Mercurial > repos > iuc > snpsift_dbnsfp

diff snpSift_dbnsfp.xml @ 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 4e21e4f2bc48
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">