Mercurial > repos > iuc > snpeff

diff snpEff.xml @ 30:0c8a8cd9dd5b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd
author iuc
date Sat, 28 Sep 2024 16:27:42 +0000
parents 4c790901c495
children b7029a54f73e
line wrap: on
line diff
--- a/snpEff.xml	Wed Aug 03 16:33:10 2022 +0000
+++ b/snpEff.xml	Sat Sep 28 16:27:42 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy1">
+<tool id="snpEff" name="SnpEff eff:" version="@WRAPPER_VERSION@.galaxy2">
     <description> annotate variants</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -9,6 +9,9 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
+        #if $intervals 
+            ln -s '${intervals}' intervals.bed &&
+        #end if 
         snpEff @JAVA_OPTIONS@ eff
         -i $inputFormat -o ${outputConditional.outputFormat} -upDownStreamLen $udLength
         #if $spliceSiteSize and str($spliceSiteSize) != '':
@@ -42,7 +45,7 @@
           -onlyTr '$transcripts'
         #end if
         #if $intervals     ### fix this for multiple dataset input
-          -interval '$intervals'
+          -interval intervals.bed
         #end if
         #if $statsFile:
           -stats '$statsFile'
@@ -156,9 +159,6 @@
             </when>
             <when value="history">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
-                    <options options_filter_attribute="metadata.snpeff_version" >
-                        <filter type="add_value" value="@SNPEFF_VERSION@" />
-                    </options>
                     <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
                 <section name="reg_section" expanded="false" title="Regulation options">
@@ -178,9 +178,6 @@
             </when>
             <when value="custom">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
-                    <options options_filter_attribute="metadata.snpeff_version" >
-                        <filter type="add_value" value="@SNPEFF_VERSION@" />
-                    </options>
                     <validator type="expression" message="This version of SnpEff will only work with @SNPEFF_VERSION@ genome databases">value is not None and value.metadata.snpeff_version == "@SNPEFF_VERSION@"</validator>
                 </param>
                 <param name="codon_table" type="select" label="Select genetic code for this sequence" help="If this sequence uses non-standard genetic code, select one from these options">
@@ -361,27 +358,56 @@
             </change_format>
         </data>
         <data name="statsFile" format="html" label="${tool.name} on ${on_string} - HTML stats">
-            <filter>generate_stats == True</filter>
+            <filter>generate_stats</filter>
         </data>
         <data name="csvFile" format="csv" label="${tool.name} on ${on_string} - CSV stats">
-            <filter>csvStats == True</filter>
+            <filter>csvStats</filter>
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="input" ftype="vcf" value="input.vcf"/>
             <param name="inputFormat" value="vcf"/>
             <param name="outputFormat" value="vcf"/>
             <param name="genomeSrc" value="named"/>
             <param name="genome_version" value="ebola_zaire"/>
             <param name="udLength" value="0"/>
-            <param name="generate_stats" value="false"/>
+            <param name="generate_stats" value="true"/>
             <output name="snpeff_output">
                 <assert_contents>
                     <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
                     <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
                 </assert_contents>
             </output>
+            <output name="statsFile">
+                <assert_contents>
+                    <has_text text="&lt;b&gt;"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- Test interval option-->
+        <test expect_num_outputs="2">
+            <param name="input" ftype="vcf" value="input.vcf"/>
+            <param name="inputFormat" value="vcf"/>
+            <param name="outputFormat" value="vcf"/>
+            <param name="genomeSrc" value="named"/>
+            <param name="interval" value="intervals.bed"/>
+            <param name="genome_version" value="ebola_zaire"/>
+            <param name="udLength" value="0"/>
+            <param name="generate_stats" value="false"/>
+            <param name="csvStats" value="true"/>
+            <output name="snpeff_output">
+                <assert_contents>
+                    <has_text_matching expression="KJ660346\t572\t.*missense_variant" />
+                    <has_text_matching expression="KJ660346\t1024\t.*synonymous_variant" />
+                </assert_contents>
+            </output>
+            <output name="csvFile">
+                <assert_contents>
+                    <has_n_lines n="185"/>
+                    <has_n_columns n="1" sep=","/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[