--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_query.xml	Wed Jul 06 07:08:15 2016 -0400
@@ -0,0 +1,126 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+    <description>Extracts fields from VCF/BCF file and prints them in user-defined format</description>
+    <macros>
+        <token name="@EXECUTABLE@">query</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+@PREPARE_ENV@
+@PREPARE_INPUT_FILES@
+#set $section = $sec_restrict
+@PREPARE_TARGETS_FILE@
+
+bcftools @EXECUTABLE@
+
+## Query section
+#set $section = $sec_query
+  --format '${section.format}'
+
+${section.allow_undef_tags}
+
+${section.print_header}
+
+## Default section
+#set $section = $sec_restrict
+@INCLUDE@
+@EXCLUDE@
+@COLLAPSE@
+@REGIONS@
+@SAMPLES@
+@TARGETS@
+
+## Primary Input/Outputs
+--vcf-list @INPUT_LIST_FILE@
+> $output_file
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_inputs" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_collapse" />
+            <expand macro="macro_samples" />
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <section name="sec_query" expanded="true" title="Query Options">
+            <param name="format" type="text" value="" label="Format for Output">
+                <help>
+                <![CDATA[ 
+                Example: %CHROM\t%POS\t%REF\t%ALT{0}\n
+                ( NOTE TAB: '\t' and new line character: '\n' )
+                ]]>
+                </help>
+                <sanitizer sanitize="False"/>
+                <validator type="empty_field" />
+            </param>
+            <param name="tsv" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Output is tab-delimited"
+                   help="Fields in your Format are separated by a TAB character: \t"/>
+            <param name="allow_undef_tags" type="boolean" truevalue="--allow-undef-tags" falsevalue="" label="Allow Undefined Tags" 
+                   help="Print &quot;.&quot; for undefined tags" />
+            <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header Line" />
+        </section>
+
+    </inputs>
+    <outputs>
+        <data name="output_file" format="txt">
+            <change_format>
+                <when input="tsv" value="True" format="tabular" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_files" ftype="vcf" value="query.vcf" />
+            <param name="format" value="%CHROM\t%POS\t%REF\t%ALT\t%DP4\t%AN[\t%GT\t%TGT]\n" />
+            <param name="tsv" value="True" />
+            <output name="output_file" file="query.out" />
+        </test>
+    </tests>
+    <help><![CDATA[ 
+=====================================
+ bcftools @EXECUTABLE@
+=====================================
+
+Extracts fields from VCF/BCF file and prints them in user-defined format
+
+  Format:
+
+  ::
+
+    ``%CHROM``          The CHROM column (similarly also other columns: POS, ID, REF, ALT, QUAL, FILTER)
+    ``%INFO/TAG``       Any tag in the INFO column
+    ``%TYPE``           Variant type (REF, SNP, MNP, INDEL, OTHER)
+    ``%MASK``           Indicates presence of the site in other files (with multiple files)
+    ``%TAG{INT}``       Curly brackets to subscript vectors (0-based)
+    ``%FIRST_ALT``      Alias for %ALT{0}
+    ``[]``              The brackets loop over all samples
+    ``%GT``             Genotype (e.g. 0/1)
+    ``%TGT``            Translated genotype (e.g. C/A)
+    ``%IUPACGT``        Genotype translated to IUPAC ambiguity codes (e.g. M instead of C/A)
+    ``%LINE``           Prints the whole line
+    ``%SAMPLE``         Sample name
+
+  Examples:
+
+  ::
+
+    ``bcftools query -f '%CHROM  %POS  %REF  %ALT{0}\n' file.vcf.gz``
+    ``bcftools query -f '%CHROM\t%POS\t%REF\t%ALT[\t%SAMPLE=%GT]\n' file.vcf.gz``
+
+@COLLAPSE_HELP@
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>