Mercurial > repos > proteore > proteore_build_protein_interaction_maps

changeset 4:ed85511368e0 draft

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planemo upload commit 0290724216a2c445b4e28842153b84a1b28f4e9a-dirty
author proteore
date Thu, 16 May 2019 08:30:16 -0400
parents 2f6cf63f8604
children 52b28dc30699
files build_protein_interaction_maps.xml proteore_biogrid_dictionaries.loc.sample proteore_bioplex_dictionaries.loc.sample proteore_humap_dictionaries.loc.sample tool_data_table_conf.xml.sample
diffstat 5 files changed, 21 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/build_protein_interaction_maps.xml	Tue Mar 12 06:56:01 2019 -0400
+++ b/build_protein_interaction_maps.xml	Thu May 16 08:30:16 2019 -0400
@@ -1,4 +1,4 @@
-<tool id="build_protein_interaction_maps" name="Build Protein-Protein interaction network" version="2019.03.12.2">
+<tool id="build_protein_interaction_maps" name="Build Protein-Protein interaction network" version="2019.05.16">
 <description>[BioGRID, BioPlex, HuMAP]</description>
     <requirements>
     </requirements>
@@ -77,7 +77,9 @@
                     <option value="GeneID" >Entrez gene ID</option>
                 </param>
                 <param name="ref_file" type="select" label="Species">
-                    <options from_data_table="proteore_biogrid_dictionaries" />
+                    <options from_data_table="proteore_biogrid_dictionaries">
+                        <filter type="sort_by" column="0"/>
+                    </options>
                 </param>
             </when>
             <when value="bioplex">
@@ -86,7 +88,9 @@
                     <option value="GeneID">Entrez gene ID</option>
                 </param>
                 <param name="ref_file" type="select" label="Species">
-                    <options from_data_table="proteore_bioplex_dictionaries" />
+                    <options from_data_table="proteore_bioplex_dictionaries">
+                        <filter type="sort_by" column="0"/>
+                    </options>
                 </param>
             </when>
             <when value="humap">
@@ -94,7 +98,9 @@
                     <option value="GeneID" >Entrez gene ID</option>
                 </param>
                 <param name="ref_file" type="select" label="Species">
-                    <options from_data_table="proteore_humap_dictionaries" />
+                    <options from_data_table="proteore_humap_dictionaries">
+                        <filter type="sort_by" column="0"/>
+                    </options>
                 </param>
             </when>
         </conditional>
--- a/proteore_biogrid_dictionaries.loc.sample	Tue Mar 12 06:56:01 2019 -0400
+++ b/proteore_biogrid_dictionaries.loc.sample	Thu May 16 08:30:16 2019 -0400
@@ -1,4 +1,4 @@
-#id	name	species	value
-Human_biogrid_01-03-2019	Human (Homo sapiens) 01/03/2019	Human	tool-data/Human_biogrid_01-03-2019.json
-Mouse_biogrid_01-03-2019	Mouse (Mus musculus) 01/03/2019	Mouse	tool-data/Mouse_biogrid_01-03-2019.json
-Rat_biogrid_01-03-2019	Rat (Rattus norvegicus) 01/03/2019	Rat	tool-data/Rat_biogrid_01-03-2019.json
+#id	release name	species	value
+9979809699	Human_biogrid_01-03-2019	Human (Homo sapiens) 01/03/2019	Human	tool-data/Human_biogrid_01-03-2019.json
+9979809699	Mouse_biogrid_01-03-2019	Mouse (Mus musculus) 01/03/2019	Mouse	tool-data/Mouse_biogrid_01-03-2019.json
+9979809699	Rat_biogrid_01-03-2019	Rat (Rattus norvegicus) 01/03/2019	Rat	tool-data/Rat_biogrid_01-03-2019.json
--- a/proteore_bioplex_dictionaries.loc.sample	Tue Mar 12 06:56:01 2019 -0400
+++ b/proteore_bioplex_dictionaries.loc.sample	Thu May 16 08:30:16 2019 -0400
@@ -1,2 +1,2 @@
-#id	name	species	value
-Human_bioplex_01-03-2019	Human (Homo sapiens) 01/03/2019	Human	tool-data/Human_bioplex_01-03-2019.json
\ No newline at end of file
+#id	release name	species	value
+9979809699	Human_bioplex_01-03-2019	Human (Homo sapiens) 01/03/2019	Human	tool-data/Human_bioplex_01-03-2019.json
--- a/proteore_humap_dictionaries.loc.sample	Tue Mar 12 06:56:01 2019 -0400
+++ b/proteore_humap_dictionaries.loc.sample	Thu May 16 08:30:16 2019 -0400
@@ -1,2 +1,2 @@
-#id	name	species	value
-Human_humap_01-03-2019	Human (Homo sapiens) 01/03/2019	Human	tool-data/Human_humap_01-03-2019.json
\ No newline at end of file
+#id	release name	species	value
+9979809699	Human_humap_01-03-2019	Human (Homo sapiens) 01/03/2019	Human	tool-data/Human_humap_01-03-2019.json
--- a/tool_data_table_conf.xml.sample	Tue Mar 12 06:56:01 2019 -0400
+++ b/tool_data_table_conf.xml.sample	Thu May 16 08:30:16 2019 -0400
@@ -1,14 +1,14 @@
 <tables>
     <table name="proteore_biogrid_dictionaries" comment_char="#">
-        <columns>id, name, species, value</columns>
+        <columns>id, release, name, species, value</columns>
         <file path="tool-data/proteore_biogrid_dictionaries.loc" />
     </table>
     <table name="proteore_bioplex_dictionaries" comment_char="#">
-        <columns>id, name, species, value</columns>
+        <columns>id, release, name, species, value</columns>
         <file path="tool-data/proteore_bioplex_dictionaries.loc" />
     </table>
     <table name="proteore_humap_dictionaries" comment_char="#">
-        <columns>id, name, species, value</columns>
+        <columns>id, release,name, species, value</columns>
         <file path="tool-data/proteore_humap_dictionaries.loc" />
     </table>
 </tables>
\ No newline at end of file