# HG changeset patch
# User iuc
# Date 1727540862 0
# Node ID 0c8a8cd9dd5baff3e07abeaec04dc53e6b24250b
# Parent  030fe29d4c47a5db9e4170c79804b530ff50fcdc
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 4bc3ef84687aa6a39f79c2497a5800a9718825cd

diff -r 030fe29d4c47 -r 0c8a8cd9dd5b snpEff.xml
--- 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[
diff -r 030fe29d4c47 -r 0c8a8cd9dd5b snpEff_create_db.xml
--- a/snpEff_create_db.xml	Wed Aug 03 16:33:10 2022 +0000
+++ b/snpEff_create_db.xml	Sat Sep 28 16:27:42 2024 +0000
@@ -1,4 +1,4 @@
-<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy5">
+<tool id="snpEff_build_gb" name="SnpEff build:" version="@WRAPPER_VERSION@.galaxy6" profile="22.01">
     <description> database from Genbank or GFF record</description>
     <macros>
         <import>snpEff_macros.xml</import>
@@ -14,25 +14,26 @@
             python3 '$__tool_directory__/gbk2fa.py' '${input_type.input}' '${output_fasta}' ${input_type.remove_version} &&
         #end if
 
-        mkdir -p '${snpeff_output.files_path}'/'${genome_version}' &&
+        mkdir -p '${snpeff_output.files_path}/${genome_version}' &&
+        mkdir -p snpeff_output/'${genome_version}' &&
 
         #if str($input_type.input_type_selector) == "gb":
             #if $input_type.input.is_of_type("genbank"):
-                ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk' &&
+                ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.gbk' &&
             #elif $input_type.input.is_of_type("genbank.gz"):
-                ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.gbk.gz' &&
+                ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.gbk.gz' &&
             #end if
         #else:
             #if $input_type.reference_source.reference_source_selector == "history":
                 #if $input_type.reference_source.input_fasta.is_of_type("fasta"):
-                    ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' &&
+                    ln -s '${input_type.reference_source.input_fasta}' 'snpeff_output/${genome_version}/sequences.fa' &&
                 #elif $input_type.reference_source.input_fasta.is_of_type("fasta.gz"):
-                    ln -s '${input_type.reference_source.input_fasta}' '${snpeff_output.files_path}/${genome_version}/sequences.fa.gz' &&
+                    ln -s '${input_type.reference_source.input_fasta}' 'snpeff_output/${genome_version}/sequences.fa.gz' &&
                 #end if
             #elif $input_type.reference_source.reference_source_selector == "cached":
-                ln -s '${input_type.reference_source.ref_file.fields.path}' '${snpeff_output.files_path}/${genome_version}/sequences.fa' &&
+                ln -s '${input_type.reference_source.ref_file.fields.path}' 'snpeff_output/${genome_version}/sequences.fa' &&
             #end if
-            ln -s '${input_type.input}' '${snpeff_output.files_path}/${genome_version}/genes.${input_type.input_type_selector}' &&
+            ln -s '${input_type.input}' 'snpeff_output/${genome_version}/genes.${input_type.input_type_selector}' &&
         #end if
 
         snpEff @JAVA_OPTIONS@ build -v
@@ -45,7 +46,8 @@
         #elif str($input_type.input_type_selector) == "gtf":
             -gtf22
         #end if
-        -dataDir '${snpeff_output.files_path}' '${genome_version}' &&
+        -dataDir "\$(pwd)/snpeff_output" '${genome_version}' &&
+        mv snpeff_output/'${genome_version}'/*.bin '${snpeff_output.files_path}/${genome_version}' &&
         echo '${genome_version}.genome : ${genome_version}' >> '${snpeff_output.files_path}'/snpEff.config &&
         echo '${genome_version}.codonTable : ${codon_table}' >> '${snpeff_output.files_path}'/snpEff.config
     ]]></command>
@@ -122,7 +124,7 @@
         </data>
     </outputs>
     <tests>
-        <test>
+        <test expect_num_outputs="2">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gb"/>
             <param name="input" value="pBR322.gbk" />
@@ -133,7 +135,7 @@
             </output>
             <output name="output_fasta" value="pBR322_test1.fna"/>
         </test>
-        <test>
+        <test expect_num_outputs="2">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gb"/>
             <param name="input" value="pBR322.gbk.gz" />
@@ -144,7 +146,7 @@
             </output>
             <output name="output_fasta" value="pBR322_test1.fna"/>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gff"/>
             <param name="reference_source_selector" value="history"/>
@@ -156,7 +158,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="pBR322"/>
             <param name="input_type_selector" value="gff"/>
             <param name="reference_source_selector" value="history"/>
@@ -168,7 +170,7 @@
                 </assert_contents>
             </output>
         </test>
-        <test>
+        <test expect_num_outputs="1">
             <param name="genome_version" value="Saccharomyces_mito"/>
             <param name="input_type_selector" value="gtf"/>
             <param name="reference_source_selector" value="history"/>
diff -r 030fe29d4c47 -r 0c8a8cd9dd5b snpeff_get_chr_names.xml
--- a/snpeff_get_chr_names.xml	Wed Aug 03 16:33:10 2022 +0000
+++ b/snpeff_get_chr_names.xml	Sat Sep 28 16:27:42 2024 +0000
@@ -50,9 +50,6 @@
             <when value="history">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <help>This can only be used on databases in your history that were downloaded using the snpEff download tool.</help>
-                    <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>
             </when>
@@ -65,9 +62,6 @@
             <when value="custom">
                 <param name="snpeff_db" type="data" format="snpeffdb" label="@SNPEFF_VERSION@ Genome Data">
                     <help>This can only be used on databases in your history that were created using the snpEff build tool.</help>
-                    <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>
             </when>
diff -r 030fe29d4c47 -r 0c8a8cd9dd5b test-data/intervals.bed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/intervals.bed	Sat Sep 28 16:27:42 2024 +0000
@@ -0,0 +1,2 @@
+chr13	32889617	32973809
+chr17	41196312	41277500