# HG changeset patch
# User iuc
# Date 1596634692 14400
# Node ID 6c6c6df09e6431795acf8d735ff963992f250f8c
# Parent  64deddb6a8ec34a00ad151bf32eab25d42ce9402
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit a8e319862d723654c372a6d71e5de76e052586a9"

diff -r 64deddb6a8ec -r 6c6c6df09e64 data_manager/macros.xml
--- a/data_manager/macros.xml	Thu Nov 28 15:48:56 2019 -0500
+++ b/data_manager/macros.xml	Wed Aug 05 09:38:12 2020 -0400
@@ -5,7 +5,7 @@
     the index versions in sync, but you should manually adjust the +galaxy
     version number. -->
     <!-- STAR version to be used -->
-    <token name="@VERSION@">2.7.2b</token>
+    <token name="@VERSION@">2.7.5b</token>
     <!-- STAR index version compatible with this version of STAR
     This is the STAR version that introduced the index structure expected
     by the current version.
@@ -13,7 +13,8 @@
     STAR -h | grep versionGenome
     or by looking for the versionGenome parameter in source/parametersDefault
     of STAR's source code -->
-    <token name="@IDX_VERSION@">2.7.1a</token>
+    <token name="@IDX_VERSION@">2.7.4a</token>
+    <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
 
     <xml name="requirements">
         <requirements>
@@ -27,7 +28,7 @@
         <param argument="--genomeDir" name="genomeDir" type="select"
         label="Select reference genome"
         help="If your genome of interest is not listed, contact the Galaxy team">
-            <options from_data_table="rnastar_index2_versioned">
+            <options from_data_table="@IDX_DATA_TABLE@">
                 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
                 <filter type="static_value" column="5" value="@IDX_VERSION@" />
                 <filter type="sort_by" column="2" />
@@ -53,7 +54,7 @@
             <conditional name="refGenomeSource.geneSource">
                 <when value="indexed">
                     <action type="metadata" name="dbkey">
-                        <option type="from_data_table" name="rnastar_index2_versioned" column="1" offset="0">
+                        <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
                             <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                             <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
                         </option>
@@ -76,10 +77,21 @@
             --genomeDir 'tempstargenomedir'
             --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
             ## Handle difference between indices with/without annotations
-            #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
-                --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
-                --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
-                #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
+            #if 'GTFconditional' in $refGenomeSource:
+                ## GTFconditional exists only in STAR, but not STARsolo
+                #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
+                    --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
+                    --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
+                    #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
+                        --sjdbGTFtagExonParentTranscript Parent
+                    #end if
+                #end if
+            #else:
+                ## ref genome selection is less complex for STARsolo cause
+                ## with-gtf is mandatory there
+                --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
+                --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
+                #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
                     --sjdbGTFtagExonParentTranscript Parent
                 #end if
             #end if
@@ -110,6 +122,13 @@
         #end if
         #end if
         ]]></token>
+    <xml name="ref_selection">
+        <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
+        <!-- Currently, this parameter is not exposed in the wrapper,
+             but used only in the tests to avoid excessive index sizes for
+             the tiny test genomes. -->
+        <param name="genomeSAindexNbases" type="hidden" value="" />
+    </xml>
     <xml name="stdio" >
         <stdio>
             <regex match="FATAL error" source="both" level="fatal"/>
@@ -119,48 +138,4 @@
             <yield />
         </stdio>
     </xml>
-    <xml name="refgenomehandling" >
-        <conditional name="refGenomeSource">
-            <param name="geneSource" type="select" label="Custom or built-in reference genome" help="Built-ins were indexed using default options">
-                <option value="indexed" selected="true">Use a built-in index</option>
-                <option value="history">Use reference genome from history and create temporary index</option>
-            </param>
-            <when value="indexed">
-                <conditional name="GTFconditional">
-                    <param name="GTFselect" type="select"
-                           label="Reference genome with or without an annotation"
-                           help="Select the '... with builtin gene-model' option to select from the list of available indexes that were built with splice junction information. Select the '... without builtin gene-model' option to select from the list of available indexes without annotated splice junctions.">
-                        <option value="without-gtf" selected='true'>use genome reference without builtin gene-model</option>
-                        <option value="with-gtf">use genome reference with builtin gene-model</option>
-                    </param>
-                    <when value="with-gtf">
-                        <expand macro="index_selection" with_gene_model="1" />
-                    </when>
-                    <when value="without-gtf">
-                        <expand macro="index_selection" with_gene_model="0" />
-                        <expand macro="@SJDBOPTIONS@" />
-                    </when>
-                </conditional>
-            </when>
-            <when value="history">
-                <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
-                <!-- Currently, this parameter is not exposed in the wrapper,
-                     but used only in the tests to avoid excessive index sizes for
-                     the tiny test genomes. -->
-                <param name="genomeSAindexNbases" type="hidden" value="" />
-                <conditional name="GTFconditional">
-                    <param name="GTFselect" type="select"
-                           label="Build index with our without known splice junctions annotation"
-                           help="To build an index with known splice junctions annotated, you will have to provide a GTF or GFF3 dataset that describes the gene models (the location of genes, transcripts and exons) known for the reference genome.">
-                        <option value="without-gtf">build index without gene-model</option>
-                        <option value="with-gtf">build index with gene-model</option>
-                    </param>
-                    <when value="with-gtf">
-                        <expand macro="@SJDBOPTIONS@" optional="false"/>
-                    </when>
-                    <when value="without-gtf" />
-                </conditional>
-            </when>
-        </conditional>
-    </xml>
 </macros>
diff -r 64deddb6a8ec -r 6c6c6df09e64 data_manager/rna_star_index_builder.xml
--- a/data_manager/rna_star_index_builder.xml	Thu Nov 28 15:48:56 2019 -0500
+++ b/data_manager/rna_star_index_builder.xml	Wed Aug 05 09:38:12 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="@IDX_VERSION@+galaxy2" profile="19.05">
+<tool id="rna_star_index_builder_data_manager" name="rnastar index versioned" tool_type="manage_data" version="@IDX_VERSION@" profile="19.05">
     <description>builder</description>
 
     <macros>
@@ -51,7 +51,7 @@
 #if str($GTFconditional.GTFselect) == "withGTF":
     --with-gene-model
 #end if
---data-table rnastar_index2_versioned
+--data-table @IDX_DATA_TABLE@
 --subdir '${subdir}'
     ]]></command>
     <inputs>
diff -r 64deddb6a8ec -r 6c6c6df09e64 data_manager_conf.xml
--- a/data_manager_conf.xml	Thu Nov 28 15:48:56 2019 -0500
+++ b/data_manager_conf.xml	Wed Aug 05 09:38:12 2020 -0400
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <data_managers>
-    <data_manager tool_file="data_manager/rna_star_index_builder.xml" id="rna_star_index_builder" version="0.0.6">
-        <data_table name="rnastar_index2_versioned">
+    <data_manager tool_file="data_manager/rna_star_index_builder.xml" id="rna_star_index_builder" version="0.0.7">
+        <data_table name="rnastar_index2x_versioned">
             <output>
                 <column name="value" />
                 <column name="dbkey" />
diff -r 64deddb6a8ec -r 6c6c6df09e64 test-data/test_star_01.data_manager_json
--- a/test-data/test_star_01.data_manager_json	Thu Nov 28 15:48:56 2019 -0500
+++ b/test-data/test_star_01.data_manager_json	Wed Aug 05 09:38:12 2020 -0400
@@ -1,1 +1,1 @@
-{"data_tables": {"rnastar_index2_versioned": \[{"dbkey": "phiX174", "name": "phiX174", "path": ".*", "value": "phiX174", "version": "2.7.1a", "with_gene_model": "0"}\]}}
\ No newline at end of file
+{"data_tables": {"rnastar_index2x_versioned": \[{"dbkey": "phiX174", "name": "phiX174", "path": ".*", "value": "phiX174", "version": "2.7.4a", "with_gene_model": "0"}\]}}
diff -r 64deddb6a8ec -r 6c6c6df09e64 tool-data/rnastar_index2_versioned.loc.sample
--- a/tool-data/rnastar_index2_versioned.loc.sample	Thu Nov 28 15:48:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-#This is a sample file distributed with Galaxy that enables tools
-#to use a directory of rna-star indexed sequences data files. You will
-#need to create these data files and then create a rnastar_index2.loc
-#file similar to this one (store it in this directory) that points to
-#the directories in which those files are stored. The rnastar_index2.loc
-#file has this format (longer white space characters are TAB characters):
-#
-#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>	<with_gene_model>	<version>
-#
-#The <with_gene_model> column should be 1 or 0, indicating whether the index
-#was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
-#or not.
-#
-#The <version> column indicates the STAR version that introduced the format of
-#the index, i.e., the oldest STAR version that could make use of the index.
-#
-#Note that STAR indices can become quite large. Consequently, it is only
-#advisable to create indices with annotations if it's known ahead of time that
-#(A) the annotations won't be frequently updated and (B) the read lengths used
-#will also rarely vary. If either of these is not the case, it's advisable to
-#create indices without annotations and then specify an annotation file and
-#maximum read length (minus 1) when running STAR.
-#
-#hg19   hg19    hg19 full   /mnt/galaxyIndices/genomes/hg19/rnastar	0	2.7.1a
-#hg19Ensembl   hg19Ensembl    hg19 full with Ensembl annotation   /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar	1	2.7.1a
-
diff -r 64deddb6a8ec -r 6c6c6df09e64 tool-data/rnastar_index2x_versioned.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/rnastar_index2x_versioned.loc.sample	Wed Aug 05 09:38:12 2020 -0400
@@ -0,0 +1,27 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of rna-star indexed sequences data files.
+#You will need to create these data files and then create a
+#rnastar_index2x_versioned.loc file similar to this one (store it in this
+directory) that points to the directories in which those files are stored.
+#The rnastar_index2x_versioned.loc file has this format (longer white space
+#characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>	<with_gene_model>	<version>
+#
+#The <with_gene_model> column should be 1 or 0, indicating whether the index
+#was built with annotations (i.e., --sjdbGTFfile and --sjdbOverhang were used)
+#or not.
+#
+#The <version> column indicates the STAR version that introduced the format of
+#the index, i.e., the oldest STAR version that could make use of the index.
+#
+#Note that STAR indices can become quite large. Consequently, it is only
+#advisable to create indices with annotations if it's known ahead of time that
+#(A) the annotations won't be frequently updated and (B) the read lengths used
+#will also rarely vary. If either of these is not the case, it's advisable to
+#create indices without annotations and then specify an annotation file and
+#maximum read length (minus 1) when running STAR.
+#
+#hg19   hg19    hg19 full   /mnt/galaxyIndices/genomes/hg19/rnastar	0	2.7.1a
+#hg19Ensembl   hg19Ensembl    hg19 full with Ensembl annotation   /mnt/galaxyIndices/genomes/hg19Ensembl/rnastar	1	2.7.1a
+
diff -r 64deddb6a8ec -r 6c6c6df09e64 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Thu Nov 28 15:48:56 2019 -0500
+++ b/tool_data_table_conf.xml.sample	Wed Aug 05 09:38:12 2020 -0400
@@ -5,8 +5,8 @@
         <file path="tool-data/all_fasta.loc" />
     </table>
     <!-- Locations of STAR indexes -->
-    <table name="rnastar_index2_versioned" comment_char="#" allow_duplicate_entries="False">
+    <table name="rnastar_index2x_versioned" comment_char="#" allow_duplicate_entries="False">
         <columns>value, dbkey, name, path, with_gene_model, version</columns>
-        <file path="tool-data/rnastar_index2_versioned.loc" />
+        <file path="tool-data/rnastar_index2x_versioned.loc" />
     </table>
 </tables>