--- a/ivar_variants.xml	Wed Jul 13 15:16:43 2022 +0000
+++ b/ivar_variants.xml	Wed Jan 11 09:53:09 2023 +0000
@@ -1,28 +1,29 @@
-<tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy2">
+<tool id="ivar_variants" name="ivar variants" version="@TOOL_VERSION@+galaxy3" profile="@PROFILE@">
     <description>Call variants from aligned BAM file</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="3">python</requirement>
-    </expand>
-    <expand macro="version_command" />
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
         ln -s '$ref' ref.fa &&
         ln -s '$input_bam' sorted.bam &&
-        samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants 
+        samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants
         -p variants
         -q $min_qual
-        -t $min_freq 
+        -t $min_freq
         #if str($output_format.choice) == "tabular" or str($output_format.choice) == "tabular_and_vcf"
-            && cp variants.tsv '$output_variants_tabular'
+            #if str($gtf) != 'None':
+                -r ref.fa
+                -g '$gtf'
+            #end if
         #end if
-        #if str($output_format.choice) == 'vcf' or str($output_format.choice) == "tabular_and_vcf"
-            && python '${__tool_directory__}/ivar_variants_to_vcf.py' 
+        #if str($output_format.choice) == "vcf" or str($output_format.choice) == "tabular_and_vcf"
+            && python '${__tool_directory__}/ivar_variants_to_vcf.py'
             ${output_format.pass_only}
-            variants.tsv '$output_variants_vcf'
+            variants.tsv variants.vcf
         #end if
-    ]]>    </command>
+    ]]></command>
     <inputs>
         <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/>
         <param name="ref" type="data" format="fasta" label="Reference"/>
@@ -35,74 +36,95 @@
                 <option value="tabular_and_vcf">Both Tabular and VCF</option>
             </param>
             <when value="vcf">
-                <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" />
+                <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters"/>
             </when>
             <when value="tabular_and_vcf">
-                <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters" />
+                <param argument="--pass_only" type="boolean" truevalue="--pass_only" falsevalue="" label="In VCF only output variants that PASS all filters"/>
+                <param name="gtf" argument="-g" optional="true" type="data" format="gff" label="Coordinates of ORFs for optional variant effect prediction" help="Provide a GFF3 dataset with annotated ORFs to have the rightmost 5 columns of the tabular output populated with mutation information at the residue level. This has no effect on the VCF output."/>
             </when>
-            <when value="tabular" />
-        </conditional>    
+            <when value="tabular">
+                <param name="gtf" argument="-g" optional="true" type="data" format="gff" label="Coordinates of ORFs for optional variant effect prediction" help="Provide a GFF3 dataset with annotated ORFs to have the rightmost 5 columns of the tabular output populated with mutation information at the residue level."/>
+            </when>
+        </conditional>
     </inputs>
     <outputs>
-        <data name="output_variants_tabular" format="tabular" label="${tool.name} tabular output on ${on_string}">
+        <data name="output_variants_tabular" from_work_dir="./variants.tsv" format="tabular" label="${tool.name} tabular output on ${on_string}">
             <filter>output_format['choice'] == 'tabular' or output_format['choice'] == 'tabular_and_vcf'</filter>
             <actions>
-                <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA" />
+                <action name="column_names" type="metadata" default="REGION,POS,REF,ALT,REF_DP,REF_RV,REF_QUAL,ALT_DP,ALT_RV,ALT_QUAL,ALT_FREQ,TOTAL_DP,PVAL,PASS,GFF_FEATURE,REF_CODON,REF_AA,ALT_CODON,ALT_AA"/>
             </actions>
         </data>
-        <data name="output_variants_vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
+        <data name="output_variants_vcf" from_work_dir="./variants.vcf" format="vcf" label="${tool.name} VCF on ${on_string}">
             <filter>output_format['choice'] == 'vcf' or output_format['choice'] == 'tabular_and_vcf'</filter>
         </data>
     </outputs>
     <tests>
         <test expect_num_outputs="1">
-            <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" />
-            <param name="ref" value="zika/db/PRV.fa" />
-            <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/>
+            <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
+            <param name="ref" value="zika/db/PRV.fa"/>
+            <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular"/>
         </test>
         <test expect_num_outputs="1">
-            <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" />
-            <param name="ref" value="zika/db/PRV.fa" />
+            <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
+            <param name="ref" value="zika/db/PRV.fa"/>
             <conditional name="output_format">
-                <param name="choice" value="vcf" />
+                <param name="choice" value="vcf"/>
             </conditional>
             <output name="output_variants_vcf" file="zika/Z52_a.vcf" ftype="vcf"/>
         </test>
         <test expect_num_outputs="2">
-            <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" />
-            <param name="ref" value="zika/db/PRV.fa" />
+            <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
+            <param name="ref" value="zika/db/PRV.fa"/>
             <conditional name="output_format">
-                <param name="choice" value="tabular_and_vcf" />
-                <param name="pass_only" value="true" />
+                <param name="choice" value="tabular_and_vcf"/>
+                <param name="pass_only" value="true"/>
             </conditional>
-            <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="10"/>
+            <output name="output_variants_tabular" file="zika/Z52_a.tsv" ftype="tabular" lines_diff="6"/>
             <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/>
         </test>
-
+        <test expect_num_outputs="1">
+            <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
+            <param name="ref" value="zika/db/PRV.fa"/>
+            <param name="gtf" value="zika/db/PRV.gff"/>
+            <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/>
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input_bam" value="zika/Z52_a.masked.sorted.bam"/>
+            <param name="ref" value="zika/db/PRV.fa"/>
+            <param name="gtf" value="zika/db/PRV.gff"/>
+            <conditional name="output_format">
+                <param name="choice" value="tabular_and_vcf"/>
+                <param name="pass_only" value="true"/>
+            </conditional>
+            <output name="output_variants_tabular" file="zika/Z52_a_annotated.tsv" ftype="tabular"/>
+            <output name="output_variants_vcf" file="zika/Z52_a_pass.vcf" ftype="vcf"/>
+        </test>
     </tests>
     <help><![CDATA[
-        iVar uses the output of the samtools mpileup command to call variants -
-        single nucleotide variants(SNVs) and indels. In order to call variants
-        correctly, the reference file used for alignment must be passed to iVar
-        using the -r flag. The output of samtools pileup is piped into ivar variants
-        to generate a .tsv file with the variants. There are two parameters that can
-        be set for variant calling using iVar - minimum quality(Default: 20) and
-        minimum frequency(Default: 0.03). Minimum quality is the minimum quality for
-        a base to be counted towards the ungapped depth to canculate iSNV frequency
-        at a given position. For insertions, the quality metric is discarded and the
-        mpileup depth is used directly. Minimum frequency is the minimum frequency
-        required for a SNV or indel to be reported.
-        
-        Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
+iVar uses the output of the samtools mpileup command to call variants -
+single nucleotide variants(SNVs) and indels. In order to call variants
+correctly, the reference file used for alignment must be passed to iVar
+using the -r flag. The output of samtools pileup is piped into ivar variants
+to generate a .tsv file with the variants. There are two parameters that can
+be set for variant calling using iVar - minimum quality(Default: 20) and
+minimum frequency(Default: 0.03). Minimum quality is the minimum quality for
+a base to be counted towards the ungapped depth to canculate iSNV frequency
+at a given position. For insertions, the quality metric is discarded and the
+mpileup depth is used directly. Minimum frequency is the minimum frequency
+required for a SNV or indel to be reported.
 
-        Optionally output is converted to VCF using a version of the `ivar_variants_to_vcf.py script <https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py>`_,
-        that has been modified to store attributes in INFO fields.
-    ]]>    </help>
+Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_.
+
+Optionally output is converted to VCF using a version of the
+`ivar_variants_to_vcf.py script <https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py>`_,
+that has been modified to store attributes in INFO fields.
+    ]]></help>
     <expand macro="citations">
         <citation type="bibtex">@misc{githubivar_variants_to_vcf,
             author = {Fernandez, Sarai Varona and Patel, Harshil},
             year = {2021},
             title = {ivar_variants_to_vcf},
             url = {https://github.com/nf-core/viralrecon/blob/dev/bin/ivar_variants_to_vcf.py}
-        }</citation>    </expand>
+        }</citation>
+    </expand>
 </tool>