Mercurial > repos > bgruening > salmonquantmerge
changeset 4:85b3dc9b6830 draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
line wrap: on
line diff
--- a/macros.xml Sat Apr 25 11:52:56 2020 -0400 +++ b/macros.xml Mon Jul 13 17:14:25 2020 -0400 @@ -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':
--- a/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Sat Apr 25 11:52:56 2020 -0400 +++ b/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv Mon Jul 13 17:14:25 2020 -0400 @@ -1,1 +1,1 @@ -RetainedTxp DuplicateTxp +RetainedRef DuplicateRef
--- a/test-data/cached_locally/prebuilt_index/header.json Sat Apr 25 11:52:56 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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
--- a/test-data/cached_locally/prebuilt_index/indexing.log Sat Apr 25 11:52:56 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/info.json Mon Jul 13 17:14:25 2020 -0400 @@ -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
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/pre_indexing.log Mon Jul 13 17:14:25 2020 -0400 @@ -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
--- a/test-data/cached_locally/prebuilt_index/quasi_index.log Sat Apr 25 11:52:56 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -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
--- a/test-data/cached_locally/prebuilt_index/refInfo.json Sat Apr 25 11:52:56 2020 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5 +0,0 @@ -{ - "ReferenceFiles": [ - "test-data/transcripts.fasta" - ] -} \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/prebuilt_index/ref_indexing.log Mon Jul 13 17:14:25 2020 -0400 @@ -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
--- a/test-data/cached_locally/prebuilt_index/versionInfo.json Sat Apr 25 11:52:56 2020 -0400 +++ b/test-data/cached_locally/prebuilt_index/versionInfo.json Mon Jul 13 17:14:25 2020 -0400 @@ -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
--- a/test-data/cached_locally/salmon_indexes_versioned.loc Sat Apr 25 11:52:56 2020 -0400 +++ b/test-data/cached_locally/salmon_indexes_versioned.loc Mon Jul 13 17:14:25 2020 -0400 @@ -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