diff data_manager/macros.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/macros.xml	Thu Aug 15 11:30:16 2019 -0400
+++ b/data_manager/macros.xml	Thu Nov 28 15:48:56 2019 -0500
@@ -1,10 +1,11 @@
 <macros>
     <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
     whenever you make changes to the following two version tokens!
-    The data manager uses a symlink to this macro file to keep the versions in
-    sync. -->
+    The data manager uses a symlink to this macro file to keep the STAR and
+    the index versions in sync, but you should manually adjust the +galaxy
+    version number. -->
     <!-- STAR version to be used -->
-    <token name="@VERSION@">2.7.2a</token>
+    <token name="@VERSION@">2.7.2b</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.
@@ -18,10 +19,11 @@
         <requirements>
             <requirement type="package" version="@VERSION@">star</requirement>
             <requirement type="package" version="1.9">samtools</requirement>
+            <yield />
         </requirements>
     </xml>
 
-    <xml name="index_selection" token_with_gene_model="1">
+    <xml name="index_selection" token_with_gene_model="0">
         <param argument="--genomeDir" name="genomeDir" type="select"
         label="Select reference genome"
         help="If your genome of interest is not listed, contact the Galaxy team">
@@ -88,7 +90,7 @@
         &&
     #end if
     ]]></token>
-    <token name="@REFGENOMEHANDLING" ><![CDATA[
+    <token name="@REFGENOMEHANDLING@" ><![CDATA[
     --runThreadN \${GALAXY_SLOTS:-4}
     --genomeLoad NoSharedMemory
     --genomeDir
@@ -97,7 +99,7 @@
     #else:
         '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
         ## Handle difference between indices with/without annotations
-        #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
+        #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
             #if $refGenomeSource.GTFconditional.sjdbGTFfile:
                 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
                 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
@@ -114,6 +116,7 @@
             <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
             <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
             <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
+            <yield />
         </stdio>
     </xml>
     <xml name="refgenomehandling" >
@@ -127,16 +130,16 @@
                     <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">use genome reference with builtin gene-model</option>
-                        <option value="with-gtf">use genome reference without builtin gene-model</option>
+                        <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>
-                    <when value="without-gtf">
-                        <expand macro="index_selection" with_gene_model="1" />
-                    </when>
                 </conditional>
             </when>
             <when value="history">