Mercurial > repos > gga > chado_expression_delete_all_biomaterials

changeset 6:596d9834ac30 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/chado commit bc69ce09372c8c2701b726c326e671af279adb4d
author gga
date Thu, 11 Jul 2019 08:36:45 -0400
parents 3a3791f72693
children 24b13e012f3e
files expression_delete_all_biomaterials.xml macros.xml
diffstat 2 files changed, 16 insertions(+), 18 deletions(-) [+]
line wrap: on
line diff
--- a/expression_delete_all_biomaterials.xml	Mon Jul 08 05:36:49 2019 -0400
+++ b/expression_delete_all_biomaterials.xml	Thu Jul 11 08:36:45 2019 -0400
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="expression_delete_all_biomaterials" name="Chado biomaterials delete all" version="@WRAPPER_VERSION@.0">
+<tool id="expression_delete_all_biomaterials" name="Chado biomaterials delete all" version="@WRAPPER_VERSION@.1">
     <description></description>
     <macros>
         <import>macros.xml</import>
@@ -14,7 +14,7 @@
 
  > '$results'
 
- && @ZIP_PSQL@
+ @ZIP_PSQL@
     ]]></command>
     <inputs>
         <expand macro="psql_target"/>
--- a/macros.xml	Mon Jul 08 05:36:49 2019 -0400
+++ b/macros.xml	Thu Jul 11 08:36:45 2019 -0400
@@ -89,32 +89,29 @@
       </conditional>
     </xml>
 
-    <token name="@AUTH@"><![CDATA[
-        if [ -z "$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
-          echo "__default: local" > '.auth.yml' &&
-          echo "local:" >> '.auth.yml' &&
-          echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
-          echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
-          echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
-          echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
-          echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
-          echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
-
-          export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
-        ; fi
-    ]]></token>
-
     <token name="@START_PSQL@"><![CDATA[
         #if $psql_target.method == 'pgtools'
             tar -xjvf '$psql_target.infile' > /dev/null &&
             . '$__tool_directory__/prepare_psql.sh' '$psql_target.schema'
         #else
-            @AUTH@
+            if [ -z "\$CHAKIN_GLOBAL_CONFIG_PATH" ]; then
+              echo "__default: local" > '.auth.yml' &&
+              echo "local:" >> '.auth.yml' &&
+              echo "    dbhost: \"\$GALAXY_CHADO_DBHOST\"" >> '.auth.yml' &&
+              echo "    dbname: \"\$GALAXY_CHADO_DBNAME\"" >> '.auth.yml' &&
+              echo "    dbpass: \"\$GALAXY_CHADO_DBPASS\"" >> '.auth.yml' &&
+              echo "    dbuser: \"\$GALAXY_CHADO_DBUSER\"" >> '.auth.yml' &&
+              echo "    dbschema: \"\$GALAXY_CHADO_DBSCHEMA\"" >> '.auth.yml' &&
+              echo "    dbport: \"\$GALAXY_CHADO_DBPORT\"" >> '.auth.yml' &&
+
+              export CHAKIN_GLOBAL_CONFIG_PATH='.auth.yml'
+            ; fi
         #end if
     ]]></token>
 
     <token name="@STOP_PSQL@"><![CDATA[
         #if $psql_target.method == 'pgtools'
+            &&
             pglite stop -d ./postgresql &&
             timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done'
             ;
@@ -125,6 +122,7 @@
 
     <token name="@ZIP_PSQL@"><![CDATA[
         #if $psql_target.method == 'pgtools'
+            &&
             pglite stop -d ./postgresql &&
             timeout 60 bash -c 'until pglite status -d ./postgresql | grep -F -q "no server running"; do sleep 1; done' &&
             tar -cvjf postgresql_out.tar.bz2 postgresql > /dev/null