--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/consensus.xml	Sat May 23 13:37:18 2020 -0400
@@ -0,0 +1,147 @@
+<tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+    <description>Assembly polishing via neural networks</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ## initialize
+        ln -s '${bam}' 'alignment.bam' &&
+        ln -s '${bam.metadata.bam_index}' 'alignment.bam.bai' &&
+
+        ## run
+        medaka consensus
+        ## optional
+        --debug ## increase log level
+        --threads \${GALAXY_SLOTS:-4}
+        --batch_size $batch_size
+        #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
+            --regions 
+            #if $regions_cond.regions_sel == 'custom'
+                '$regions_cond.custom'
+            #else if $regions_cond.regions_sel == 'bed'
+                '$regions_cond.bed'
+            #end if
+        #end if
+        --chunk_len $chunk_len
+        --chunk_ovlp $chunk_ovlp
+        --model '$model'
+        $disable_cudnn
+        $check_output
+        $save_features
+        #if $RG
+            --RG '$RG'
+        #end if
+        #if $tag_name
+            --tag_name '$tag_name'
+        #end if
+        #if $tag_value
+            --tag_value $tag_value
+        #end if
+        $tag_keep_missing
+        ## required
+        'alignment.bam' ## bam
+        'result.hdf' ## output
+
+        |& tee 'log.txt'
+    ]]></command>
+    <inputs>
+        <param argument="bam" type="data" format="bam" label="Select input alignment"/>
+        <expand macro="model" argument="--model"/>
+        <expand macro="b" argument="--batch_size"/>
+        <conditional name="regions_cond">
+            <param name="regions_sel" type="select" label="Specify regions to analyse via">
+                <option value="none">None</option>
+                <option value="custom">Custom input</option>
+                <option value="bed">BED file</option>
+            </param>
+            <when value="custom">
+                <param argument="custom" type="text" value="" optional="true" label="Set genomic regions to analyse"/>
+            </when>
+            <when value="bed">
+                <param argument="bed" type="data" format="bed" optional="true" label="Select file with genomic regions to analyse"/>
+            </when>
+            <when value="none"/>
+        </conditional>
+        <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/>
+        <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/>
+        <param argument="--disable_cudnn" type="boolean" truevalue="--disable_cudnn" falsevalue="" label="Disable use of cuDNN model layers?"/>
+        <param argument="--check_output" type="boolean" truevalue="--check_output" falsevalue="" label="Verify integrity of output file after inference?"/>
+        <param argument="--save_features" type="boolean" truevalue="--save_features" falsevalue="" label="Save features with consensus?"/>
+        <param argument="--RG" type="text" value="" optional="true" label="Set read group"/>
+        <param argument="--tag_name" type="text" value="" optional="true" label="Set tag name" help="Two letters."/>
+        <param argument="--tag_value" type="integer" value="" optional="true" label="Set tag value"/>
+        <param argument="--tag_keep_missing" type="boolean" truevalue="--tag_keep_missing" falsevalue="" label="Keep alignments when tag is missing?"/>
+        <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="h5" from_work_dir="result.hdf" label="${tool.name} on ${on_string}: Result">
+            <filter>'result' in out</filter>
+        </data>
+        <!-- optional -->
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
+            <filter>'log' in out</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!-- #1 default -->
+        <test expect_num_outputs="1">
+            <param name="bam" value="alignment.bam"/>
+            <output name="out_result">
+                <assert_contents>
+                    <has_size value="32624"/>
+                </assert_contents>
+            </output>
+        </test>
+        <!-- #2 -->
+        <test expect_num_outputs="2">
+            <param name="bam" value="alignment.bam"/>
+            <param name="model" value="r941_min_fast_g303"/>
+            <param name="batch_size" value="99"/>
+            <param name="chunk_len" value="9999"/>
+            <param name="chunk_ovlp" value="999"/>
+            <param name="disable_cudnn" value="true"/>
+            <param name="check_output" value="true"/>
+            <param name="save_features" value="true"/>
+            <param name="tag_keep_missing" value="true"/>
+            <param name="out" value="result,log"/>
+            <output name="out_result">
+                <assert_contents>
+                    <has_size value="38400"/>
+                </assert_contents>
+            </output>
+            <output name="out_log">
+                <assert_contents>
+                    <has_text_matching expression=".+Validating and finalising output data."/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+.. class:: infomark
+
+**What it does**
+
+@WID@
+
+The module *consensus* runs inference from a trained model and alignments.
+
+**Input**
+
+Alignment (BAM)
+
+**Output**
+
+Results (H5/HDF)
+
+**References**
+
+@REFERENCES@
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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