--- 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':

Binary file test-data/cached_locally/prebuilt_index/complete_ref_lens.bin has changed

Binary file test-data/cached_locally/prebuilt_index/ctable.bin has changed

Binary file test-data/cached_locally/prebuilt_index/ctg_offsets.bin has changed

--- 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

Binary file test-data/cached_locally/prebuilt_index/hash.bin has changed

--- 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

Binary file test-data/cached_locally/prebuilt_index/mphf.bin has changed

Binary file test-data/cached_locally/prebuilt_index/pos.bin has changed

--- /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

Binary file test-data/cached_locally/prebuilt_index/rank.bin has changed

Binary file test-data/cached_locally/prebuilt_index/refAccumLengths.bin has changed

--- 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

Binary file test-data/cached_locally/prebuilt_index/reflengths.bin has changed

Binary file test-data/cached_locally/prebuilt_index/refseq.bin has changed

Binary file test-data/cached_locally/prebuilt_index/rsd.bin has changed

Binary file test-data/cached_locally/prebuilt_index/sa.bin has changed

Binary file test-data/cached_locally/prebuilt_index/seq.bin has changed

Binary file test-data/cached_locally/prebuilt_index/txpInfo.bin has changed

--- 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