--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_view.xml	Wed Jul 06 07:09:28 2016 -0400
@@ -0,0 +1,351 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+    <description>VCF/BCF conversion, view, subset and filter VCF/BCF files</description>
+    <macros>
+        <token name="@EXECUTABLE@">view</token>
+        <import>macros.xml</import>
+        <xml name="macro_types_options">
+            <option value="snps">snps</option>
+            <option value="indels">indels</option>
+            <option value="mnps">mnps</option>
+            <option value="other">mnps</option>
+        </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@
+
+## Subset section
+#set $section = $sec_subset
+${section.trim_alt_alleles}
+${section.no_update}
+@SAMPLES@
+${section.force_samples}
+
+
+## Filter section
+#set $section = $sec_filter
+#if $section.min_ac:
+  --min-ac "${section.min_ac}"
+#end if
+#if $section.max_ac:
+  --max-ac "${section.max_ac}"
+#end if
+#if str($section.select_genotype) != "__none__":
+  --genotype "${section.select_genotype}"
+#end if
+## known or novel
+#if $section.known_or_novel:
+${section.known_or_novel}
+#end if
+#if $section.min_alleles:
+  --min-alleles "${section.min_alleles}"
+#end if
+#if $section.max_alleles:
+  --max-alleles "${section.max_alleles}"
+#end if
+#if $section.phased:
+${section.phased}
+#end if
+#if $section.min_af:
+  --min-af "${section.min_af}"
+#end if
+#if $section.max_af:
+  --max-af "${section.max_af}"
+#end if
+#if $section.uncalled:
+${section.uncalled}
+#end if
+#if $section.types:
+  --types "${section.types}"
+#end if
+#if $section.exclude_types:
+  --exclude-types "${section.exclude_types}"
+#end if
+#if $section.private:
+${section.private}
+#end if
+
+## Output section
+#set $section = $sec_output
+${section.drop_genotypes}
+#if $section.header:
+${section.header}
+#end if
+#if $section.compression_level:
+  --compression-level "${section.compression_level}"
+#end if
+
+#set $section = $sec_restrict
+@APPLY_FILTERS@
+@INCLUDE@
+@EXCLUDE@
+@REGIONS@
+@TARGETS@
+
+@OUTPUT_TYPE@
+@THREADS@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+> "$output_file"
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_apply_filters" />
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <section name="sec_subset" expanded="false" title="Subset Options">
+            <expand macro="macro_samples" />
+            <param name="force_samples" type="boolean" truevalue="--force-samples" falsevalue="" label="Force Samples" 
+                   help="Only warn about unknown subset samples" />
+            <param name="no_update" type="boolean" truevalue="--no-update" falsevalue="" label="No Update" 
+                   help="Do not (re)calculate INFO fields for the subset (currently INFO/AC and INFO/AN)" />
+            <param name="trim_alt_alleles" type="boolean" truevalue="--trim-alt-alleles" falsevalue="" label="Trim Alt Alleles" 
+                   help="Trim alternate alleles not seen in the subset" />
+        </section>
+        <section name="sec_filter" expanded="false" title="Filter Options">
+            <param name="min_ac" type="integer" label="Min Ac" default="nref" optional="True" 
+                   help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
+            <param name="max_ac" type="integer" label="Max Ac" default="nref" optional="True" 
+                   help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
+            <param name="select_genotype" type="select">
+                <option value="__none__" selected="True">No selection</option>
+                <option value="require one or more hom/het/missing genotype or" />
+                <option value="if prefixed with &quot;^&quot;" />
+                <option value="exclude sites with hom/het/missing genotypes" />
+            </param>
+
+            <param name="types" type="select" label="Select Types"  multiple="true" optional="True">
+                <help>
+                 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested. 
+                 Types are determined by comparing the REF and ALT alleles in the VCF record.
+                </help>
+                <expand macro="macro_types_options" />
+            </param>
+
+            <param name="exclude_types" type="select" label="Exclude Types"  multiple="true" optional="True">
+                <help>
+                 List of variant types to exclude. Site is excluded if any of the ALT alleles is of the type requested. 
+                 Types are determined by comparing the REF and ALT alleles in the VCF record.
+                </help>
+                <expand macro="macro_types_options" />
+              </param>
+
+
+              <param name="known_or_novel" type="select" label="filter known or novel ID" optional="true">
+                  <option value="--novel">(-k) print novel sites only (ID column is ".")</option>
+                  <option value="--known">(-n) print known sites only (ID column is not ".")</option>
+              </param>
+
+              <param name="min_alleles" type="integer" label="Min Alleles" optional="True" 
+                     help="(-m) Minimum number of alleles listed in REF and ALT (e.g. -m2)" />
+              <param name="max_alleles" type="integer" label="Max Alleles" optional="True" 
+                     help="(-M) Maximum number of alleles listed in REF and ALT (e.g. -M2 for biallelic sites)" />
+
+              <param name="phased" type="select" label="filter phased" optional="true">
+                  <help>
+                  Haploid genotypes are considered phased. Missing genotypes considered unphased unless the phased bit is set. 
+                  </help>
+                  <option value="--phased">(-p) print sites where all samples are phased</option>
+                  <option value="--exclude-phased">(-P) exclude sites where all samples are phased</option>
+              </param>
+
+              <!-- TODO optional select for type: nref,alt1,minor,major,sum -->
+              <param name="min_af" type="float" label="Min Af" default="nref" optional="True" 
+                     help="(-q) Minimum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
+              <param name="max_af" type="float" label="Max Af" default="nref" optional="True" 
+                     help="(-Q) Maximum frequency for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
+
+              <param name="uncalled" type="select" label="filter on genotype uncalled" optional="true">
+                  <option value="--uncalled">uncalled - print sites without a called genotype</option>
+                  <option value="--exclude-uncalled">exclude-uncalled - exclude sites without a called genotype</option>
+              </param>
+
+              <param name="private" type="select" label="filter on private" optional="true">
+                  <help><![CDATA[
+                   Private: Where only the subset samples carry an non-reference allele.
+                   ( Ignored if samples are not included )
+                  ]]></help>
+                  <option value="--private">(-x) private - print sites where only the subset samples carry an non-reference allele</option>
+                  <option value="--exclude-private">(-X) exclude-private - exclude sites where only the subset samples carry an non-reference allele</option>
+              </param>
+
+        </section>
+
+        <section name="sec_output" expanded="false" title="Output Options">
+            <param name="drop_genotypes" type="boolean" truevalue="--drop-genotypes" falsevalue="" label="Drop Genotypes" 
+                   help="Drop individual genotype information (after subsetting if -s option set)" />
+            <param name="header" type="select" label="output header" optional="true">
+                <option value="--no-header">(-h) no-header</option>
+                <option value="--header-only">(-H) header-only</option>
+            </param>
+            <param name="compression_level" type="integer" min="0" max="9" label="Compression Level" default="-1" optional="True" 
+                   help="Compression level: 0 uncompressed, 1 best speed, 9 best compression" />
+            <param name="invert_targets_file" type="boolean" truevalue="^" falsevalue="" label="Invert Targets File" 
+                   help="Inverts the query/filtering applied by Targets File" />
+        </section>
+        <expand macro="macro_select_output_type" />
+    </inputs>
+    <outputs>
+        <expand macro="macro_vcf_output" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="min_ac" value="1" />
+            <param name="max_ac" value="1" />
+            <param name="samples" value="NA00002" />
+            <param name="types" value="snps" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="rs2298108" /> 
+                    <not_has_text text="rs6111385" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="known_or_novel" value="--novel" />
+            <param name="private" value="--exclude-private" />
+            <param name="samples" value="NA00003" />
+            <param name="regions" value="20,Y" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="8657215" /> 
+                    <not_has_text text="rs6111385" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="known_or_novel" value="--known" />
+            <param name="private" value="--exclude-private" />
+            <param name="apply_filters" value="PASS" />
+            <param name="samples" value="NA00003" />
+            <param name="regions" value="20,Y" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="rs6111385" /> 
+                    <not_has_text text="8657215" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="private" value="--private" />
+            <param name="samples" value="NA00003" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="rs62584840" /> 
+                    <not_has_text text="8657215" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="include" value="QUAL==999 &amp;&amp; (FS&lt;20 || FS&gt;=41.02) &amp;&amp; ICF&gt;-0.1 &amp;&amp; HWE*2&gt;1.2" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="rs5939407" /> 
+                    <not_has_text text="8657215" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="phased" value="--phased" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="rs78249411" /> 
+                    <not_has_text text="rs6111385" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="phased" value="--exclude-phased" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="rs6111385" /> 
+                    <not_has_text text="rs78249411" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="min_alleles" value="2" />
+            <param name="max_alleles" value="2" />
+            <param name="min_af" value="0.3" />
+            <param name="max_af" value="0.7" />
+            <param name="header" value="--header-only" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="##bcftools_viewCommand" /> 
+                    <not_has_text text="rs78249411" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="uncalled" value="--uncalled" />
+            <param name="header" value="--no-header" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <not_has_text text="##bcftools_viewCommand" /> 
+                    <has_text text="5464562" /> 
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <param name="exclude_types" value="snps" />
+            <param name="drop_genotypes" value="true" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <not_has_text text="##FORMAT=&lt;ID=GT" /> 
+                    <not_has_text text="rs62584840" /> 
+                    <has_text text="2343543" /> 
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@
+=====================================
+
+VCF/BCF conversion, view, subset and filter VCF/BCF files.
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>