diff macros.xml @ 10:d72192ec8e39 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 08015be1ee8a784e0619f961aaa724857debfd6f"

--- a/macros.xml	Mon Jul 29 10:09:54 2019 -0400
+++ b/macros.xml	Mon Dec 02 05:46:45 2019 -0500
@@ -1,14 +1,10 @@
 <?xml version="1.0"?>
 <macros>
-  <token name="@WRAPPER_VERSION@">4.0.0</token>
+  <token name="@WRAPPER_VERSION@">4.1</token>
 
   <xml name="requirements">
     <requirements>
-      <requirement type="package" version="2.7">python</requirement>
-      <requirement type="package" version="1.65">biopython</requirement>
-      <requirement type="package" version="0.6.2">bcbiogff</requirement>
-      <requirement type="package" version="2.12.4">requests</requirement>
-      <requirement type="package" version="1.11.0">six</requirement>
+      <requirement type="package" version="4.1">apollo</requirement>
       <yield/>
     </requirements>
   </xml>
@@ -19,20 +15,27 @@
   <token name="@URL@">
 "\$GALAXY_WEBAPOLLO_URL"
   </token>
-  <token name="@ADMIN_AUTH@">
-"\$GALAXY_WEBAPOLLO_URL"
-"\$GALAXY_WEBAPOLLO_USER"
-"\$GALAXY_WEBAPOLLO_PASSWORD"
-  </token>
+
+  <token name="@AUTH@"><![CDATA[
+      if [ -z "\$ARROW_GLOBAL_CONFIG_PATH" ]; then
+        echo "__default: local" > '.auth.yml' &&
+        echo "local:" >> '.auth.yml' &&
+        echo "    url: \"\$GALAXY_WEBAPOLLO_URL\"" >> '.auth.yml' &&
+        echo "    username: \"\$GALAXY_WEBAPOLLO_USER\"" >> '.auth.yml' &&
+        echo "    password: \"\$GALAXY_WEBAPOLLO_PASSWORD\"" >> '.auth.yml' &&
+
+        export ARROW_GLOBAL_CONFIG_PATH='.auth.yml'
+      ; fi &&
+  ]]></token>
 
   <token name="@ORG_OR_GUESS@">
 <![CDATA[
 #if $org_source.source_select == "auto_json":
-    --org_json "${org_source.org_file}"
+    --org_json '${org_source.org_file}'
 #elif $org_source.source_select == "select":
-    --org_id "${org_source.org_select}"
+    --org_id '${org_source.org_select}'
 #else:
-    --org_raw "${org_source.org_raw}"
+    --org_raw '${org_source.org_raw}'
 #end if
 ]]>
   </token>
@@ -42,13 +45,13 @@
 
 #if $cn_source.source_select == "auto":
     #if str($cn_source.cn_file) != "None":
-        --seq_fasta $cn_source.cn_file
+        --seq_fasta '$cn_source.cn_file'
     #end if
 #else
     #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
         --seq_raw
         #for $item in $cn_source.refseqs:
-            "${item.refseq}"
+            '${item.refseq}'
         #end for
     #end if
 #end if
@@ -93,12 +96,6 @@
     </conditional>
   </xml>
 
-  <xml name="test_result">
-      <assert_stderr>
-          <has_text text="MissingSchema" />
-      </assert_stderr>
-  </xml>
-
   <xml name="citations">
       <citations>
         <citation type="doi">10.1371/journal.pcbi.1006790</citation>
@@ -109,12 +106,12 @@
   </xml>
   <token name="@GENOME_SELECTOR_PRE@">
 #if $reference_genome.reference_genome_source == 'history':
-    ln -s $reference_genome.genome_fasta genomeref.fa;
+    ln -s '$reference_genome.genome_fasta' genomeref.fa;
 #end if
   </token>
   <token name="@GENOME_SELECTOR@">
 #if $reference_genome.reference_genome_source == 'cached':
-    "${reference_genome.fasta_indexes.fields.path}"
+    '${reference_genome.fasta_indexes.fields.path}'
 #elif $reference_genome.reference_genome_source == 'history':
     genomeref.fa
 #end if