# HG changeset patch
# User iuc
# Date 1698222277 0
# Node ID 01ccd366690d14444626ea6615a8829ad84e950a
# Parent  3d61a698e5e1fff1bd1a03d8e34fb7df33185c11
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/arriba commit 3a528b3f87cff585baf4abb8ebe0be95a24044ea

diff -r 3d61a698e5e1 -r 01ccd366690d arriba.xml
--- a/arriba.xml	Fri Mar 24 08:12:45 2023 +0000
+++ b/arriba.xml	Wed Oct 25 08:24:37 2023 +0000
@@ -472,8 +472,8 @@
         <test expect_num_outputs="4"> 
             <param name="input" ftype="sam" value="Aligned.out.sam"/>
             <conditional name="genome">
-                <param name="genome_source" value="history"/>
-                <param name="assembly" ftype="fasta" value="genome.fasta.gz"/>
+                <param name="genome_source" value="cached"/>
+                <param name="ref_file" value="genome_id"/>
             </conditional>
             <conditional name="genome_gtf">
                 <param name="gtf_source" value="history"/>
diff -r 3d61a698e5e1 -r 01ccd366690d macros.xml
--- a/macros.xml	Fri Mar 24 08:12:45 2023 +0000
+++ b/macros.xml	Wed Oct 25 08:24:37 2023 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">2.4.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">arriba</requirement>
@@ -53,7 +53,7 @@
         ln -sf '$genome.assembly' $genome_assembly &&
     #end if
 #elif str($genome.genome_source) == "cached"
-    #set $genome_assembly = $genome.ref_file.fields.fasta
+    #set $genome_assembly = $genome.ref_file.fields.path
 #end if
     ]]></token>
     <token name="@GTF_SOURCE@"><![CDATA[
@@ -63,7 +63,7 @@
     ]]></token>
 
     <xml name="visualization_options">
-                <param name="cytobands" argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
+                <param argument="--cytobands" type="data" format="tabular" optional="true" label="Cytobands"/>
                 <section name="options" expanded="false" title="Draw Fusion Options">
                     <param argument="--sampleName" type="text" value="" optional="true" label="Sample Name printed as the title on every page"/>
                     <param argument="--transcriptSelection" type="select" optional="true" label="Transcript selection">
diff -r 3d61a698e5e1 -r 01ccd366690d test-data/all_fasta.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/all_fasta.loc	Wed Oct 25 08:24:37 2023 +0000
@@ -0,0 +1,19 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id>	<dbkey>	<display_name>	<file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3	apiMel3	Honeybee (Apis mellifera): apiMel3	/path/to/genome/apiMel3/apiMel3.fa
+#hg19canon	hg19	Human (Homo sapiens): hg19 Canonical	/path/to/genome/hg19/hg19canon.fa
+#hg19full	hg19	Human (Homo sapiens): hg19 Full	/path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#
+genome_id	dbkey	genome_name	${__HERE__}/genome.fasta.gz
\ No newline at end of file
diff -r 3d61a698e5e1 -r 01ccd366690d test-data/genome.fasta.gz
Binary file test-data/genome.fasta.gz has changed
diff -r 3d61a698e5e1 -r 01ccd366690d test-data/genome.fasta.gz.fai
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome.fasta.gz.fai	Wed Oct 25 08:24:37 2023 +0000
@@ -0,0 +1,2 @@
+22	269079	4	269079	269080
+9	515509	269087	515509	515510
diff -r 3d61a698e5e1 -r 01ccd366690d test-data/genome.fasta.gz.gzi
Binary file test-data/genome.fasta.gz.gzi has changed
diff -r 3d61a698e5e1 -r 01ccd366690d tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed Oct 25 08:24:37 2023 +0000
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, dbkey, name, path</columns>
+        <file path="${__HERE__}/test-data/all_fasta.loc" />
+    </table>
+</tables>