--- a/bcftools_convert_from_vcf.xml	Sat Mar 11 17:58:33 2017 -0500
+++ b/bcftools_convert_from_vcf.xml	Thu Apr 13 17:44:12 2017 -0400
@@ -12,6 +12,37 @@
             <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" 
                    label="convert haploid genotypes to diploid homozygotes"  help="(\-\-haploid2diploid)"/>
         </xml>
+        <xml name="macro_sexinfo">
+            <conditional name="sex_info">
+                <param name="sex_info_src" type="select" label="sex column">
+                    <help><![CDATA[
+SampleName SexDesignation:
+<br>MaleSample    M
+<br>FemaleSample  F
+                    ]]></help>
+                    <option value="none">None</option>
+                    <option value="history">designations from history dataset</option>
+                    <option value="entry">designations from text input</option>
+                </param>
+                <when value="none"/>
+                <when value="history">
+                    <param name="sex_info_file" type="data" format="tabular" label="per sample sex designation file"/>
+                </when>
+                <when value="entry">
+                    <param name="sex_info_lines" type="text" area="True" label="per sample sex designation" >
+                        <validator type="regex" message="sample M or F separated by TAB">^(\S+[ \t][MF](\n\S+[ \t][MF])*)$</validator>
+                        <sanitizer sanitize="False"/>
+                    </param>
+                </when>
+            </conditional>
+        </xml>
+        <token name="@SAMPLE_SEX@">
+#if $convert.sex_info.sex_info_src == 'entry':
+  --sex "$entered_sex_file"
+#elif $convert.sex_info.sex_info_src == 'history':
+  --sex "$convert.sex_info.sex_info_file"
+#end if
+        </token>
     </macros>
     <expand macro="requirements" />
     <expand macro="version_command" />
@@ -20,6 +51,7 @@
 @PREPARE_INPUT_FILE@
 #set $section = $sec_restrict
 @PREPARE_TARGETS_FILE@
+@PREPARE_REGIONS_FILE@
 
 bcftools @EXECUTABLE@
 
@@ -33,6 +65,7 @@
 $convert.vcf_ids $convert.haploid2diploid
 --haplegendsample "$output_hap,$output_legend,$output_samples"
 #end if
+@SAMPLE_SEX@
 
 ## VCF input section
 #set $section = $sec_restrict
@@ -46,6 +79,12 @@
 "$input_file" .
 ]]>
     </command>
+    <configfiles>
+        <configfile name="entered_sex_file"><![CDATA[#slurp
+#if $convert.sex_info.sex_info_src == 'entry':
+$convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
+#end if]]></configfile>
+    </configfiles>
     <inputs>
         <expand macro="macro_input" />
         <section name="sec_restrict" expanded="false" title="Restrict to">
@@ -73,14 +112,17 @@
                 <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"/>
+                <expand macro="macro_sexinfo"/>
             </when>
             <when value="hap_sample">
                 <expand macro="macro_haploid2diploid"/>
                 <expand macro="macro_vcf_ids"/>
+                <expand macro="macro_sexinfo"/>
             </when>
             <when value="hap_legend_sample">
                 <expand macro="macro_haploid2diploid"/>
                 <expand macro="macro_vcf_ids"/>
+                <expand macro="macro_sexinfo"/>
             </when>
         </conditional>
     </inputs>