diff bcftools_isec.xml @ 0:a994b57c9a7d 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_isec.xml	Wed Jul 06 07:03:54 2016 -0400
@@ -0,0 +1,104 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
+    <description>Create intersections, unions and complements of VCF files</description>
+    <macros>
+        <token name="@EXECUTABLE@">isec</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@
+
+## Default section
+#set $section = $sec_default
+${section.complement}
+#if $section.nfiles:
+  --nfiles "${section.nfiles}"
+#end if
+
+#set $section = $sec_restrict
+@REGIONS@
+@TARGETS@
+@COLLAPSE@
+@APPLY_FILTERS@
+@INCLUDE@
+@EXCLUDE@
+
+@OUTPUT_TYPE@
+@THREADS@
+
+## Primary Input/Outputs
+@INPUT_FILES@
+> "$output_file"
+
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_inputs" />
+        <section name="sec_restrict" expanded="false" title="Restrict to">
+            <expand macro="macro_collapse" />
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+            <expand macro="macro_apply_filters" />
+            <expand macro="macro_regions" />
+            <expand macro="macro_targets" />
+        </section>
+        <section name="sec_default" expanded="true" title="Isec Options">
+            <param name="nfiles" type="text" label="Nfiles" optional="True" 
+                 help="Output positions present in this many (=), this many or more (+), this many or fewer (-), the exact (~) files" >
+                <validator type="regex" message="bitmask zero or one">^([=+-]?\d+|~[01]+)?$</validator>
+            </param>
+            <param name="complement" type="boolean" truevalue="--complement" falsevalue="" label="Complement" 
+                   help="Output positions present only in the first file but missing in the others" />
+            <param name="prefix" type="boolean" truevalue="--prefix subset" falsevalue="" checked="false" label="subset each of the input files" 
+                   help="(-p)" />
+            <param name="write" type="text" label="Files to write" optional="True" 
+                 help="(-write) The output files to write " >
+                <validator type="regex" message="">^([=+-]?\d+|~[01]+)?$</validator>
+            </param>
+        </section>
+        <expand macro="macro_select_output_type" />
+    </inputs>
+    <outputs>
+        <expand macro="macro_vcf_output"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_files" ftype="vcf" value="isec.b.vcf,isec.a.vcf" />
+            <param name="nfiles" value="=2" />
+            <param name="output_type" value="v" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="3157410" />
+                    <has_text text="3162006" />
+                    <not_has_text text="3062915" />
+                </assert_contents>
+            </output>
+        </test>
+
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@
+=====================================
+
+Create intersections, unions and complements of VCF files.
+
+@COLLAPSE_HELP@
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>