diff variant.xml @ 0:3cde72a6e37c draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 1b97fa7a21a2c85bf4891aed1b7df92685b346c3"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant.xml	Sat May 23 13:36:47 2020 -0400
@@ -0,0 +1,111 @@
+<?xml version="1.0"?>
+<tool id="medaka_variant" name="medaka: Variant" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Probability decoding</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ## initialize
+        @REF_FASTA@
+
+        ## run
+        medaka variant
+        ## optional
+        --debug
+        #if $region
+            --region '${region}'
+        #end if
+        $verbose
+        ## required
+        'reference.fa'
+        #for $current in $inputs
+            '$current'
+        #end for
+        'result.vcf' ## output
+
+        |& tee log.txt
+        ]]></command>
+    <inputs>
+        <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
+        <expand macro="reference"/>
+        <param argument="--region" type="text" value="" optional="true" label="Set reference names to limit variant calling" help="Separated by ','."/>
+        <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" label="Populate VCF info fields?"/>
+        <param name="out" type="select" multiple="true" optional="false" label="Select output file(s)">
+            <option value="result" selected="true">Result</option>
+            <option value="log">Log</option>
+        </param>
+    </inputs>
+    <outputs>
+        <!-- standard -->
+        <data name="out_result" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result">
+            <filter>'result' in out</filter>
+        </data>
+        <!-- optional -->
+        <data name="out_log" format="tabular" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
+            <filter>'log' in out</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- #1 default -->
+        <test expect_num_outputs="1">
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="bwa-mem-mt-genome"/>
+            </conditional>
+            <param name="inputs" value="consensus.hdf"/>
+            <output name="out_result">
+                <assert_contents>
+                    <has_n_lines n="6"/>
+                    <has_line line="##fileformat=VCFv4.1"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 -->
+        <test expect_num_outputs="2">
+            <conditional name="reference_source">
+                <param name="reference_source_selector" value="cached"/>
+                <param name="ref_file" value="bwa-mem-mt-genome"/>
+            </conditional>
+            <param name="inputs" value="consensus.hdf"/>
+            <param name="verbose" value="true"/>
+            <param name="out" value="result,log"/>
+            <output name="out_result">
+                <assert_contents>
+                    <has_n_lines n="13"/>
+                    <has_line line="##fileformat=VCFv4.1"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_n_lines n="17"/>
+                    <has_text_matching expression=".+Loaded.+"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+The module *variant* decodes probabilities.
+
+**Input**
+
+- reference sequence (FASTA)
+- (several) consensus files (H5/HDF)
+
+**Output**
+
+- decoded probabilities (VCF)
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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