Mercurial > repos > gga > tripal_analysis_load_go

changeset 3:60d3281859a0 draft

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planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/tripal commit d21999bb3e142fd972a3338b70216989a257d5b1
author gga
date Mon, 06 Aug 2018 04:43:30 -0400
parents 976020e5c924
children 590495cec185
files analysis_load_go.xml macros.xml
diffstat 2 files changed, 21 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/analysis_load_go.xml	Thu Jun 21 08:47:37 2018 -0400
+++ b/analysis_load_go.xml	Mon Aug 06 04:43:30 2018 -0400
@@ -5,6 +5,7 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
+    <code file="tripal.py"/>
     <expand macro="stdio"/>
     <command><![CDATA[
         tmp_dir=`mktemp -d -p "@DATA_DIR@"` && chmod a+rx "\${tmp_dir}"
@@ -19,9 +20,21 @@
 
         tripaille analysis load_go
 
+            --organism_id '${organism}'
+
             @ANALYSIS@
 
-            @MATCHING@
+            #if str($matching.query_re):
+                --re_name '${matching.query_re}'
+            #end if
+
+            #if $matching.query_uniquename:
+                --query_matching 'uniquename'
+            #else
+                --query_matching 'uniquename'
+            #end if
+
+            --query_type '$matching.query_type'
 
             "\${tmp_dir}/blast2go.gaf"
 
@@ -35,6 +48,11 @@
                format="txt"
                label="Blast2Go results (GAF file)" />
 
+        <param argument="--organism"
+               type="select"
+               dynamic_options="list_organisms()"
+               label="Organism" />
+
         <expand macro="matching"/>
         <expand macro="analysis" />
         <expand macro="wait_for"/>
--- a/macros.xml	Thu Jun 21 08:47:37 2018 -0400
+++ b/macros.xml	Mon Aug 06 04:43:30 2018 -0400
@@ -2,7 +2,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.0.4">python-tripal</requirement>
+            <requirement type="package" version="3.0">python-tripal</requirement>
             <yield/>
         </requirements>
     </xml>
@@ -15,7 +15,7 @@
         </stdio>
     </xml>
 
-    <token name="@WRAPPER_VERSION@">2.0.4</token>
+    <token name="@WRAPPER_VERSION@">3.0</token>
 
     <xml name="citation">
         <citations>