diff bcftools_filter.xml @ 0:061729be105d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_filter.xml	Wed Jul 06 07:03:12 2016 -0400
@@ -0,0 +1,218 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+    <description>Apply fixed-threshold filters</description>
+    <macros>
+        <token name="@EXECUTABLE@">filter</token>
+        <import>macros.xml</import>
+    </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@
+
+## Filter section
+#set $section = $sec_filter
+#if $section.SnpGap:
+  --SnpGap "${section.SnpGap}"
+#end if
+#if $section.IndelGap:
+  --IndelGap "${section.IndelGap}"
+#end if
+#if $section.mode:
+  #set $mode = str($section.mode).replace(',','')
+  --mode '$mode'
+#end if
+#if $section.soft_filter:
+  --soft-filter "${section.soft_filter}"
+#end if
+#if $section.select_set_GTs:
+  --set-GTs "${section.select_set_GTs}"
+#end if
+
+#set $section = $sec_restrict
+@REGIONS@
+@TARGETS@
+@INCLUDE@
+@EXCLUDE@
+
+@OUTPUT_TYPE@
+@THREADS@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+> "$output_file"
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+        </section>
+        <section name="sec_filter" expanded="false" title="Filter Options">
+            <param name="SnpGap" type="integer" label="Snpgap" optional="True" help="(-g) Filter SNPs within &lt;int&gt; base pairs of an indel" />
+            <param name="IndelGap" type="integer" label="Indelgap" optional="True" help="(-G) Filter clusters of indels separated by &lt;int&gt; or fewer base pairs allowing only one to pass" />
+            <param name="mode" type="select" label="Mode FILTER annotation" optional="true" multiple="true" display="checkboxes">
+                <help>(-m)
+                 The default mode replaces existing filters of failed sites with a new FILTER string 
+                 while leaving sites which pass untouched when non-empty 
+                 and setting to "PASS" when the FILTER string is absent.
+                </help>
+                <option value="+">(+) append new FILTER strings of failed sites instead of replacing them</option>
+                <option value="x">(x) resets filters of sites which pass to "PASS"</option>
+            </param>
+            <param name="soft_filter" type="text" value="" label="Soft Filter" optional="true">
+                <help><![CDATA[ (-s) 
+                   Annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d").
+                ]]></help>
+            </param>
+            <param name="select_set_GTs" type="select" ladel="Set genotypes of failed samples"  optional="true" help="(-S)">
+                <option value=".">to missing (.)</option>
+                <option value="0">to REF (0)</option>
+            </param>
+        </section>
+        <expand macro="macro_select_output_type" />
+    </inputs>
+    <outputs>
+        <expand macro="macro_vcf_output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.1.vcf" />
+            <param name="mode" value="x" />
+            <param name="SnpGap" value="2" />
+            <param name="IndelGap" value="2" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="PASS" />
+                    <not_has_text text="1006" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.2.vcf" />
+            <param name="exclude" value="QUAL==59.2 || (INDEL=0 &amp; (FMT/GQ=25 | FMT/DP=10))" />
+            <param name="soft_filter" value="Modified" />
+            <param name="select_set_GTs" value="." />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="Modified" />
+                    <has_text text="AN=2;AC=1" />
+                    <has_text_matching expression="TAAAA\tTA,T\t61.5\tModified" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.3.vcf" />
+            <param name="exclude" value="DP=19" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <not_has_text text="3162006" />
+                    <has_text text="3162007" />
+                </assert_contents>
+            </output>
+        </test>
+
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.3.vcf" />
+            <param name="exclude" value="DP=19" />
+            <param name="soft_filter" value="XX" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="\tXX\tDP=19" />
+                    <has_text_matching expression="\tq20\tAO" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.3.vcf" />
+            <param name="exclude" value="DP=19" />
+            <param name="soft_filter" value="XX" />
+            <param name="mode" value="+" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="\tq20;XX\tDP=19" />
+                    <has_text_matching expression="\tq20\tAO" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.3.vcf" />
+            <param name="exclude" value="DP=19" />
+            <param name="soft_filter" value="XX" />
+            <param name="mode" value="x" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="\tXX\tDP=19" />
+                    <has_text_matching expression="\tPASS\tAO" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.3.vcf" />
+            <param name="exclude" value="DP=19" />
+            <param name="soft_filter" value="XX" />
+            <param name="mode" value="+,x" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text_matching expression="\tq20;XX\tDP=19" />
+                    <has_text_matching expression="\tPASS\tAO" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.3.vcf" />
+            <param name="exclude" value="FMT/GT=&quot;0/2&quot;" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <not_has_text text="3162006" />
+                    <has_text text="3162007" />
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="input_file" ftype="vcf" value="filter.2.vcf" />
+            <param name="include" value="FMT/GT=&quot;0/0&quot; &amp;&amp; AC[*]=2" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="AN=4;AC=2" />
+                    <not_has_text text="AN=4;AC=0" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@
+=====================================
+
+Apply fixed-threshold filters.
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>