diff variant.xml @ 10:9fb055604648 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 0faf0ade3f13d7c78d93869823ea9fdf25c21b13"

--- a/variant.xml	Mon Mar 29 20:05:39 2021 +0000
+++ b/variant.xml	Thu Apr 22 20:25:35 2021 +0000
@@ -1,12 +1,10 @@
 <?xml version="1.0"?>
-<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy7" profile="@PROFILE@">
+<tool id="medaka_variant" name="medaka variant tool" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
     <description>Probability decoding</description>
     <macros>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements">
-        <requirement type="package" version="1.4.1">scipy</requirement>
-    </expand>
+    <expand macro="requirements"/>
 
     <expand macro="version_command"/>
 
@@ -39,13 +37,14 @@
         --regions '${regions}'
     #end if
     $verbose
+    ${ambig_ref}
+    ${gvcf}
     ## required
     reference.fa
     #for $current in $pool.inputs
         '$current'
     #end for
     '$out_result' ## output
-
     2>&1 | tee '$out_log'
 #elif $pool.pool_mode == "No":
     ## run
@@ -56,26 +55,27 @@
         --regions '${regions}'
     #end if
     $verbose
+    ${ambig_ref}
+    ${gvcf}
     ## required
     reference.fa
     '$pool.input'
     '$out_result' ##output
     2>&1 | tee '$out_log'
 #end if
-
 #if $out_annotated:
     ## medaka annotate errors out if the reference is lower case at a position it's annotating because it checks vs the ref base in the vcf
     && python '$convert_fasta' reference.fa  upper_reference.fa
     && ln -s '$output_annotated.in_bam' in.bam
     && ln -s '$output_annotated.in_bam.metadata.bam_index' in.bai
-    && medaka tools annotate --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf
-    && '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated'
+    && medaka tools annotate --dpsp --pad $output_annotated.pad '$out_result' upper_reference.fa in.bam tmp.vcf
+    && python '$__tool_directory__/convert_VCF_info_fields.py' tmp.vcf '$out_annotated'
 #end if
     ]]></command>
     <inputs>
         <conditional name="pool">
             <param name="pool_mode"  type="select" label="Are you pooling HDF5 datasets?">
-                <option value="No" selected="True">No</option>
+                <option value="No" selected="true">No</option>
                 <option value="Yes">Yes</option>
             </param>
             <when value="Yes">
@@ -96,6 +96,8 @@
             </sanitizer>
         </param>
         <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
+        <param argument="--ambig_ref" type="boolean" truevalue="--ambig_ref" falsevalue="" label="Decode variants at ambiguous reference positions?" checked="false"/>
+        <param argument="--gvcf" type="boolean" truevalue="--gvcf" falsevalue="" label="Output VCF records for reference loci predicted to be non-variant?" checked="false"/>
         <conditional name="output_annotated">
             <param name="output_annotated_select" type="select" label="Output annotated VCF?" help="Annotate allele frequency, depth of coverage, etc for each variant (requires BAM file)">
                 <option value="true" selected="true">Output annotated VCF</option>
@@ -129,8 +131,9 @@
             </conditional>
             <conditional name="reference_source">
                 <param name="reference_source_selector" value="history"/>
-                <param name="ref_file" value="ref.fasta"/>
+                <param name="ref_file" value="ref.fasta.gz"/>
             </conditional>
+            <param name="ambig_ref" value="true"/>
             <conditional name="output_annotated">
                 <param name="output_annotated_select" value="true"/>
                 <param name="in_bam" value="medaka_test.bam"/>
@@ -146,7 +149,7 @@
             </output>
             <output name="out_annotated">
                 <assert_contents>
-                    <has_n_lines n="22"/>
+                    <has_n_lines n="23"/>
                     <has_line line="##fileformat=VCFv4.1" />
                     <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                     <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />
@@ -168,6 +171,7 @@
                 <param name="reference_source_selector" value="history"/>
                 <param name="ref_file" value="ref.fasta.gz" ftype="fasta.gz"/>
             </conditional>
+            <param name="ambig_ref" value="true"/>
             <conditional name="output_annotated">
                 <param name="output_annotated_select" value="true"/>
                 <param name="in_bam" value="medaka_test.bam"/>
@@ -183,7 +187,7 @@
             </output>
             <output name="out_annotated">
                 <assert_contents>
-                    <has_n_lines n="22"/>
+                    <has_n_lines n="23"/>
                     <has_line line="##fileformat=VCFv4.1" />
                     <has_line_matching expression="##medaka_version=[0-9]+\.[0-9]+\.[0-9]+" />
                     <has_line_matching expression="##convert_VCF_info_fields=[0-9]+\.[0-9]+" />