Mercurial > repos > proteore > proteore_data_manager

changeset 10:e6b8f0e5fe16 draft

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planemo upload commit 567ba7934c0ca55529dfeb5e7ca0935ace260ad7-dirty
author proteore
date Wed, 13 Mar 2019 06:09:49 -0400
parents cdd29444e0af
children ac2cd728c40e
files data_manager/resource_building.xml data_manager_conf.xml tool_data_table_conf.xml.sample
diffstat 3 files changed, 20 insertions(+), 1 deletions(-) [+]
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--- a/data_manager/resource_building.xml	Tue Mar 12 06:40:37 2019 -0400
+++ b/data_manager/resource_building.xml	Wed Mar 13 06:09:49 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.12.1" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.13" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
--- a/data_manager_conf.xml	Tue Mar 12 06:40:37 2019 -0400
+++ b/data_manager_conf.xml	Wed Mar 13 06:09:49 2019 -0400
@@ -1,6 +1,21 @@
 <?xml version="1.0"?>
 <data_managers>
     <data_manager tool_file="data_manager/resource_building.xml" id="resource_building">
+        <data_table name="proteore_peptide_atlas">
+            <output>
+                <column name="id"/>
+                <column name="name" />
+                <column name="tissue" />
+                <column name="value" output_ref="output" >
+                    <move type="file">
+                        <!--source>${path}/${value}.tsv</source-->
+                        <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">peptide_atlas/</target>
+                    </move>
+                    <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/peptide_atlas/${id}.tsv</value_translation>
+                    <value_translation type="function">abspath</value_translation>
+                </column>
+            </output>
+        </data_table>
         <data_table name="proteore_protein_atlas_normal_tissue">
             <output>
                 <column name="id"/>
--- a/tool_data_table_conf.xml.sample	Tue Mar 12 06:40:37 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Wed Mar 13 06:09:49 2019 -0400
@@ -1,5 +1,9 @@
 <?xml version="1.0"?>
 <tables>
+    <table name='proteore_peptide_atlas' comment_char="#">
+      <columns>id, name, tissue, value</columns>
+      <file path="tool-data/proteore_peptide_atlas.loc"/>
+    </table>
     <table name="proteore_protein_atlas_normal_tissue" comment_char="#">
       <columns>id, name, tissue, value</columns>
       <file path="tool-data/proteore_protein_atlas_normal_tissue.loc" />