# HG changeset patch
# User bgruening
# Date 1594674865 14400
# Node ID 85b3dc9b68304526f34244956b28e0df1c03f2af
# Parent  f6e3a10a88e564ac0edb0a40558dad5c80e77ca5
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"

diff -r f6e3a10a88e5 -r 85b3dc9b6830 macros.xml
--- 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':
diff -r f6e3a10a88e5 -r 85b3dc9b6830 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 f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/ctable.bin
Binary file test-data/cached_locally/prebuilt_index/ctable.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/ctg_offsets.bin
Binary file test-data/cached_locally/prebuilt_index/ctg_offsets.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv
--- 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/hash.bin
Binary file test-data/cached_locally/prebuilt_index/hash.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/header.json
--- 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/indexing.log
--- 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 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 17:14:25 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/mphf.bin
Binary file test-data/cached_locally/prebuilt_index/mphf.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/pos.bin
Binary file test-data/cached_locally/prebuilt_index/pos.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 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 17:14:25 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/quasi_index.log
--- 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/rank.bin
Binary file test-data/cached_locally/prebuilt_index/rank.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/refAccumLengths.bin
Binary file test-data/cached_locally/prebuilt_index/refAccumLengths.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/refInfo.json
--- 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 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 17:14:25 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/reflengths.bin
Binary file test-data/cached_locally/prebuilt_index/reflengths.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/refseq.bin
Binary file test-data/cached_locally/prebuilt_index/refseq.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/rsd.bin
Binary file test-data/cached_locally/prebuilt_index/rsd.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/sa.bin
Binary file test-data/cached_locally/prebuilt_index/sa.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/seq.bin
Binary file test-data/cached_locally/prebuilt_index/seq.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/txpInfo.bin
Binary file test-data/cached_locally/prebuilt_index/txpInfo.bin has changed
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/prebuilt_index/versionInfo.json
--- 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
diff -r f6e3a10a88e5 -r 85b3dc9b6830 test-data/cached_locally/salmon_indexes_versioned.loc
--- 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