--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/callvariants.xml	Tue Oct 05 20:05:50 2021 +0000
@@ -0,0 +1,110 @@
+<tool id="bbtools_callvariants" name="BBTools: call variants" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
+    <description>in aligned Bam files</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+#import os
+
+#if str($ref_source_cond.ref_source) == 'cached'
+    #set ref = str($ref_source_cond.reference.fields.path)
+#else:
+    #set ref = $ref_source_cond.reference
+#end if
+
+## callvariants uses the file extension to determine the input format.
+#set input_name = str($os.path.basename($input.file_name)) + '.bam'
+ln -s '${input}' '${input_name}' &&
+
+callvariants.sh in='${input_name}' threads=\${GALAXY_SLOTS:-4} ref='${ref}' ploidy=$ploidy
+#if $output_variant_score_hist:
+    shist='$output_scorehist'
+#end if
+#if $output_zygosity_hist:
+    zhist='$output_zygosityhist'
+#end if
+#if $output_quality_hist:
+    qhist='$output_qualityhist'
+#end if
+#if str($output_format) == 'vcf':
+    vcf='out.vcf' && mv 'out.vcf' '$output'
+#elif str($output_format) == 'gff':
+    outgff='out.gff' && mv 'out.gff' '$output'
+#else:
+    out='output.txt' && mv 'output.txt' '$output'
+#end if
+]]></command>
+    <inputs>
+        <param name="input" type="data" format="bam" label="Bam file" help="Bam files produced by BBMap are recommended"/>
+        <expand macro="reference_source_cond"/>
+        <param name="ploidy" type="integer" value="1" min="1" label="Ploidy" help="See help section below"/>
+        <param name="output_format" type="select" label="Select output format">
+            <option value="vcf" selected="true">vcf</option>
+            <option value="gff">gff</option>
+            <option value="txt">txt</option>
+        </param>
+        <param name="output_variant_score_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output variant score histogram?"/>
+        <param name="output_zygosity_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output zygosity histogram?"/>
+        <param name="output_quality_hist" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output quality histogram?"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="vcf">
+            <change_format>
+                <when input="output_format" value="gff" format="gff"/>
+                <when input="output_format" value="txt" format="txt"/>
+            </change_format>
+        </data>
+        <data name="output_scorehist" format="tabular" label="${tool.name} on ${on_string} (scorehist)">
+            <filter>output_variant_score_hist</filter>
+        </data>
+        <data name="output_zygosityhist" format="tabular" label="${tool.name} on ${on_string} (zygosityhist)">
+            <filter>output_zygosity_hist</filter>
+        </data>
+        <data name="output_qualityhist" format="tabular" label="${tool.name} on ${on_string} (qualityhist)">
+            <filter>output_quality_hist</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="4">
+            <param name="input" value="cv_input.bam" ftype="bam"/>
+            <param name="ploidy" value="2"/>
+            <param name="output_variant_score_hist" value="yes"/>
+            <param name="output_zygosity_hist" value="yes"/>
+            <param name="output_quality_hist" value="yes"/>
+            <output name="output" file="cv_output.vcf" ftype="vcf" compare="contains"/>
+            <output name="output_scorehist" file="cv_scorehist_output.tabular" ftype="tabular" compare="contains"/>
+            <output name="output_zygosityhist" file="cv_zygosityhist_output.tabular" ftype="tabular" compare="contains"/>
+            <output name="output_qualityhist" file="cv_qualityhist_output.tabular" ftype="tabular" compare="contains"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="cv_input.bam" ftype="bam"/>
+            <param name="ploidy" value="2"/>
+            <param name="output_format" value="gff"/>
+            <output name="output" file="cv_output.gff" ftype="gff" compare="contains"/>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input" value="cv_input.bam" ftype="bam"/>
+            <param name="ploidy" value="2"/>
+            <param name="output_format" value="txt"/>
+            <output name="output" file="cv_output.txt" ftype="txt" compare="contains"/>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+CallVariants is a high-speed, multithreaded variant caller that accepts bam files, and output VCF files.  It is capable
+of indel realignment, multi-sample variant-calling, and processing samples with arbitrary ploidy.
+
+BBMap is the recommended mapping program for CallVariants, but output from any aligner is acceptable.  Reads can be
+realigned with the "realign" flag.  This is slower, but is highly recommended if the input is from any mapping tool
+other than BBMap. Output from BBMap should not be realigned.
+
+**Options**
+
+ * **Ploidy** - Arbitrary ploidy is supported - the default is 1 which works for haploid organisms.  Allele fractions lower than those expected for the ploidy (for example, anything below 0.5 for a diploid, or 0.25 for a tetraploid) will incur a score penalty. When calling variants on non-haploid organisms, it is crucial to set the ploidy.
+
+    </help>
+    <expand macro="citations"/>
+</tool>
+