# HG changeset patch
# User bgruening
# Date 1594674723 0
# Node ID df8e5d1bfe707cea88db6e872056e5c8241eaa61
# Parent  818b16dd05a1a644c74c50afedb72bca13e827f5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"

diff -r 818b16dd05a1 -r df8e5d1bfe70 macros.xml
--- a/macros.xml	Sat Apr 25 15:44:01 2020 +0000
+++ b/macros.xml	Mon Jul 13 21:12:03 2020 +0000
@@ -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':
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/complete_ref_lens.bin
Binary file test-data/cached_locally/prebuilt_index/complete_ref_lens.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/ctable.bin
Binary file test-data/cached_locally/prebuilt_index/ctable.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/ctg_offsets.bin
Binary file test-data/cached_locally/prebuilt_index/ctg_offsets.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv
--- a/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv	Sat Apr 25 15:44:01 2020 +0000
+++ b/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv	Mon Jul 13 21:12:03 2020 +0000
@@ -1,1 +1,1 @@
-RetainedTxp	DuplicateTxp
+RetainedRef	DuplicateRef
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/hash.bin
Binary file test-data/cached_locally/prebuilt_index/hash.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/header.json
--- a/test-data/cached_locally/prebuilt_index/header.json	Sat Apr 25 15:44:01 2020 +0000
+++ /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
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/indexing.log
--- a/test-data/cached_locally/prebuilt_index/indexing.log	Sat Apr 25 15:44:01 2020 +0000
+++ /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
diff -r 818b16dd05a1 -r df8e5d1bfe70 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 21:12:03 2020 +0000
@@ -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
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/mphf.bin
Binary file test-data/cached_locally/prebuilt_index/mphf.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/pos.bin
Binary file test-data/cached_locally/prebuilt_index/pos.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 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 21:12:03 2020 +0000
@@ -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
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/quasi_index.log
--- a/test-data/cached_locally/prebuilt_index/quasi_index.log	Sat Apr 25 15:44:01 2020 +0000
+++ /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
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/rank.bin
Binary file test-data/cached_locally/prebuilt_index/rank.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/refAccumLengths.bin
Binary file test-data/cached_locally/prebuilt_index/refAccumLengths.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/refInfo.json
--- a/test-data/cached_locally/prebuilt_index/refInfo.json	Sat Apr 25 15:44:01 2020 +0000
+++ /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
diff -r 818b16dd05a1 -r df8e5d1bfe70 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 21:12:03 2020 +0000
@@ -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
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/reflengths.bin
Binary file test-data/cached_locally/prebuilt_index/reflengths.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/refseq.bin
Binary file test-data/cached_locally/prebuilt_index/refseq.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/rsd.bin
Binary file test-data/cached_locally/prebuilt_index/rsd.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/sa.bin
Binary file test-data/cached_locally/prebuilt_index/sa.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/seq.bin
Binary file test-data/cached_locally/prebuilt_index/seq.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/txpInfo.bin
Binary file test-data/cached_locally/prebuilt_index/txpInfo.bin has changed
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/prebuilt_index/versionInfo.json
--- a/test-data/cached_locally/prebuilt_index/versionInfo.json	Sat Apr 25 15:44:01 2020 +0000
+++ b/test-data/cached_locally/prebuilt_index/versionInfo.json	Mon Jul 13 21:12:03 2020 +0000
@@ -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
diff -r 818b16dd05a1 -r df8e5d1bfe70 test-data/cached_locally/salmon_indexes_versioned.loc
--- a/test-data/cached_locally/salmon_indexes_versioned.loc	Sat Apr 25 15:44:01 2020 +0000
+++ b/test-data/cached_locally/salmon_indexes_versioned.loc	Mon Jul 13 21:12:03 2020 +0000
@@ -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