--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_call.xml	Mon May 02 17:27:10 2016 -0400
@@ -0,0 +1,159 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+  <description>SNP/indel variant calling from VCF/BCF</description>
+  <macros>
+    <token name="@EXECUTABLE@">call</token>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="version_command" />
+  <command detect_errors="aggressive"><![CDATA[
+bcftools @EXECUTABLE@
+
+## Consensus/variant calling section
+#if $sec_consensus_variant_calling.select_caller == "consensus":
+    --consensus-caller
+#else:
+    --multiallelic-caller
+#end if
+
+#if $sec_consensus_variant_calling.constraints.constrain_select == "alleles":
+  --constrain alleles
+#elif $sec_consensus_variant_calling.constraints.constrain_select == "trio":
+  --constrain trio
+  --novel-rate ${sec_consensus_variant_calling.constraints.novel_snp},${sec_consensus_variant_calling.constraints.novel_ins},${sec_consensus_variant_calling.constraints.novel_del}
+  --pval-threshold "${sec_consensus_variant_calling.constraints.pval_threshold}"
+#end if
+
+#if $sec_consensus_variant_calling.prior:
+  --prior "${sec_consensus_variant_calling.prior}"
+#end if
+${sec_consensus_variant_calling.chromosome_X}
+${sec_consensus_variant_calling.chromosome_Y}
+
+
+## File format section
+#if str($sec_default.select_output_type) != "__none__":
+  --output-type "${sec_default.select_output_type}"
+#end if
+@SEC_DEF_REGIONS@
+@SEC_DEF_SAMPLES@
+@SEC_DEF_TARGETS@
+
+
+## Input/output section
+${sec_input_output.keep_alts}
+#set values_sec_input_output_format_fields = '","'.join([str($value) for $value in $sec_input_output.format_fields_repeat])
+#if $values_sec_input_output_format_fields:
+  --format-fields "${values_sec_input_output_format_fields}"
+#end if
+
+#if str($sec_input_output.gvcf) != "":
+  --gvcf "${sec_input_output.gvcf}"
+#end if
+
+${sec_input_output.insert_missed}
+${sec_input_output.keep_masked_ref}
+
+#if str($sec_input_output.skip_variants) != "__none__":
+  --skip-variants "${sec_input_output.skip_variants}"
+#end if
+
+${sec_input_output.variants_only}
+
+## Primary Input/Outputs
+
+$input_file
+>
+$output_file
+]]>
+</command>
+  <inputs>
+    <param name="input_file" label="VCF/BCF Data" type="data" format="vcf,bcf,vcf_bgz,bcf_bgz" />
+    <section name="sec_consensus_variant_calling" expanded="true" title="Consensus/variant calling Options">
+      <param name="select_caller" label="Calling Method" type="select">
+        <option value="consensus">the original calling method (-c, --consensus-caller)</option>
+        <option value="multiallelic">alternative model for multiallelic and rare-variant calling (-m, --multiallelic-caller)</option>
+      </param>
+      <conditional name="constraints" label="Constraints">
+        <param name="constrain_select" label="Constraints" type="select" argument="-C">
+          <option value="__none__" selected="True">No constraints</option>
+          <option value="alleles">call genotypes given alleles (alleles)</option>
+          <option value="trio">call genotypes given the father-mother-child constraint (trio)</option>
+        </param>
+        <when value="__none__" />
+        <when value="alleles" />
+        <when value="trio">
+          <param name="novel_snp" label="Novel Rate: SNPs" type="float" default="1e-8" optional="True" help="mutation rate of SNPs" argument="--novel-rate"/>
+          <param name="novel_ins" label="Novel Rate: Insertions" type="float" default="1e-9" optional="True" help="mutation rate of insertions according to their length" argument="--novel-rate" />
+          <param name="novel_del" label="Novel Rate: Deletions" type="float" default="1e-9" optional="True" help="mutation rate of deletions according to their length" argument="--novel-rate" />
+          <param name="pval_threshold" label="Pval Threshold" type="float" default="0.5" optional="True" help="variant if P(ref|D)&lt;FLOAT with -c" argument="--pval-treshold"/>
+        </when>
+      </conditional>
+      <param name="prior" label="Prior" type="float" default="1.1e-3" optional="True" help="mutation rate (use bigger for greater sensitivity)" argument="--prior" />
+      <param name="chromosome_X" label="Chromosome X" type="boolean" truevalue="--chromosome-X" falsevalue="" help="haploid output for male samples (requires PED file with -s)" argument="--chromosome-X"/>
+      <param name="chromosome_Y" label="Chromosome Y" type="boolean" truevalue="--chromosome-Y" falsevalue="" help="haploid output for males and skips females (requires PED file with -s)" argument="--chromosome-Y"/>
+    </section>
+    <section name="sec_default" expanded="true" title="Default Options">
+      <expand macro="macro_select_output_type" />
+      <expand macro="macro_regions" />
+      <expand macro="macro_samples" />
+      <expand macro="macro_targets" />
+    </section>
+    <section name="sec_input_output" expanded="true" title="Input/output Options">
+      <param name="keep_alts" label="Keep Alts" type="boolean" truevalue="--keep-alts" falsevalue="" help="keep all possible alternate alleles at variant sites" argument="--keep-alts"/>
+      <repeat name="format_fields_repeat" title="Format Fields">
+        <param name="format_fields" type="text" label="Format Fields" help="output format fields: e.g. GQ, GP (lowercase allowed)" argument="--format-fields" />
+      </repeat>
+      <param name="gvcf" label="Gvcf" type="integer" optional="True" help="output gVCF blocks of homozygous REF calls. The parameter is the minimum per-sample depth required to include a site in the non-variant block." argument="--gvcf"/>
+      <param name="insert_missed" label="Insert Missed" type="boolean" truevalue="--insert-missed" falsevalue="" help="output also sites missed by mpileup but present in -T" argument="--insert-missed"/>
+      <param name="keep_masked_ref" label="Keep Masked Ref" type="boolean" truevalue="--keep-masked-ref" falsevalue="" help="keep sites with masked reference allele (REF=N)" argument="--keep-masked-ref"/>
+      <param name="skip_variants" label="Skip Variants" type="select" help="Skip indels/SNP sites" argument="--skip-variants">
+        <option value="__none__" selected="True">Don't skip any</option>
+        <option value="indels">Skip indels</option>
+        <option value="snps">Skip snps</option>
+      </param>
+      <param name="variants_only" label="Variants Only" type="boolean" truevalue="--variants-only" falsevalue="" help="output variant sites only" argument="--variants-only"/>
+    </section>
+  </inputs>
+  <outputs>
+    <data name="output_file" format="vcf">
+      <change_format>
+        <when input="sec_file_format|select_output_type" value="b" format="bcf_bgz" />
+        <when input="sec_file_format|select_output_type" value="u" format="bcf" />
+        <when input="sec_file_format|select_output_type" value="z" format="vcf_bgz" />
+        <when input="sec_file_format|select_output_type" value="v" format="vcf" />
+      </change_format>
+    </data>
+  </outputs>
+  <tests>
+      <test>
+          <param name="input_file" value="mpileup.vcf" />
+          <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
+          <param name="sec_input_output|variants_only" value="--variants-only" />
+          <param name="sec_file_format|select_output_type" value="v" />
+          <output name="output_file" file="mpileup.1.out" lines_diff="2" ftype="vcf" />
+      </test>
+      <test>
+          <param name="input_file" value="mpileup.vcf" />
+          <param name="sec_consensus_variant_calling|select_caller" value="multiallelic" />
+          <param name="sec_input_output|variants_only" value="--variants-only" />
+          <param name="sec_input_output|gvcf" value="0" />
+          <param name="sec_file_format|select_output_type" value="v" />
+          <output name="output_file" file="mpileup.2.out" lines_diff="2" ftype="vcf" />
+      </test>
+  </tests>
+  <help>
+      <![CDATA[
+      **bcftools call**
+
+      SNP/indel variant calling from VCF/BCF. To be used in conjunction with
+      samtools mpileup. This command replaces the former "bcftools view"
+      caller. Some of the original functionality has been temporarily lost in
+      the process of transition to htslib, but will be added back on popular
+      demand. The original calling model can be invoked with the -c
+      option.
+      ]]>
+  </help>
+  <expand macro="citations" />
+</tool>