diff bcftools_plugin_color_chrs.xml @ 8:47ee1925fe9e draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_plugin_color_chrs.xml	Wed Jun 05 12:59:21 2019 -0400
@@ -0,0 +1,105 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@TOOL_VERSION@+galaxy1">
+    <description>plugin Color shared chromosomal segments, requires phased GTs</description>
+    <macros>
+        <token name="@EXECUTABLE@">color-chrs</token>
+        <token name="@PLUGIN_ID@">color_chrs</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@
+@PREPARE_REGIONS_FILE@
+
+bcftools plugin @EXECUTABLE@
+
+## VCF input section
+#set $section = $sec_restrict
+@REGIONS@
+@TARGETS@
+@INCLUDE@
+@EXCLUDE@
+
+@THREADS@
+
+## Primary Input/Outputs
+@INPUT_FILE@
+
+## Plugin options
+#if $sample_relation.sample_rel_sel == 'trio':
+-- --trio '${sample_relation.mother},${sample_relation.father},${sample_relation.child}'
+#else:
+-- --unrelated '${sample_relation.sample_a},${sample_relation.sample_b}'
+#end if
+-p output_tmp
+&& color-chrs.pl output_tmp.dat -p output_tmp
+&& mv output_tmp.dat '$output_data'
+&& mv output_tmp.svg '$output_svg'
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+        <conditional name="sample_relation"> 
+            <param name="sample_rel_sel" type="select" label="Sample relationship">
+                <option value="trio">trio - mother,father,child</option>
+                <option value="unrelated">unrelated sample pair</option>
+            </param>
+            <when value="trio">
+               <param name="mother" type="text" value="" label="name of mother"/>
+               <param name="father" type="text" value="" label="name of father"/>
+               <param name="child" type="text" value="" label="name of child"/>
+            </when>
+            <when value="unrelated">
+               <param name="sample_a" type="text" value="" label="name of sample A"/>
+               <param name="sample_b" type="text" value="" label="name of sample B"/>
+            </when>
+        </conditional>
+        <section name="sec_restrict" expanded="false" title="Restrict analysis to">
+            <expand macro="macro_include" />
+            <expand macro="macro_exclude" />
+            <expand macro="macro_restrict" />
+            <expand macro="macro_restrict" type="target" label_type="Target" />
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_data" format="tabular" />
+        <data name="output_svg" format="svg" />
+    </outputs>
+    <tests>
+        <test expect_num_outputs="2">
+            <param name="input_file" ftype="vcf" value="stats.a.vcf" />
+            <conditional name="sample_relation">
+                <param name="sample_rel_sel" value="trio" />
+                <param name="mother" value="A" />
+                <param name="father" value="C" />
+                <param name="child" value="B" />
+            </conditional>
+            <output name="output_data" ftype="tabular" file="color_chrs.dat" />
+        </test>
+        <test expect_num_outputs="2">
+            <param name="input_file" ftype="vcf" value="stats.a.vcf" />
+            <conditional name="sample_relation">
+                <param name="sample_rel_sel" value="unrelated" />
+                <param name="sample_a" value="A" />
+                <param name="sample_b" value="B" />
+            </conditional>
+            <output name="output_data" ftype="tabular" file="color_chrs_unrelated.dat" />
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@ plugin
+=====================================
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+]]>
+</help>
+    <expand macro="citations" />
+</tool>