| Previous changeset 13:e3d32471da11 (2020-04-25) Next changeset 15:cc05793bb896 (2020-10-03) |
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Commit message:
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" |
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modified:
macros.xml test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv test-data/cached_locally/prebuilt_index/versionInfo.json test-data/cached_locally/salmon_indexes_versioned.loc |
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added:
test-data/cached_locally/prebuilt_index/complete_ref_lens.bin test-data/cached_locally/prebuilt_index/ctable.bin test-data/cached_locally/prebuilt_index/ctg_offsets.bin test-data/cached_locally/prebuilt_index/info.json test-data/cached_locally/prebuilt_index/mphf.bin test-data/cached_locally/prebuilt_index/pos.bin test-data/cached_locally/prebuilt_index/pre_indexing.log test-data/cached_locally/prebuilt_index/rank.bin test-data/cached_locally/prebuilt_index/refAccumLengths.bin test-data/cached_locally/prebuilt_index/ref_indexing.log test-data/cached_locally/prebuilt_index/reflengths.bin test-data/cached_locally/prebuilt_index/refseq.bin test-data/cached_locally/prebuilt_index/seq.bin |
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removed:
test-data/cached_locally/prebuilt_index/hash.bin test-data/cached_locally/prebuilt_index/header.json test-data/cached_locally/prebuilt_index/indexing.log test-data/cached_locally/prebuilt_index/quasi_index.log test-data/cached_locally/prebuilt_index/refInfo.json test-data/cached_locally/prebuilt_index/rsd.bin test-data/cached_locally/prebuilt_index/sa.bin test-data/cached_locally/prebuilt_index/txpInfo.bin |
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| diff -r e3d32471da11 -r b265be7af3db macros.xml --- a/macros.xml Sat Apr 25 11:49:15 2020 -0400 +++ b/macros.xml Mon Jul 13 17:13:55 2020 -0400 |
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| @@ -1,15 +1,15 @@ <macros> - <token name="@VERSION@">0.14.1.2</token> + <token name="@VERSION@">1.3.0</token> <token name="@GALAXY_VERSION@">galaxy0</token> - <token name="@IDX_VERSION@">q6</token> + <token name="@IDX_VERSION@">q7</token> <xml name="requirements"> <requirements> + <requirement type="package" version="@VERSION@">salmon</requirement> <requirement type="package" version="1.3">seqtk</requirement> - <requirement type="package" version="0.14.1">salmon</requirement> <requirement type="package" version="1.10">samtools</requirement> <requirement type="package" version="0.2.0">vpolo</requirement> - <requirement type="package" version="0.25.1">pandas</requirement> - <requirement type="package" version="1.3.1">scipy</requirement> + <requirement type="package" version="1.0.3">pandas</requirement> + <requirement type="package" version="1.4.1">scipy</requirement> </requirements> </xml> <xml name="stranded"> @@ -358,7 +358,7 @@ #end if salmon quant - --index $index_path + --index '$index_path' #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single': --libType ${quant_type.input.single_or_paired.strandedness} #if $compressed == 'GZ': |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/complete_ref_lens.bin |
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| Binary file test-data/cached_locally/prebuilt_index/complete_ref_lens.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/ctable.bin |
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| Binary file test-data/cached_locally/prebuilt_index/ctable.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/ctg_offsets.bin |
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| Binary file test-data/cached_locally/prebuilt_index/ctg_offsets.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv --- a/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Sat Apr 25 11:49:15 2020 -0400 +++ b/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Mon Jul 13 17:13:55 2020 -0400 |
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| @@ -1,1 +1,1 @@ -RetainedTxp DuplicateTxp +RetainedRef DuplicateRef |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/hash.bin |
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| Binary file test-data/cached_locally/prebuilt_index/hash.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/header.json --- a/test-data/cached_locally/prebuilt_index/header.json Sat Apr 25 11:49:15 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,14 +0,0 @@ -{ - "value0": { - "IndexType": 1, - "IndexVersion": "q6", - "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 e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/indexing.log --- a/test-data/cached_locally/prebuilt_index/indexing.log Sat Apr 25 11:49:15 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,2 +0,0 @@ -[2019-09-08 20:35:10.408] [jLog] [info] building index -[2019-09-08 20:35:10.448] [jLog] [info] done building index |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/info.json --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/info.json Mon Jul 13 17:13:55 2020 -0400 |
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| @@ -0,0 +1,22 @@ +{ + "index_version": 4, + "reference_gfa": [ + "foo" + ], + "sampling_type": "dense", + "k": 31, + "num_kmers": 18902, + "num_contigs": 23, + "seq_length": 19592, + "have_ref_seq": true, + "have_edge_vec": false, + "SeqHash": "238a71484cdcf251805629c612f7edd515eb1a23d9be2e2014b62fd5931eb4ac", + "NameHash": "2fc64c34c65a78d18fec933772e1aa454cfed52b2b48d43eb75d2933a22feb04", + "SeqHash512": "a45ea3d0c5f11c16a45b8b75f902f908996117d7486d72b3d19a8ae619b07b22f3ca0888f5ee6e9dbabf639ae51f7fc74b8eea8808435bbb2ec70b96162849aa", + "NameHash512": "6123f1c58bf2153fca204e97fa72a2d25460242f14b886e421316ff251cc57293e77c02d536122e97f46d2508c626e42a35a1798209766359904ddf49fb7bf33", + "DecoySeqHash": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", + "DecoyNameHash": "e3b0c44298fc1c149afbf4c8996fb92427ae41e4649b934ca495991b7852b855", + "num_decoys": 0, + "first_decoy_index": 18446744073709551615, + "keep_duplicates": false +} \ No newline at end of file |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/mphf.bin |
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| Binary file test-data/cached_locally/prebuilt_index/mphf.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/pos.bin |
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| Binary file test-data/cached_locally/prebuilt_index/pos.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/pre_indexing.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/pre_indexing.log Mon Jul 13 17:13:55 2020 -0400 |
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| @@ -0,0 +1,3 @@ +[2020-07-09 14:16:39.483] [jLog] [warning] The salmon index is being built without any decoy sequences. It is recommended that decoy sequence (either computed auxiliary decoy sequence or the genome of the organism) be provided during indexing. Further details can be found at https://salmon.readthedocs.io/en/latest/salmon.html#preparing-transcriptome-indices-mapping-based-mode. +[2020-07-09 14:16:39.484] [jLog] [info] building index +[2020-07-09 14:16:39.619] [jLog] [info] done building index |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/quasi_index.log --- a/test-data/cached_locally/prebuilt_index/quasi_index.log Sat Apr 25 11:49:15 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -[2019-09-08 20:35:10.409] [jointLog] [info] [Step 1 of 4] : counting k-mers -[2019-09-08 20:35:10.412] [jointLog] [info] Replaced 0 non-ATCG nucleotides -[2019-09-08 20:35:10.412] [jointLog] [info] Clipped poly-A tails from 0 transcripts -[2019-09-08 20:35:10.412] [jointLog] [info] Building rank-select dictionary and saving to disk -[2019-09-08 20:35:10.412] [jointLog] [info] done -[2019-09-08 20:35:10.412] [jointLog] [info] Writing sequence data to file . . . -[2019-09-08 20:35:10.412] [jointLog] [info] done -[2019-09-08 20:35:10.412] [jointLog] [info] Building 32-bit suffix array (length of generalized text is 28,577) -[2019-09-08 20:35:10.413] [jointLog] [info] Building suffix array . . . -[2019-09-08 20:35:10.445] [jointLog] [info] khash had 18,902 keys -[2019-09-08 20:35:10.445] [jointLog] [info] saving hash to disk . . . -[2019-09-08 20:35:10.447] [jointLog] [info] done |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/rank.bin |
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| Binary file test-data/cached_locally/prebuilt_index/rank.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/refAccumLengths.bin |
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| Binary file test-data/cached_locally/prebuilt_index/refAccumLengths.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/refInfo.json --- a/test-data/cached_locally/prebuilt_index/refInfo.json Sat Apr 25 11:49:15 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,5 +0,0 @@ -{ - "ReferenceFiles": [ - "test-data/transcripts.fasta" - ] -} \ No newline at end of file |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/ref_indexing.log --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/ref_indexing.log Mon Jul 13 17:13:55 2020 -0400 |
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| @@ -0,0 +1,29 @@ +[2020-07-09 14:16:39.484] [puff::index::jointLog] [info] Running fixFasta +[2020-07-09 14:16:39.490] [puff::index::jointLog] [info] Replaced 0 non-ATCG nucleotides +[2020-07-09 14:16:39.490] [puff::index::jointLog] [info] Clipped poly-A tails from 0 transcripts +[2020-07-09 14:16:39.491] [puff::index::jointLog] [info] Filter size not provided; estimating from number of distinct k-mers +[2020-07-09 14:16:39.494] [puff::index::jointLog] [info] ntHll estimated 54811 distinct k-mers, setting filter size to 2^20 +[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Starting the Pufferfish indexing by reading the GFA binary file. +[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Setting the index/BinaryGfa directory foo +[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Done wrapping the rank vector with a rank9sel structure. +[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] contig count for validation: 23 +[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Total # of Contigs : 23 +[2020-07-09 14:16:39.546] [puff::index::jointLog] [info] Total # of numerical Contigs : 23 +[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Total # of contig vec entries: 36 +[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] bits per offset entry 6 +[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Done constructing the contig vector. 24 +[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] # segments = 23 +[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] total length = 19,592 +[2020-07-09 14:16:39.547] [puff::index::jointLog] [info] Reading the reference files ... +[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] positional integer width = 15 +[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] seqSize = 19,592 +[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] rankSize = 19,592 +[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] edgeVecSize = 0 +[2020-07-09 14:16:39.548] [puff::index::jointLog] [info] num keys = 18,902 +[2020-07-09 14:16:39.614] [puff::index::jointLog] [info] mphf size = 0.0125198 MB +[2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk size = 9,796 +[2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk 0 = [0, 9,796) +[2020-07-09 14:16:39.614] [puff::index::jointLog] [info] chunk 1 = [9,796, 19,562) +[2020-07-09 14:16:39.618] [puff::index::jointLog] [info] finished populating pos vector +[2020-07-09 14:16:39.618] [puff::index::jointLog] [info] writing index components +[2020-07-09 14:16:39.619] [puff::index::jointLog] [info] finished writing dense pufferfish index |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/reflengths.bin |
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| Binary file test-data/cached_locally/prebuilt_index/reflengths.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/refseq.bin |
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| Binary file test-data/cached_locally/prebuilt_index/refseq.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/rsd.bin |
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| Binary file test-data/cached_locally/prebuilt_index/rsd.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/sa.bin |
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| Binary file test-data/cached_locally/prebuilt_index/sa.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/seq.bin |
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| Binary file test-data/cached_locally/prebuilt_index/seq.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/txpInfo.bin |
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| Binary file test-data/cached_locally/prebuilt_index/txpInfo.bin has changed |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/prebuilt_index/versionInfo.json --- a/test-data/cached_locally/prebuilt_index/versionInfo.json Sat Apr 25 11:49:15 2020 -0400 +++ b/test-data/cached_locally/prebuilt_index/versionInfo.json Mon Jul 13 17:13:55 2020 -0400 |
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| @@ -1,6 +1,7 @@ { - "indexVersion": 4, + "indexVersion": 5, "hasAuxIndex": false, "auxKmerLength": 31, - "indexType": 1 + "indexType": 2, + "salmonVersion": "1.3.0" } \ No newline at end of file |
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| diff -r e3d32471da11 -r b265be7af3db test-data/cached_locally/salmon_indexes_versioned.loc --- a/test-data/cached_locally/salmon_indexes_versioned.loc Sat Apr 25 11:49:15 2020 -0400 +++ b/test-data/cached_locally/salmon_indexes_versioned.loc Mon Jul 13 17:13:55 2020 -0400 |
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| @@ -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 q6 +hg19_transcript_subset hg19 Human (Homo sapiens): hg19 transcript test subset ${__HERE__}/prebuilt_index q7 |