Mercurial > repos > iuc > data_manager_primer_scheme_bedfiles

changeset 1:cce5d9327cd6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit c78a20041ead5aa639003db5311d7a0d88e204b6"
author iuc
date Fri, 24 Apr 2020 16:10:30 -0400
parents ae730ecdc7e7
children b3710e492ee4
files data_manager/install_primer_scheme_bedfiles.py data_manager/install_primer_scheme_bedfiles.xml tool-data/primer_scheme_bedfiles.loc.sample tool_data_table_conf.xml.sample
diffstat 4 files changed, 11 insertions(+), 11 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/install_primer_scheme_bedfiles.py	Sun Apr 19 09:22:19 2020 -0400
+++ b/data_manager/install_primer_scheme_bedfiles.py	Fri Apr 24 16:10:30 2020 -0400
@@ -17,9 +17,9 @@
 
 def fetch_artic_primers(output_directory, primers):
     primer_sets = {
-        "ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed",
-        "ARTICv2": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed",
-        "ARTICv3": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed",
+        "SARS-CoV-2-ARTICv1": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V1/nCoV-2019.bed",
+        "SARS-CoV-2-ARTICv2": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V2/nCoV-2019.bed",
+        "SARS-CoV-2-ARTICv3": "https://raw.githubusercontent.com/artic-network/artic-ncov2019/master/primer_schemes/nCoV-2019/V3/nCoV-2019.bed",
     }
 
     data = []
--- a/data_manager/install_primer_scheme_bedfiles.xml	Sun Apr 19 09:22:19 2020 -0400
+++ b/data_manager/install_primer_scheme_bedfiles.xml	Fri Apr 24 16:10:30 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.8" tool_type="manage_data" profile="19.05">
+<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.10" tool_type="manage_data" profile="19.05">
     <requirements>
         <requirement type="package">python</requirement>
         <requirement type="package" version="2.22.0">requests</requirement>
@@ -23,9 +23,9 @@
             </param>
             <when value="ARTIC">                    
                 <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch">
-                    <option value="ARTICv1" selected="true">ARTIC v1</option>
-                    <option value="ARTICv2" selected="true">ARTIC v2</option>
-                    <option value="ARTICv3" selected="true">ARTIC v3</option>
+                    <option value="SARS-CoV-2-ARTICv1" selected="true">SARS-CoV-2 ARTIC v1</option>
+                    <option value="SARS-CoV-2-ARTICv2" selected="true">SARS-CoV-2 ARTIC v2</option>
+                    <option value="SARS-CoV-2-ARTICv3" selected="true">SARS-CoV-2 ARTIC v3</option>
                 </param>
             </when>
             <when value="history">
@@ -42,7 +42,7 @@
     <tests>
         <test>
             <param name="input_type" value="ARTIC" />
-            <param name="primers" value="ARTICv1,ARTICv2,ARTICv3"/>
+            <param name="primers" value="SARS-CoV-2-ARTICv1,SARS-CoV-2-ARTICv2,SARS-CoV-2-ARTICv3"/>
             <output name="output_file">
                 <assert_contents>
                     <has_text text="ARTIC"/>
@@ -61,4 +61,4 @@
             </output>        
         </test>
     </tests>
-</tool>
\ No newline at end of file
+</tool>
--- a/tool-data/primer_scheme_bedfiles.loc.sample	Sun Apr 19 09:22:19 2020 -0400
+++ b/tool-data/primer_scheme_bedfiles.loc.sample	Fri Apr 24 16:10:30 2020 -0400
@@ -5,4 +5,4 @@
 # value  description path
 #
 # for example
-# ARTICv1   ARTIC v1 primers    /data/galaxy/tool_data/artic_primers/ARTICv1.bed
\ No newline at end of file
+# SARS-CoV-2-ARTICv1	SARS-CoV-2 ARTIC v1 primers	/data/galaxy/tool_data/artic_primers/SARS-CoV-2-ARTICv1.bed
--- a/tool_data_table_conf.xml.sample	Sun Apr 19 09:22:19 2020 -0400
+++ b/tool_data_table_conf.xml.sample	Fri Apr 24 16:10:30 2020 -0400
@@ -1,6 +1,6 @@
 <tables>
     <!-- Locations of primer scheme BED files -->
-    <table name="primer_scheme_bedfiles" comment_char="#">
+    <table name="primer_scheme_bedfiles" comment_char="#" allow_duplicate_entries="False">
         <columns>value, description, path</columns>
         <file path="tool-data/primer_scheme_bedfiles.loc" />
     </table>