diff data_manager/rna_star_index_builder.xml @ 6:64deddb6a8ec draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_star_index_builder commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"

--- a/data_manager/rna_star_index_builder.xml	Thu Aug 15 11:30:16 2019 -0400
+++ b/data_manager/rna_star_index_builder.xml	Thu Nov 28 15:48:56 2019 -0500
@@ -1,11 +1,13 @@
-<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="2.7.1a" profile="17.01">
+<tool id="rna_star_index_builder_data_manager" name="rnastar index2" tool_type="manage_data" version="@IDX_VERSION@+galaxy2" profile="19.05">
     <description>builder</description>
 
     <macros>
         <import>macros.xml</import>
     </macros>
 
-    <expand macro="requirements" />
+    <expand macro="requirements">
+        <requirement type="package" version="3.7">python</requirement>
+    </expand>
 
     <command><![CDATA[
 if [ -z "\$GALAXY_MEMORY_MB" ] ; then
@@ -14,17 +16,16 @@
     GALAXY_MEMORY_BYTES=\$((GALAXY_MEMORY_MB * 1000000)) ;
 fi ;
 
-#import json, os
-#set params = json.loads(open(str($out_file)).read())
-#set target_directory = $params['output_data'][0]['extra_files_path'].encode('ascii', 'replace')
-#set subdir = os.path.basename(target_directory)
+#import os
+#set $target_directory = str($out_file.extra_files_path)
+#set $subdir = os.path.basename($target_directory)
 
-mkdir -p '${target_directory}/${subdir}' &&
+mkdir '${target_directory}' &&
 
 STAR
 --runMode genomeGenerate
 --genomeFastaFiles '${all_fasta_source.fields.path}'
---genomeDir '${target_directory}/${subdir}'
+--genomeDir '${target_directory}'
 --limitGenomeGenerateRAM \${GALAXY_MEMORY_BYTES}
 #if $GTFconditional.GTFselect == "withGTF":
     --sjdbGTFfile '${GTFconditional.sjdbGTFfile}'
@@ -100,25 +101,26 @@
         <data name="out_file" format="data_manager_json"/>
     </outputs>
 
-    <!-- not available in planemo at the moment of writing
     <tests>
         <test>
-            <param name="all_fasta_source" value="phiX.fa"/>
+            <param name="all_fasta_source" value="phiX174"/>
             <param name="sequence_name" value="phiX"/>
             <param name="sequence_id" value="minimal-settings"/>
             <param name="modelformat" value="None"/>
 
-            <output name="out_file" file="test_star_01.data_manager_json"/>
+            <output name="out_file" file="test_star_01.data_manager_json" compare="re_match"/>
         </test>
     </tests>
-    -->
 
     <help><![CDATA[
 .. class:: infomark
 
 *What it does*
 
-This is a Galaxy datamanager for the rna STAR gap-aware RNA aligner.
+This is a Galaxy data manager tool for the gap-aware RNA aligner STAR.
+
+This version of the tool builds STAR indices of the format first introduced
+with STAR version @IDX_VERSION@.
 
 Please read the fine manual - that and the google group are the places to learn about the options above.