--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_convert_from_vcf.xml	Wed Jul 06 07:02:27 2016 -0400
@@ -0,0 +1,185 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@ from vcf" id="bcftools_@EXECUTABLE@_from_vcf" version="@VERSION@.0">
+    <description>Converts VCF/BCF to IMPUTE2/SHAPEIT formats</description>
+    <macros>
+        <token name="@EXECUTABLE@">convert</token>
+        <import>macros.xml</import>
+        <xml name="macro_vcf_ids">
+            <param name="vcf_ids" type="boolean" truevalue="--vcf-ids" falsevalue="" checked="false" 
+                   label="Output VCF IDs instead of CHROM:POS_REF_ALT" help="(\-\-vcf_ids)"/>
+        </xml>
+        <xml name="macro_haploid2diploid">
+            <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" 
+                   label="convert haploid genotypes to diploid homozygotes"  help="(\-\-haploid2diploid)"/>
+        </xml>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+@PREPARE_ENV@
+@PREPARE_INPUT_FILE@
+#set $section = $sec_restrict
+@PREPARE_TARGETS_FILE@
+
+bcftools @EXECUTABLE@
+
+#if $convert.convert_to == 'gen_sample':
+--tag $convert.tag $convert.chrom $convert.vcf_ids
+--gensample "$output_gen,$output_samples"
+#elif $convert.convert_to == 'hap_sample':
+$convert.vcf_ids $convert.haploid2diploid
+--hapsample "$output_hap,$output_samples"
+#elif $convert.convert_to == 'hap_legend_sample':
+$convert.vcf_ids $convert.haploid2diploid
+--haplegendsample "$output_hap,$output_legend,$output_samples"
+#end if
+
+## VCF input section
+#set $section = $sec_restrict
+@INCLUDE@
+@EXCLUDE@
+@REGIONS@
+@TARGETS@
+@SAMPLES@
+
+## Primary Input/Outputs
+"$input_file" .
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+            <expand macro="macro_samples" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <conditional name="convert">
+            <param name="convert_to" type="select" label="convert to">
+                <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
+                <option value="hap_sample">hap sample - IMPUTE2 or SHAPEIT</option>
+                <option value="hap_legend_sample">hap legend sample - IMPUTE2 or SHAPEIT</option>
+            </param>
+            <when value="gen_sample">
+                <param name="tag" type="select" label="tag to take values for .gen file: GT,PL,GL,GP">
+                    <option value="GT">GT</option>
+                    <option value="PL">PL</option>
+                    <option value="GP">GP</option>
+                    <!--
+                    <option value="GL">GL</option>
+                    -->
+                </param>
+                <param name="chrom" type="boolean" truevalue="--chrom" falsevalue="" checked="false" 
+                   label="Output chromosome in first column instead of CHROM:POS_REF_ALT" help="(\-\-chrom)"/>
+                <expand macro="macro_vcf_ids"/>
+            </when>
+            <when value="hap_sample">
+                <expand macro="macro_haploid2diploid"/>
+                <expand macro="macro_vcf_ids"/>
+            </when>
+            <when value="hap_legend_sample">
+                <expand macro="macro_haploid2diploid"/>
+                <expand macro="macro_vcf_ids"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen">
+            <filter>convert['convert_to'] == 'gen_sample'</filter> 
+        </data>
+        <data name="output_hap" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.haps">
+            <filter>convert['convert_to'] in ('hap_sample','hap_legend_sample')</filter> 
+        </data>
+        <data name="output_legend" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.legend">
+            <filter>convert['convert_to'] == 'hap_legend_sample'</filter> 
+        </data>
+        <data name="output_samples" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.samples"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="convert.vcf" />
+            <param name="convert_to"  value="gen_sample" />
+            <output name="output_gen">
+                <assert_contents>
+                    <has_text text="X:2698560_G_A X:2698560_G_A 2698560 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0"/>
+                </assert_contents>
+            </output>
+            <output name="output_samples">
+                <assert_contents>
+                    <has_text text="NA00001 NA00001 0"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="convert.vcf" />
+            <param name="convert_to"  value="gen_sample" />
+            <param name="tag"  value="GP" />
+            <param name="chrom"  value="True" />
+            <output name="output_gen">
+                <assert_contents>
+                    <has_text text="X X:2698560_G_A 2698560 G A 1.00"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="check.vcf" />
+            <param name="convert_to"  value="gen_sample" />
+            <param name="tag"  value="GT" />
+            <param name="chrom"  value="True" />
+            <param name="vcf_ids"  value="True" />
+            <output name="output_gen">
+                <assert_contents>
+                    <has_text text="1 id3D 3062915 GTTT G 0 1 0 0 1 0"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="convert.vcf" />
+            <param name="convert_to"  value="hap_sample" />
+            <output name="output_hap">
+                <assert_contents>
+                    <has_text text="X X:2698769_AAG_A 2698769 AAG A 1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="convert.vcf" />
+            <param name="convert_to"  value="hap_legend_sample" />
+            <output name="output_hap">
+                <assert_contents>
+                    <has_text text="1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/>
+                </assert_contents>
+            </output>
+            <output name="output_legend">
+                <assert_contents>
+                    <has_text text="X:2698769_AAG_A 2698769 AAG A"/>
+                </assert_contents>
+            </output>
+            <output name="output_samples">
+                <assert_contents>
+                    <has_text text="sample population group sex"/>
+                    <has_text text="NA00001 NA00001 NA00001 2"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@ from vcf
+=====================================
+
+Converts VCF/BCF to other formats. See man page for file formats details. 
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>