Mercurial > repos > iuc > data_manager_selection_background

changeset 2:e4f07770b340 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_selection_background commit f3390425582c26c4018eb13eb0f8f2a85189ce08"
author iuc
date Tue, 24 Aug 2021 17:58:31 +0000
parents 0bd1cd5eac51
children 10ac95ec81d9
files data_manager/data_manager_selection_background.py data_manager/data_manager_selection_background.xml data_manager_conf.xml test-data/selection-out1.json tool-data/selection_background.loc.sample tool_data_table_conf.xml.sample
diffstat 5 files changed, 10 insertions(+), 10 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_selection_background.py	Sat Aug 21 07:51:54 2021 +0000
+++ b/data_manager/data_manager_selection_background.py	Tue Aug 24 17:58:31 2021 +0000
@@ -125,7 +125,7 @@
     # Update Data Manager JSON and write to file
     data_manager_entry = {
         'data_tables': {
-            'bealign_selection': {'value': args.dbkey, 'label': args.label, 'path': table_entry}
+            'selection_background': {'value': args.dbkey, 'label': args.label, 'path': table_entry}
         }
     }
 
--- a/data_manager/data_manager_selection_background.xml	Sat Aug 21 07:51:54 2021 +0000
+++ b/data_manager/data_manager_selection_background.xml	Tue Aug 24 17:58:31 2021 +0000
@@ -1,5 +1,5 @@
 <?xml version="1.0"?>
-<tool id="data_manager_selection_background" name="Add background sequences" tool_type="manage_data" version="1.0.1">
+<tool id="data_manager_selection_background" name="Add background sequences" tool_type="manage_data" version="1.0.2">
     <description>for selection analysis</description>
     <command detect_errors="exit_code">
     <![CDATA[
@@ -38,7 +38,7 @@
             <param name="label" value="SARS-CoV-2: ORF6" />
             <param name="source_selector" value="history" />
             <param name="dataset" value="selection-in1.fa" />
-            <output name="out_file" file="selection-out1.json" />
+            <output name="selection_background_json" file="selection-out1.json" />
         </test>
     </tests>
     <help>
--- a/data_manager_conf.xml	Sat Aug 21 07:51:54 2021 +0000
+++ b/data_manager_conf.xml	Tue Aug 24 17:58:31 2021 +0000
@@ -5,12 +5,12 @@
             <output>
                 <column name="value" />
                 <column name="label" />
-                <column name="path" output_ref="out_file" >
+                <column name="path" output_ref="selection_background_json" >
                     <move type="file">
                         <source>${path}</source>
-                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${value}/selection/${path}</target>
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">selection_background/${value}/${path}</target>
                     </move>
-                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/selection/${path}</value_translation>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/selection_background/${value}/${path}</value_translation>
                     <value_translation type="function">abspath</value_translation>
                 </column>
             </output>
--- a/test-data/selection-out1.json	Sat Aug 21 07:51:54 2021 +0000
+++ b/test-data/selection-out1.json	Tue Aug 24 17:58:31 2021 +0000
@@ -1,1 +1,1 @@
-{"data_tables": {"bealign_selection": {"label": "SARS-CoV-2: ORF6", "path": "CoV2-ORF6.fa", "value": "CoV2-ORF6"}}}
\ No newline at end of file
+{"data_tables": {"selection_background": {"label": "SARS-CoV-2: ORF6", "path": "CoV2-ORF6.fa", "value": "CoV2-ORF6"}}}
\ No newline at end of file
--- a/tool_data_table_conf.xml.sample	Sat Aug 21 07:51:54 2021 +0000
+++ b/tool_data_table_conf.xml.sample	Tue Aug 24 17:58:31 2021 +0000
@@ -1,7 +1,7 @@
 <tables>
-    <!-- Locations of dbkeys and len files under genome directory -->
-    <table name="bealign_selection" comment_char="#">
+    <!-- Locations of background sequences for clade analysis -->
+    <table name="selection_background" comment_char="#">
         <columns>value, label, path</columns>
-        <file path="tool-data/bealign_selection.loc" />
+        <file path="tool-data/selection_background.loc" />
     </table>
 </tables>