Mercurial > repos > dfornika > mentalist

changeset 10:4ab1c1edb543 draft

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planemo upload for repository https://github.com/WGS-TB/MentaLiST/tree/master/galaxy commit 7e8b159e34b91cb5e76ba86feaea24158565606b-dirty
author dfornika
date Wed, 11 Oct 2017 16:31:13 -0400
parents 2f2860ab7d3c
children 2c384f9d9a83
files data_managers/data_manager_conf.xml data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py
diffstat 2 files changed, 10 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/data_managers/data_manager_conf.xml	Wed Oct 11 14:27:37 2017 -0400
+++ b/data_managers/data_manager_conf.xml	Wed Oct 11 16:31:13 2017 -0400
@@ -7,9 +7,9 @@
         <column name="name" />
         <column name="path" output_ref="out_file">
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target>
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${path}</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
@@ -22,9 +22,9 @@
         <column name="name" />
         <column name="path" output_ref="out_file">
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target>
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${path}</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
@@ -37,9 +37,9 @@
         <column name="name" />
         <column name="path" output_ref="out_file">
           <move type="directory" relativize_symlinks="True">
-            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${value}</target>
+            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">mentalist_databases/${path}</target>
           </move>
-          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${value}</value_translation>
+          <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/mentalist_databases/${path}</value_translation>
           <value_translation type="function">abspath</value_translation>
         </column>
       </output>
--- a/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 14:27:37 2017 -0400
+++ b/data_managers/data_manager_mentalist_download_pubmlst/data_manager/mentalist_download_pubmlst.py	Wed Oct 11 16:31:13 2017 -0400
@@ -18,7 +18,10 @@
     if return_code:
         print("Error building database.", file=sys.stderr)
         sys.exit( return_code )
-    data_table_entry = dict( value=database_name, dbkey=database_name, name=database_name, path=database_name )
+    data_table_path = scheme.lower().replace(" ", "_").translate(None, string.punctuation) + "_k" + str(kmer_size) + "_pubmlst"
+    data_table_value = data_table_path + ".h5"
+    data_table_name = scheme.lower() + " k=" + str(kmer_size) + " (PubMLST)"
+    data_table_entry = dict( value=data_table_value, dbkey='PubMLST', name=data_table_name, path=database_name )
     for data_table_name in data_table_names:
         _add_data_table_entry( data_manager_dict, data_table_name, data_table_entry )