTCTCTTTCACCACGCGCCTCCTCCTCCTCGCTCCCTTGCTAGCTCGTT\n+CTCGGCTTGTCTACAGGCCCTTTTCCCCGTCCAGGCCTTGGGGGCTCGGACCCTGAACTC\n+AGACTCTACAGATTGCCCTCCAAGTGAGGACTTGGCTCCCCCACTCCTTCGACGCCCCCA\n+CCCCCGCCCCCCGTGCAGAGAGCCGGCTCCTGGGCCTGCTGGGGCCTCTGCTCCAGGGCC\n+TCAGGGCCCGGCCTGGCAGCCGGGGAGGGCCGGAGGCCCAAGGAGGGCGCGCCTTGGCCC\n+CACACCAACCCCCAGGGCCTCCCCGCAGTCCCTGCCTAGCCCCTCTGCCCCAGCAAATGC\n+CCAGCCCAGGCAAATTGTATTTAAAGAATCCTGGGGGTCATTATGGCATTTTACAAACTG\n+TGACCGTTTCTGTGTGAAGATTTTTAGCTGTATTTGTGGTCTCTGTATTTATATTTATGT\n+TTAGCACCGTCAGTGTTCCTATCCAATTTCAAAAAAGGAAAAAAAAGAGGGAAAATTACA\n+AAAAGAGAGAAAAAAAGTGAATGACGTTTGTTTAGCCAGTAGGAGAAAATAAATAAATAA\n+ATAAATCCCTTCGTGTTACCCTCCTGTATAAATCCAACCTCTGGGTCCGTTCTCGAATAT\n+TTAATAAAACTGATATTATTTTTAAAACTTTA\n+>NM_173860\n+ATGGGCGAGCATAATCTCCTGAATCCCGGGTTTGTGGGGCCGCTGGTAAACATCCACACG\n+GGAGACACCTTCTACTTCCCCAACTTCCGCGCGTCCGGGGCGCAGCTTCCCGGGCTGCCT\n+TCGCTGTCCTACCCACGCCGCGACAACGTGTGCTCCCTGTCCTGGCCGTCGGCGGAGCCG\n+TGCAATGGCTACCCGCAGCCCTACCTCGGCAGCCCAGTGTCTCTCAACCCTCCCTTCGGC\n+CGCACGTGCGAGCTGGCGCGCGTGGAGGACGGCAAGGGTTACTACCGCGAGCCGTGCGCC\n+GAGGGTGGCGGCGGGGGCCTGAAGCGTGAGGAGCGCGGGCGCGACCCGGGAGCCGGGCCC\n+GGGGCAGCGCTGCTCCCGCTGGAGCCGTCGGGGCCGCCTGCGCTCGGCTTCAAGTACGAC\n+TACGCGGCGGGCGGCGGCGGTGGCGACGGCGGCGGCGGCGCAGGACCTCCGCACGACCCG\n+CCCTCCTGCCAGTCGCTGGAATCCGACTCCAGTTCGTCCCTGCTCAACGAGGGCAACAAG\n+GGCGCCGGCGCAGGCGACCCCGGCAGCTTGGTATCGCCGTTGAACCCCGGCGGCGGGCTC\n+TCGGCCAGCGGCGCGCCCTGGTACCCGATCAACAGCCGCTCTCGGAAGAAGCGCAAGCCC\n+TATTCGAAGTTGCAACTGGCAGAGCTGGAGGGCGAGTTTCTGGTCAACGAGTTCATCACA\n+CGCCAGCGCCGGAGGGAACTCTCAGACCGCTTGAATCTTAGTGACCAGCAGGTCAAGATC\n+TGGTTTCAGAACCGGAGAATGAAAAAGAAAAGACTTCTGTTGAGGGAGCAAGCTCTCTCC\n+TTCTTTTAA\n+>NR_003084\n+TTATTGTGGTTTGTCCGTTCCGAGCGCTCCGCAGAACAGTCCTCCCTGTAAGAGCCTAAC\n+CATTGCCAGGGAAACCTGCCCTGGGCGCTCCCTTCATTAGCAGTATTTTTTTTAAATTAA\n+TCTGATTAATAATTATTTTTCCCCCATTTAATTTTTTTTCCTCCCAGGTGGAGTTGCCGA\n+AGCTGGGGGCAGCTGGGGAGGGTGGGGATGGGAGGGGAGAGACAGAAGTTGAGGGCATCT\n+CTCTCTTCCTTCCCGACCCTCTGGCCCCCAAGGGGCAGGAGGAATGCAGGAGCAGGAGTT\n+GAGCTTGGGAGCTGCAGATGCCTCCGCCCCTCCTCTCTCCCAGGCTCTTCCTCCTGCCCC\n+CTTCTTGCAACTCTCCTTAATTTTGTTTGGCTTTTGGATGATTATAATTATTTTTATTTT\n+TGAATTTATATAAAGTATATGTGTGTGTGTGTGGAGCTGAGACAGGCTCGGCAGCGGCAC\n+AGAATGAGGGAAGACGAGAAAGAGAGTGGGAGAGAGAGAGGCAGAGAGGGAGAGAGGGAG\n+AGTGACAGCAGCGCTCGAGACGGACGGCAAGCGGTCCCGAACCAGTTACACGCGCTACCA\n+GACTCTGGAACTCGAGAAAGAATTCCACTTTAACCGCTACCTCACTCGCCGCAGGCGCAT\n+AGAGATCGCCAACAACTTGTGTCTCAATGAGAGACAGATCAAGATCTGGTTCCAGAACCG\n+CAGGATGAAGTGGAAGAAAGATTCCAAAATGAAAAGCAAAGAGGCTCTTTAGAGGCAGCG\n+GGGGAGGCCCGCAGAGCGCGCCCCTAGCCGGTTCCTGTCCCTGCGCCTTTCCTTTTCGCC\n+TTTCCTCTCTATATTTCGGGTCGGGGGCAGGTGCTGGAGCACTGGGCTCCCGGGCCCCAC\n+AGACAAAAGCGCTTTTCCTTGGCATTCCGCATCCCTACCGACCCAGGGTTCCCGCGGGGC\n+TGTCGGCGCTGCCCCATCTCCCCTCAGCTCGGCTCAGCTCGGTACCCGGGGCCCAGGGCA\n+AGCTCCGCAGGACTTCCCCGGAGGGCTGCGGCGTACAGGCTGGCGCAGAACGAACCTTGG\n+CCTGGGCCGTATCTCCGGCTCCCAGCCTCAGCGCGGCCCTCCCGAGTTAAGGTGGGCCCG\n+GCCCGCGCCACAGGACCCTCGCCGGACCCTCTAACCTCGCCCTCTCCTTTGTTCCCGGCT\n+GGACGGGTTAGACAGCCAAAGGCTGGCGAGAGTCTGGCCCTAGACTCGGGGTGCTTCCTT\n+GTAGCGACTAAACTAGATTTTCACTTATGAATGATTTGCATATGAAAGGAGAGCATCGGC\n+CTAGGGCCCCCACAGTTGCTCTATGCTTTCCAAACCTTATCTCCACAACCTCTTCCCCCC\n+AAAACCCGGGAACCTCCCCAGCCTGCGCCTGCTGCATGCCCTCTCAGGCCGGCAGCCCCA\n+GCCTGCTAGCTAGCTCAACTAGTGGGGTTTCCTGGCACTGGACCCCAGCAAGTGGTCCTA\n+GAGGCCCTTTGCTGTCCCATAGTCCCTGCCACGAATTTCTGTGCCCTCCTGACCCATTGC\n+TGTTGTCCAACTATTTATTGACTCTGGGTCCTTCCTGAAACTATATTTTGTCATATCAAA\n+TAAAGAGAGAACAGGACTAA\n' |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/tool-data/salmon_indexes_versioned.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/tool-data/salmon_indexes_versioned.loc.sample Wed Oct 02 04:31:53 2019 -0400 |
| b |
| @@ -0,0 +1,32 @@ +# salmon_indexes_versioned.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 Salmon. +# 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 salmon_indexes_versioned.loc.sample 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> <version> +# +# The <version> column can be retrieved from the header.json file in the index folder. e.g "IndexVersion": "q5" + + + +# So, for example, if you had sacCer3 indexes stored in: +# +# /depot/data2/galaxy/sacCer3/salmon_indexes/ +# +# then the salmon_indexes.loc entry could look like this: +# +#sacCer3 sacCer3 S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3) /depot/data2/galaxy/sacCer3/salmon_indexes/version_3/ q6 +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/salmon_indexes/mm10/version_2 q4 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 +# +# |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/tool_data_table_conf.xml.sample Wed Oct 02 04:31:53 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of indexes in salmon mapper format --> + <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path, version</columns> + <file path="tool-data/salmon_indexes_versioned.loc" /> + </table> +</tables> |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 old/tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/old/tool_data_table_conf.xml.test Wed Oct 02 04:31:53 2019 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of indexes in salmon mapper format --> + <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False"> + <columns>value, dbkey, name, path, version</columns> + <file path="${__HERE__}/test-data/cached_locally/salmon_indexes_versioned.loc" /> + </table> +</tables> |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 salmonquant.xml --- a/salmonquant.xml Mon Sep 09 11:11:22 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,267 +0,0 @@\n-<tool id="salmon" name="Salmon quant" version="@VERSION@">\n- <description>Perform dual-phase, reads or mapping-based estimation of transcript abundance from RNA-seq reads</description>\n- <macros>\n- <import>macros.xml</import>\n- </macros>\n- <expand macro="requirements"/>\n- <command detect_errors="aggressive"><![CDATA[\n- #if $quant_type.qtype == "reads":\n- @indexing@\n- @salreads@\n- #else:\n- @salalign@\n- #end if\n- @salquant@\n- #if $quant_type.qtype == "reads":\n- #if $quant_type.writeMappings:\n- && samtools view -S -b ./output/samout.sam > ./output/bamout.bam\n- #end if\n- #end if\n- #if $quant_type.qtype == "alignment":\n- #if $quant_type.sampleOut:\n- && samtools sort -@ 4 -o ./output/postSample_sorted.bam ./output/postSample.bam\n- #end if\n- #end if\n- ]]>\n- </command>\n- <inputs>\n- <conditional name="quant_type">\n- <param name="qtype" type="select" label="Select salmon quantification mode:">\n- <option value="reads" selected="True">Reads</option>\n- <option value="alignment">Alignment</option>\n- </param>\n- <when value="reads">\n- <expand macro="index"/>\n- <expand macro="reads"/>\n- </when>\n- <when value="alignment">\n- <expand macro="align"/>\n- </when>\n- </conditional>\n- <expand macro="quantboth"/>\n- </inputs>\n- <outputs>\n- <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />\n- <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">\n- <filter>geneMap</filter>\n- </data>\n- <data name="output_bam" format="bam" from_work_dir="output/bamout.bam" label="${tool.name} on ${on_string} (BAM format)">\n- <filter>quant_type[\'qtype\'] == "reads" and quant_type[\'writeMappings\']</filter>\n- </data>\n- <data name="postSample" format="bam" from_work_dir="./output/postSample_sorted.bam" label="Sampled input alignments on ${on_string}(BAM format)">\n- <filter>quant_type[\'qtype\'] == "alignment" and quant_type[\'sampleOut\']</filter>\n- </data>\n- </outputs>\n- <tests>\n- <test expect_num_outputs="2">\n- <conditional name="quant_type">\n- <param name="qtype" value="reads"/>\n- <conditional name="refTranscriptSource">\n- <param name="TranscriptSource" value="history"/>\n- <section name="s_index">\n- <param name="fasta" value="transcripts.fasta"/>\n- </section>\n- </conditional>\n- <section name="input">\n- <param name="single_or_paired.single_or_paired_opts" value="paired" />\n- <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />\n- <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />\n- <param name="single_or_paired.strandedness" value="U"/>\n- </section>\n- <param name="writeMappings" value="true"/>\n- </conditional>\n- <output name="output_quant" ftype="tabular">\n- <assert_contents>\n- <has_text text="EffectiveLength" />\n- <has_text text="TPM" />\n- <has_text text="NM_001168316" />\n- <has_text text="NM_174914" />\n- <has_text text="NM_018953" />\n- <has_text text="NR_003084" />\n- <has_text text="NM_017410" />\n- <has_text text="NM_153693" />\n- <has_text'..b'allowDovetail"/>\n- <param name="recoverOrphans" value="--recoverOrphans"/>\n- </conditional>\n- <output name="output_quant" ftype="tabular">\n- <assert_contents>\n- <has_text text="EffectiveLength" />\n- <has_text text="TPM" />\n- <has_text text="NM_001168316" />\n- <has_text text="NM_174914" />\n- <has_text text="NM_018953" />\n- <has_n_columns n="5" />\n- </assert_contents>\n- </output>\n- </test>\n- <test expect_num_outputs="1">\n- <conditional name="quant_type">\n- <param name="qtype" value="reads"/>\n- <conditional name="refTranscriptSource">\n- <param name="TranscriptSource" value="history"/>\n- <section name="s_index">\n- <param name="fasta" value="transcripts.fasta"/>\n- </section>\n- </conditional>\n- <section name="input">\n- <param name="single_or_paired.single_or_paired_opts" value="paired" />\n- <param name="single_or_paired.input_mate1" value="fastqs/reads_1.fastq" />\n- <param name="single_or_paired.input_mate2" value="fastqs/reads_2.fastq" />\n- <param name="single_or_paired.strandedness" value="U"/>\n- </section>\n- </conditional>\n- <param name="seqBias" value="--seqBias"/>\n- <param name="gcBias" value="--gcBias"/>\n- <section name="adv">\n- <param name="dumpEq" value="--dumpEq"/>\n- <param name="minAssignedFrags" value="10"/>\n- <param name="noLengthCorrection"/>\n- <param name="initUniform" value="--initUniform"/>\n- <param name="useEM" value="--useEM"/>\n- <param name="noGammaDraw" value="--noGammaDraw"/>\n- </section>\n- <output name="output_quant" ftype="tabular">\n- <assert_contents>\n- <has_text text="EffectiveLength" />\n- <has_text text="TPM" />\n- <has_n_columns n="5" />\n- </assert_contents>\n- </output>\n- </test>\n- <test expect_num_outputs="1">\n- <conditional name="quant_type">\n- <param name="qtype" value="reads"/>\n- <conditional name="refTranscriptSource">\n- <param name="TranscriptSource" value="indexed"/>\n- <param name="index" value="hg19_transcript_subset" />\n- </conditional>\n- <section name="input">\n- <conditional name="single_or_paired">\n- <param name="single_or_paired_opts" value="paired" />\n- <param name="input_mate1" value="fastqs/reads_1.fastq" />\n- <param name="input_mate2" value="fastqs/reads_2.fastq" />\n- <param name="strandedness" value="U"/>\n- </conditional>\n- </section>\n- </conditional>\n- <output name="output_quant" ftype="tabular">\n- <assert_contents>\n- <has_text text="EffectiveLength" />\n- <has_text text="TPM" />\n- <has_text text="NM_001168316" />\n- <has_text text="NM_174914" />\n- <has_text text="NM_018953" />\n- <has_text text="NR_003084" />\n- <has_text text="NM_017410" />\n- <has_text text="NM_153693" />\n- <has_text text="NR_031764" />\n- <has_n_columns n="5" />\n- </assert_contents>\n- </output>\n- </test>\n- </tests>\n- <help><![CDATA[\n- @salmonhelp@\n- ]]></help>\n- <expand macro="citations"/>\n-</tool>\n' |
| b |
| diff -r 4de6e2e40c7a -r 666bb48b1007 test-data/cached_locally/salmon_indexes_versioned.loc --- a/test-data/cached_locally/salmon_indexes_versioned.loc Mon Sep 09 11:11:22 2019 -0400 +++ b/test-data/cached_locally/salmon_indexes_versioned.loc Wed Oct 02 04:31:53 2019 -0400 |
| b |
| @@ -30,4 +30,4 @@ #dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/salmon_indexes/dm3/version_1 q5 # # -hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q5 +hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q6 |
