Mercurial > repos > iuc > data_manager_snpeff

changeset 4:847b0f43c0e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_snpeff commit 8652f36a3a3838dca989426961561e81432acf4f
author iuc
date Tue, 04 Apr 2017 18:14:37 -0400
parents e5a471c4630e
children 3d9dd4b9fb09
files data_manager/data_manager_snpEff_databases.py data_manager/data_manager_snpEff_databases.xml data_manager/data_manager_snpEff_download.py data_manager/data_manager_snpEff_download.xml data_manager/snpEff_macros.xml tool_data_table_conf.xml.sample
diffstat 6 files changed, 41 insertions(+), 67 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/data_manager_snpEff_databases.py	Mon Oct 31 08:13:11 2016 -0400
+++ b/data_manager/data_manager_snpEff_databases.py	Tue Apr 04 18:14:37 2017 -0400
@@ -71,5 +71,6 @@
     # save info to json file
     open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
 
+
 if __name__ == "__main__":
     main()
--- a/data_manager/data_manager_snpEff_databases.xml	Mon Oct 31 08:13:11 2016 -0400
+++ b/data_manager/data_manager_snpEff_databases.xml	Tue Apr 04 18:14:37 2017 -0400
@@ -1,23 +1,20 @@
-<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
-    <description>Read the list of available snpEff databases</description>
-    <macros>
-        <import>snpEff_macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command><![CDATA[
-        @CONDA_SNPEFF_JAR_PATH@ &&
-        python '$__tool_directory__/data_manager_snpEff_databases.py' 
-            --jar_path '\$SNPEFF_JAR_PATH/snpEff.jar'
-            '$out_file'
-        ]]>
-    </command>
-    <inputs>
-    </inputs>
-    <outputs>
+<tool id="data_manager_snpeff_databases" name="SnpEff Databases" version="4.1.0" tool_type="manage_data">
+	<description>Read the list of available snpEff databases</description>
+	<requirements>
+		<requirement type="package" version="4.1">snpEff</requirement>
+	</requirements>
+        <stdio>
+          <exit_code range=":-1"  level="fatal"   description="Error: Cannot open file" />
+          <exit_code range="1:"  level="fatal"   description="Error" />
+        </stdio>
+	<command interpreter="python">
+        data_manager_snpEff_databases.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" "$out_file"
+        </command>
+	<inputs>
+	</inputs>
+	<outputs>
            <data name="out_file" format="data_manager_json"/>
-    </outputs>
+	</outputs>
         <tests>
             <test>
                 <output name="out_file">
@@ -28,7 +25,7 @@
                 </output>
             </test>
         </tests>
-    <help>
+	<help>
 
 This tool updatess the list of SnpEff databases for the SnpEff Download data manager.
 It should only need to be run once for a snpEff version, 
@@ -39,7 +36,9 @@
 Please cite:
 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
 
-    </help>
-    <expand macro="citations" />
+	</help>
+      <citations>
+        <citation type="doi">10.4161/fly.19695</citation>
+      </citations>
 </tool>
 
--- a/data_manager/data_manager_snpEff_download.py	Mon Oct 31 08:13:11 2016 -0400
+++ b/data_manager/data_manager_snpEff_download.py	Tue Apr 04 18:14:37 2017 -0400
@@ -196,5 +196,6 @@
     # save info to json file
     open( filename, 'wb' ).write( json.dumps( data_manager_dict ) )
 
+
 if __name__ == "__main__":
     main()
--- a/data_manager/data_manager_snpEff_download.xml	Mon Oct 31 08:13:11 2016 -0400
+++ b/data_manager/data_manager_snpEff_download.xml	Tue Apr 04 18:14:37 2017 -0400
@@ -1,17 +1,16 @@
-<tool id="data_manager_snpeff_download" name="SnpEff Download" version="@WRAPPER_VERSION@.0" tool_type="manage_data">
+<tool id="data_manager_snpeff_download" name="SnpEff Download" version="4.1.0" tool_type="manage_data">
     <description>Download a new database</description>
-    <macros>
-        <import>snpEff_macros.xml</import>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command><![CDATA[
-        @CONDA_SNPEFF_JAR_PATH@ &&
-        python $__tool_directory__/data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
+    <requirements>
+        <requirement type="package" version="4.1">snpEff</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
+        <exit_code range="1:" level="fatal" description="Error" />
+    </stdio>
+    <command interpreter="python">
+        data_manager_snpEff_download.py --jar_path "\$SNPEFF_JAR_PATH/snpEff.jar" --config "\$SNPEFF_JAR_PATH/snpEff.config"
           --genome_version "$genome_version" "$out_file"
-        ]]>
-    </command>
+        </command>
     <inputs>
         <param name="genome_version" type="text" value="" label="Snpff Genome Version Name (e.g. GRCh38.76)">
             <help>https://snpeff-data.galaxyproject.org/databases/</help>
@@ -50,6 +49,8 @@
 "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.", Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM. Fly (Austin). 2012 Apr-Jun;6(2):80-92. PMID: 22728672 [PubMed - in process]
 
     </help>
-    <expand macro="citations" />
+      <citations>
+        <citation type="doi">10.4161/fly.19695</citation>
+      </citations>
 </tool>
 
--- a/data_manager/snpEff_macros.xml	Mon Oct 31 08:13:11 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-<macros>
-    <xml name="requirements">
-        <requirements>
-            <requirement type="package" version="4.1">snpEff</requirement>
-        </requirements>
-    </xml>
-  <xml name="stdio">
-    <stdio>
-        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
-        <exit_code range="1:"  level="fatal" description="Error" />
-    </stdio>
-  </xml>
-  <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
-  <xml name="version_command">
-    <version_command><![CDATA[
-    if [ -z "$SNPEFF_JAR_PATH" ]; then
-        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
-    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
-    ]]></version_command>
-  </xml>
-  <token name="@WRAPPER_VERSION@">4.1</token>
-  <xml name="citations">
-      <citations>
-        <citation type="doi">10.4161/fly.19695</citation>
-        <yield />
-      </citations>
-  </xml>
-</macros>
--- a/tool_data_table_conf.xml.sample	Mon Oct 31 08:13:11 2016 -0400
+++ b/tool_data_table_conf.xml.sample	Tue Apr 04 18:14:37 2017 -0400
@@ -1,17 +1,17 @@
 <tables>
-    <table name="snpeffv_genomedb" comment_char="#">
+    <table name="snpeffv_genomedb" comment_char="#" allow_duplicate_entries="False">
         <columns>key, version, value, name, path</columns>
         <file path="tool-data/snpeffv_genomedb.loc" />
     </table>
-    <table name="snpeffv_regulationdb" comment_char="#">
+    <table name="snpeffv_regulationdb" comment_char="#" allow_duplicate_entries="False">
         <columns>key, version, genome, value, name</columns>
         <file path="tool-data/snpeffv_regulationdb.loc" />
     </table>
-    <table name="snpeffv_annotations" comment_char="#">
+    <table name="snpeffv_annotations" comment_char="#" allow_duplicate_entries="False">
         <columns>key, version, genome, value, name</columns>
         <file path="tool-data/snpeffv_annotations.loc" />
     </table>
-    <table name="snpeffv_databases" comment_char="#">
+    <table name="snpeffv_databases" comment_char="#" allow_duplicate_entries="False">
         <columns>key, version, value, name</columns>
         <file path="tool-data/snpeffv_databases.loc" />
     </table>