Mercurial > repos > iuc > snpsift_genesets

changeset 5:d12a810c837e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift_genesets/ commit fbc18d9128669e461e76ed13307ee88dd774afa5
author iuc
date Mon, 12 Jun 2017 10:25:57 -0400
parents ea2e7d299365
children
files snpSift_geneSets.xml snpSift_macros.xml
diffstat 2 files changed, 42 insertions(+), 45 deletions(-) [+]
line wrap: on
line diff
--- a/snpSift_geneSets.xml	Mon Dec 19 11:57:27 2016 -0500
+++ b/snpSift_geneSets.xml	Mon Jun 12 10:25:57 2017 -0400
@@ -1,6 +1,6 @@
-<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.1">
+<tool id="snpSift_geneSets" name="SnpSift GeneSets" version="@WRAPPER_VERSION@.0">
     <description>Annotating GeneSets, such as Gene Ontology, KEGG, Reactome</description>
-    <!-- 
+    <!--
         You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory)
     -->
     <macros>
@@ -10,22 +10,22 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
-        @CONDA_SNPSIFT_JAR_PATH@ &&
-        java -Xmx2G -jar "\$SNPSIFT_JAR_PATH/SnpSift.jar" geneSets -v
-        #if $db_opts.db_opts_selector == "db"
-          "${db_opts.database.fields.path}"
-        #elif $db_opts.db_opts_selector == "histdb"
-          "$db_opts.histdb"
-        #end if
-        "$input" 2> "$log" > "$output"
-]]>
-    </command>
+SnpSift -Xmx2G geneSets -v
+#if $db_opts.db_opts_selector == 'db'
+    '${db_opts.database.fields.path}'
+#elif $db_opts.db_opts_selector == 'histdb'
+    '$db_opts.histdb'
+#end if
+'$input'
+2> '$log'
+> '$output'
+    ]]></command>
     <inputs>
-        <param format="vcf" name="input" type="data" label="Variant input file in VCF format"/>
+        <param name="input" type="data" format="vcf" label="Variant input file in VCF format"/>
         <conditional name="db_opts">
             <param name="db_opts_selector" type="select" label="Select Annotation database" help="">
-              <option value="db" selected="True">Locally installed database</option>
-              <option value="histdb">database from your history</option>
+                <option value="db" selected="True">Locally installed database</option>
+                <option value="histdb">database from your history</option>
             </param>
             <when value="db">
                 <param name="database" type="select" label="Molecular Signatures Database (MSigDB)">
@@ -39,8 +39,8 @@
         </conditional>
     </inputs>
     <outputs>
-        <data format="vcf" name="output" label="${tool.name} on ${on_string}: VCF" />
-        <data format="txt" name="log" label="${tool.name} on ${on_string}: log" />
+        <data name="output" format="vcf" label="${tool.name} on ${on_string}: VCF" />
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: log" />
     </outputs>
     <tests>
     </tests>
@@ -56,8 +56,7 @@
 @EXTERNAL_DOCUMENTATION@
 
 .. _MSigDB: http://www.broadinstitute.org/gsea/msigdb/
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations">
         <citation type="doi">10.1073/pnas.0506580102</citation><!-- MSigDB citation -->
     </expand>
--- a/snpSift_macros.xml	Mon Dec 19 11:57:27 2016 -0500
+++ b/snpSift_macros.xml	Mon Jun 12 10:25:57 2017 -0400
@@ -1,33 +1,31 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="4.1">snpsift</requirement>
+            <requirement type="package" version="4.3.1p">snpsift</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_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><![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@">
+    <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_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><![CDATA[
+SnpSift dbnsfp 2>&1|head -n 1
+        ]]></version_command>
+    </xml>
+    <token name="@WRAPPER_VERSION@">4.3</token>
+    <token name="@EXTERNAL_DOCUMENTATION@">
+For details about this tool, please go to:
 
-For details about this tool, please go to:
-	http://snpeff.sourceforge.net/SnpEff_manual.html
-
-  </token>
-  <xml name="citations">
-      <citations>
-        <citation type="doi">10.3389/fgene.2012.00035</citation>
-        <yield />
-      </citations>
-  </xml>
+- http://snpeff.sourceforge.net/SnpEff_manual.html
+    </token>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.3389/fgene.2012.00035</citation>
+            <yield />
+        </citations>
+    </xml>
 </macros>