Mercurial > repos > iuc > snpsift_dbnsfp

changeset 2:c838e7136a40 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_dbnsfp commit d12355cea76843e3ed6f09d96c3e9fe22afe4a4f
author iuc
date Mon, 05 Dec 2016 12:06:13 -0500
parents 13191d4914f7
children 563d1bdb7b80
files snpSift_dbnsfp.xml snpSift_macros.xml tool_dependencies.xml
diffstat 3 files changed, 16 insertions(+), 26 deletions(-) [+]
line wrap: on
line diff
--- a/snpSift_dbnsfp.xml	Tue Jun 07 10:04:48 2016 -0400
+++ b/snpSift_dbnsfp.xml	Mon Dec 05 12:06:13 2016 -0500
@@ -1,4 +1,4 @@
-<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.0">
+<tool id="snpSift_dbnsfp" name="SnpSift dbNSFP" version="@WRAPPER_VERSION@.1">
     <description>Add Annotations from dbNSFP or similar annotation DBs</description>
     <macros>
         <import>snpSift_macros.xml</import>
@@ -7,7 +7,8 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        java -Xmx6G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" dbnsfp -v
+        @CONDA_SNPSIFT_JAR_PATH@ &&
+        java -Xmx6G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp -v
         #if $db.dbsrc == 'cached':
           -db "$db.dbnsfp"
           #if $db.annotations and str($db.annotations) != '':
@@ -60,17 +61,21 @@
         <data format="vcf" name="output" />
     </outputs>
     <tests>
+        <!-- This cannot be tested at the moment because test_dbnsfpdb.tabular
+             is converted from dbnsfp.tabular to snpsiftdbnsfp format on-the-fly
+             when this tool is run and annotation metadata is not available
+             until after the conversion is completed.
         <test>
-            <param name="input" ftype="vcf" value="test_annotate_in.vcf.vcf"/>
+            <param name="input" ftype="vcf" value="test_annotate_in.vcf"/>
             <param name="dbsrc" value="history"/>
             <param name="dbnsfpdb" value="test_dbnsfpdb.tabular" ftype="dbnsfp.tabular" />
-            <annotations value="aaref,aaalt,genename,aapos,SIFT_score"/>
+            <param name="annotations" value="aaref,aaalt,genename,aapos,SIFT_score"/>
             <output name="output">
                 <assert_contents>
                     <has_text text="dbNSFP_SIFT_score=0.15" />
                 </assert_contents>
             </output>
-        </test>
+        </test> -->
     </tests>
     <help><![CDATA[
 
@@ -279,9 +284,6 @@
 
 @EXTERNAL_DOCUMENTATION@
 	http://snpeff.sourceforge.net/SnpSift.html#dbNSFP
-
-@CITATION_SECTION@
-
 ]]>
     </help>
     <expand macro="citations">
--- a/snpSift_macros.xml	Tue Jun 07 10:04:48 2016 -0400
+++ b/snpSift_macros.xml	Mon Dec 05 12:06:13 2016 -0500
@@ -1,7 +1,7 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1">snpEff</requirement>
+            <requirement type="package" version="4.1">snpsift</requirement>
         </requirements>
     </xml>
   <xml name="stdio">
@@ -10,8 +10,12 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
+  <token name="@CONDA_SNPSIFT_JAR_PATH@">if [ -z "\$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=\$(dirname \$(readlink -e \$(which SnpSift))); fi</token>
   <xml name="version_command">
-    <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command>
+    <version_command><![CDATA[
+    if [ -z "$SNPSIFT_JAR_PATH" ]; then export SNPSIFT_JAR_PATH=$(dirname $(readlink -e $(which SnpSift))); fi &&
+    java -jar "$SNPSIFT_JAR_PATH/SnpSift.jar" dbnsfp 2>&1|head -n 1
+    ]]></version_command>
   </xml>
   <token name="@WRAPPER_VERSION@">4.1</token>
   <token name="@EXTERNAL_DOCUMENTATION@">
@@ -20,16 +24,6 @@
 	http://snpeff.sourceforge.net/SnpEff_manual.html
 
   </token>
-  <token name="@CITATION_SECTION@">------
-
-**Citation**
-
-For the underlying tool, please cite the following two publications:
-
-SnpSift citation:
-"Using Drosophila melanogaster as a model for genotoxic chemical mutational studies with a new program, SnpSift", Cingolani, P., et. al., Frontiers in Genetics, 3:35, 2012.
-
-  </token>
   <xml name="citations">
       <citations>
         <citation type="doi">10.3389/fgene.2012.00035</citation>
--- a/tool_dependencies.xml	Tue Jun 07 10:04:48 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="snpEff" version="4.1">
-        <repository changeset_revision="374c7f8421fb" name="package_snpeff_4_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>