Mercurial > repos > iuc > bcftools_query_list_samples

diff bcftools_query_list_samples.xml @ 0:1af52ffc90e3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
author iuc
date Wed, 06 Jul 2016 07:08:29 -0400
parents
children 5272100dd270
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bcftools_query_list_samples.xml	Wed Jul 06 07:08:29 2016 -0400
@@ -0,0 +1,49 @@
+<?xml version='1.0' encoding='utf-8'?>
+<tool name="bcftools List Samples" id="bcftools_@EXECUTABLE@_list_samples" version="@VERSION@.0">
+    <description>in VCF/BCF file</description>
+    <macros>
+        <token name="@EXECUTABLE@">query</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <command detect_errors="aggressive"><![CDATA[
+@PREPARE_ENV@
+@PREPARE_INPUT_FILE@
+bcftools @EXECUTABLE@ --list-samples
+## Primary Input/Outputs
+@INPUT_FILE@
+| tee $output_file | tr '\n' ','
+]]>
+    </command>
+    <inputs>
+        <expand macro="macro_input" />
+    </inputs>
+    <outputs>
+        <data name="output_file" format="tabular"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_file" ftype="vcf" value="query.vcf" />
+            <output name="output_file">
+                <assert_contents>
+                    <has_text text="C" />
+                    <not_has_text text="A" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+=====================================
+ bcftools List Samples @EXECUTABLE@
+=====================================
+
+Lists Samples from a VCF/BCF file
+
+@BCFTOOLS_MANPAGE@#@EXECUTABLE@
+
+@BCFTOOLS_WIKI@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>