Mercurial > repos > proteore > proteore_data_manager

changeset 7:77db6c42a212 draft

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planemo upload commit 5df487b88ce2146c4be8e1d9f419006583185f6a-dirty
author proteore
date Mon, 11 Mar 2019 04:37:01 -0400
parents f281a1eb83d6
children d5badf9de1b0
files data_manager/resource_building.xml data_manager_conf.xml tool-data/proteore_peptide_atlas.loc.sample tool_data_table_conf.xml.sample
diffstat 4 files changed, 1 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/resource_building.xml	Mon Mar 11 04:30:28 2019 -0400
+++ b/data_manager/resource_building.xml	Mon Mar 11 04:37:01 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.10" tool_type="manage_data">
+<tool id="data_manager_proteore" name="Get source files for proteore tools" version="2019.03.10.1" tool_type="manage_data">
 <description>
 to create or update reference files for proteore tools
 </description>
--- a/data_manager_conf.xml	Mon Mar 11 04:30:28 2019 -0400
+++ b/data_manager_conf.xml	Mon Mar 11 04:37:01 2019 -0400
@@ -29,21 +29,6 @@
                 </column>
             </output>
         </data_table>
-        <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_id_mapping_Human">
             <output>
                 <column name="id" />
--- a/tool-data/proteore_peptide_atlas.loc.sample	Mon Mar 11 04:30:28 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,10 +0,0 @@
-#This file lists the locations name and values of reference files for number of MS/MS observations in a tissue
-#This is a tab separated file (TAB, not 4 spaces !)
-#<id>	<name>	<tissue>	<value>
-#Human_Heart_20-07-2018	Human Heart 20/07/2018	Human_Heart	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Heart_20-07-2018.tsv
-#Human_Liver_20-07-2018	Human Liver 20/07/2018	Human_Liver	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Liver_20-07-2018.tsv
-#Human_Urine_20-07-2018	Human Urine 20/07/2018	Human_Urine	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Urine_20-07-2018.tsv
-#Human_Brain_20-07-2018	Human Brain 20/07/2018	Human_Brain	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Brain_20-07-2018.tsv
-#Human_Kidney_20-07-2018	Human Kidney 20/07/2018	Human_Kidney	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Kidney_20-07-2018.tsv
-#Human_Plasma_20-07-2018	Human Plasma 20/07/2018	Human_Plasma	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_Plasma_20-07-2018.tsv
-#Human_CSF_20-07-2018	Human CSF 20/07/2018	Human_CSF	/projet/galaxydev/galaxy/tool-data/peptide_atlas/Human_CSF_20-07-2018.tsv
--- a/tool_data_table_conf.xml.sample	Mon Mar 11 04:30:28 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Mon Mar 11 04:37:01 2019 -0400
@@ -1,9 +1,5 @@
 <?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" />