diff bcftools_plugin_counts.xml @ 0:06cd2a0252dc 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_plugin_counts.xml	Wed Jul 06 07:04:58 2016 -0400
@@ -0,0 +1,81 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools @EXECUTABLE@" id="bcftools_plugin_@PLUGIN_ID@" version="@VERSION@.0">
+    <description>plugin  counts number of samples, SNPs, INDELs, MNPs and total sites</description>
+    <macros>
+        <token name="@EXECUTABLE@">counts</token>
+        <token name="@PLUGIN_ID@">counts</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 plugin @EXECUTABLE@
+
+## VCF input section
+#set $section = $sec_restrict
+@INCLUDE@
+@EXCLUDE@
+@REGIONS@
+@TARGETS@
+
+## Primary Input/Outputs
+@INPUT_FILE@ | tee counts_file.txt  
+&& sed 's/^.* \([a-zA-Z]*\):[ ]*\([0-9]*\)$/\1 \2/' counts_file.txt | python $transform > "$output_file"
+]]>
+    </command>
+    <configfiles>
+        <configfile name="transform">
+import sys
+header = []
+value = []
+for line in sys.stdin:
+  h,v = line.strip().split()
+  header.append(h)
+  value.append(v)
+print >> sys.stdout, '#%s\n' % '\t'.join(header)
+print >> sys.stdout, '%s\n' % '\t'.join(value)
+        </configfile>
+    </configfiles>
+    <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>
+    </inputs>
+    <outputs>
+        <data name="output_file" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="view.vcf" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="SNPs"/>
+                    <has_text text="11"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools @EXECUTABLE@ plugin
+=====================================
+
+Counts number of samples, SNPs, INDELs, MNPs and total number of sites.
+
+@REGIONS_HELP@
+@TARGETS_HELP@
+@EXPRESSIONS_HELP@
+
+
+
+    ]]></help>
+    <expand macro="citations" />
+</tool>