# HG changeset patch
# User bgruening
# Date 1564245467 14400
# Node ID 2c0ca397d3025a740e49123b5b3b891023fb6092
# Parent  6b0ba6de14249b47143a5ed043f5086dcd7e6912
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4cc21e8c47d99cee4560bb7634c859b551c4ea72-dirty

diff -r 6b0ba6de1424 -r 2c0ca397d302 salmon.xml
--- a/salmon.xml	Thu Aug 23 15:58:26 2018 -0400
+++ b/salmon.xml	Sat Jul 27 12:37:47 2019 -0400
@@ -18,6 +18,7 @@
             </param>
         </xml>
         <token name="@VERSION@">0.11.2</token>
+        <token name="@IDX_VERSION@">q5</token>
     </macros>
 
     <requirements>
@@ -230,8 +231,9 @@
             </param>
             <when value="indexed">
                 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
-                    <options from_data_table="salmon_indexes">
+                    <options from_data_table="salmon_indexes_versioned">
                         <filter type="sort_by" column="2"/>
+                        <filter type="static_value" column="4" value="@IDX_VERSION@" />
                         <validator type="no_options" message="No indexes are available for the selected input dataset"/>
                     </options>
                 </param>
@@ -441,6 +443,28 @@
                 </assert_contents>
             </output>
         </test>
+        <test> <!--test use of built-in index-->
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq" />
+            <param name="input_mate2" value="reads_2.fastq" />
+            <param name="biasCorrect" value="False" />
+            <param name="TranscriptSource" value="indexed" />
+            <param name="index" value="hg19_transcript_subset" />
+            <output name="output_quant">
+                <assert_contents>
+                    <has_text text="EffectiveLength" />
+                    <has_text text="TPM" />
+                    <has_text text="NM_001168316" />
+                    <has_text text="NM_174914" />
+                    <has_text text="NM_018953" />
+                    <has_text text="NR_003084" />
+                    <has_text text="NM_017410" />
+                    <has_text text="NM_153693" />
+                    <has_text text="NR_031764" />
+                    <has_n_columns n="5" />
+                </assert_contents>
+            </output>
+        </test>
         <test> <!-- gzipped input -->
             <param name="single_or_paired_opts" value="paired" />
             <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/prebuilt_index/duplicate_clusters.tsv	Sat Jul 27 12:37:47 2019 -0400
@@ -0,0 +1,1 @@
+RetainedTxp	DuplicateTxp
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/hash.bin
Binary file test-data/cached_locally/prebuilt_index/hash.bin has changed
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/header.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/prebuilt_index/header.json	Sat Jul 27 12:37:47 2019 -0400
@@ -0,0 +1,14 @@
+{
+    "value0": {
+        "IndexType": 1,
+        "IndexVersion": "q5",
+        "UsesKmers": true,
+        "KmerLen": 31,
+        "BigSA": false,
+        "PerfectHash": false,
+        "SeqHash": "238a71484cdcf251805629c612f7edd515eb1a23d9be2e2014b62fd5931eb4ac",
+        "NameHash": "2fc64c34c65a78d18fec933772e1aa454cfed52b2b48d43eb75d2933a22feb04",
+        "SeqHash512": "a45ea3d0c5f11c16a45b8b75f902f908996117d7486d72b3d19a8ae619b07b22f3ca0888f5ee6e9dbabf639ae51f7fc74b8eea8808435bbb2ec70b96162849aa",
+        "NameHash512": "6123f1c58bf2153fca204e97fa72a2d25460242f14b886e421316ff251cc57293e77c02d536122e97f46d2508c626e42a35a1798209766359904ddf49fb7bf33"
+    }
+}
\ No newline at end of file
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/indexing.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/prebuilt_index/indexing.log	Sat Jul 27 12:37:47 2019 -0400
@@ -0,0 +1,2 @@
+[2019-07-25 13:45:20.599] [jLog] [info] building index
+[2019-07-25 13:45:20.654] [jLog] [info] done building index
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/quasi_index.log
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/refInfo.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/prebuilt_index/refInfo.json	Sat Jul 27 12:37:47 2019 -0400
@@ -0,0 +1,5 @@
+{
+    "ReferenceFiles": [
+        "tools/salmon/test-data/transcripts.fasta"
+    ]
+}
\ No newline at end of file
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/rsd.bin
Binary file test-data/cached_locally/prebuilt_index/rsd.bin has changed
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/sa.bin
Binary file test-data/cached_locally/prebuilt_index/sa.bin has changed
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/txpInfo.bin
Binary file test-data/cached_locally/prebuilt_index/txpInfo.bin has changed
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/prebuilt_index/versionInfo.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/prebuilt_index/versionInfo.json	Sat Jul 27 12:37:47 2019 -0400
@@ -0,0 +1,6 @@
+{
+    "indexVersion": 2,
+    "hasAuxIndex": false,
+    "auxKmerLength": 31,
+    "indexType": 1
+}
\ No newline at end of file
diff -r 6b0ba6de1424 -r 2c0ca397d302 test-data/cached_locally/salmon_indexes_versioned.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cached_locally/salmon_indexes_versioned.loc	Sat Jul 27 12:37:47 2019 -0400
@@ -0,0 +1,33 @@
+# salmon_indexes_versioned.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Salmon.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample), 
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path> <version>
+#
+# The <version> column can be retrieved from the header.json file in the index folder. e.g   "IndexVersion": "q5"
+
+
+
+# So, for example, if you had sacCer3 indexes stored in:
+#
+#    /depot/data2/galaxy/sacCer3/salmon_indexes/
+#
+# then the salmon_indexes.loc entry could look like this:
+#
+#sacCer3	sacCer3	S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)	/depot/data2/galaxy/sacCer3/salmon_indexes/version_3/	q6
+#
+#More examples:
+#
+#mm10	mm10	Mouse (mm10)	/depot/data2/galaxy/salmon_indexes/mm10/version_2	q4
+#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	q5
diff -r 6b0ba6de1424 -r 2c0ca397d302 tool-data/salmon_indexes.loc.sample
--- a/tool-data/salmon_indexes.loc.sample	Thu Aug 23 15:58:26 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-# This is a sample file distributed with Galaxy that is used to define a
-# list of salmon indices, using three columns tab separated:
-#
-# salmon_index_id{tab}Salmon Index desciption{tab}/data/salmon_indexes/salmon_index_id/
-#
-# An index can be created with the following command:
-#
-# salmon index
-#     --transcripts your_transcripts.fasta
-#     --kmerSize 21
-#     --out /data/salmon_indexes/salmon_index_id/
-#     --threads 4
-#
-
diff -r 6b0ba6de1424 -r 2c0ca397d302 tool-data/salmon_indexes_versioned.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/salmon_indexes_versioned.loc.sample	Sat Jul 27 12:37:47 2019 -0400
@@ -0,0 +1,32 @@
+# salmon_indexes_versioned.loc.sample
+# This is a *.loc.sample file distributed with Galaxy that enables tools
+# to use a directory of indexed data files. This one is for Salmon.
+# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
+# First create these data files and save them in your own data directory structure.
+# Then, create a salmon_indexes_versioned.loc.sample file to use those indexes with tools.
+# Copy this file, save it with the same name (minus the .sample), 
+# follow the format examples, and store the result in this directory.
+# The file should include an one line entry for each index set.
+# The path points to the "basename" for the set, not a specific file.
+# It has four text columns seperated by TABS.
+#
+# <unique_build_id>	<dbkey>	<display_name>	<file_base_path> <version>
+#
+# The <version> column can be retrieved from the header.json file in the index folder. e.g   "IndexVersion": "q5"
+
+
+
+# So, for example, if you had sacCer3 indexes stored in:
+#
+#    /depot/data2/galaxy/sacCer3/salmon_indexes/
+#
+# then the salmon_indexes.loc entry could look like this:
+#
+#sacCer3	sacCer3	S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)	/depot/data2/galaxy/sacCer3/salmon_indexes/version_3/	q6
+#
+#More examples:
+#
+#mm10	mm10	Mouse (mm10)	/depot/data2/galaxy/salmon_indexes/mm10/version_2	q4
+#dm3	dm3		D. melanogaster (dm3)	/depot/data2/galaxy/salmon_indexes/dm3/version_1	q5
+#
+#
diff -r 6b0ba6de1424 -r 2c0ca397d302 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Thu Aug 23 15:58:26 2018 -0400
+++ b/tool_data_table_conf.xml.sample	Sat Jul 27 12:37:47 2019 -0400
@@ -1,6 +1,7 @@
 <tables>
-    <table name="salmon_indexes" comment_char="#">
-        <columns>value, name, path</columns>
-        <file path="tool-data/salmon_indexes.loc" />
+    <!-- Locations of indexes in salmon mapper format -->
+    <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path, version</columns>
+        <file path="tool-data/salmon_indexes_versioned.loc" />
     </table>
 </tables>
diff -r 6b0ba6de1424 -r 2c0ca397d302 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Sat Jul 27 12:37:47 2019 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of indexes in salmon mapper format -->
+    <table name="salmon_indexes_versioned" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path, version</columns>
+        <file path="${__HERE__}/test-data/cached_locally/salmon_indexes_versioned.loc" />
+    </table>
+</tables>