--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hapog.xml	Fri Sep 16 13:48:54 2022 +0000
@@ -0,0 +1,121 @@
+<tool id="hapog" name="Hapo-G" profile="21.05" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>genome polishing</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.3.3</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">hapog</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+hapog
+--genome '${genome}'
+--output output/
+
+--threads \${GALAXY_SLOTS:-1}
+
+#if str( $reads.type ) == "short":
+    #for $i in $reads.pe1
+        --pe1 '${i}'
+    #end for
+    #for $i in $reads.pe2
+        --pe2 '${i}'
+    #end for
+#elif str( $reads.type ) == "short_collection":
+    #for $i in $reads.pecol
+        --pe1 '${i.forward}'
+        --pe2 '${i.reverse}'
+    #end for
+#elif str( $reads.type ) == "long":
+    --single '${single}'
+#elif str( $reads.type ) == "bam":
+    -b '${bam}'
+#end if
+
+$u
+    ]]></command>
+    <inputs>
+        <param argument="--genome" type="data" format="fasta" label="Genome assembly to polish"/>
+        <conditional name="reads">
+            <param name="type" type="select" label="Type of data used for polishing">
+                <option value="short">Short (paired) reads</option>
+                <option value="short_collection">Short (paired) reads collection</option>
+                <option value="long">Long reads</option>
+                <option value="bam">Pre-aligned reads (BAM)</option>
+            </param>
+            <when value="short">
+                <param argument="--pe1" type="data" format="fastq,fastq.gz" multiple="true" label="First set of short reads"/>
+                <param argument="--pe2" type="data" format="fastq,fastq.gz" multiple="true" label="Second set of short reads"/>
+            </when>
+            <when value="short_collection">
+                <param name="pecol" type="data_collection" collection_type="paired" format="fastq,fastq.gz" label="Paired collection of short reads"/>
+            </when>
+            <when value="long">
+                <param argument="--single" type="data" format="fastq,fastq.gz" label="Long reads"/>
+            </when>
+            <when value="bam">
+                <param name="bam" type="data" format="bam" label="Pre-aligned reads"/>
+            </when>
+        </conditional>
+        <param argument="-u" type="boolean" truevalue="-u" falsevalue="" checked="False" label="Include unpolished sequences in final output" />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" from_work_dir="output/hapog_results/hapog.fasta"/>
+        <data format="tsv" name="changes" from_work_dir="output/hapog_results/hapog.changes"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="genome" value="genome.fa" />
+            <conditional name="reads">
+                <param name="type" value="short" />
+                <param name="pe1" value="fastq1.fq" />
+                <param name="pe2" value="fastq2.fq" />
+            </conditional>
+            <output name="output" file="hapog_short.fasta" />
+            <output name="changes" file="hapog_short.changes" />
+        </test>
+        <test>
+            <param name="genome" value="genome.fa" />
+            <conditional name="reads">
+                <param name="type" value="short" />
+                <param name="pe1" value="fastq1.fq.gz" />
+                <param name="pe2" value="fastq2.fq.gz" />
+            </conditional>
+            <output name="output" file="hapog_short.fasta"/>
+            <output name="changes" file="hapog_short.changes" />
+        </test>
+        <test>
+            <param name="genome" value="genome.fa" />
+            <conditional name="reads">
+                <param name="type" value="long" />
+                <param name="single" value="fastq1.fq" />
+            </conditional>
+            <output name="output" file="hapog_long.fasta" />
+            <output name="changes" file="hapog_long.changes" />
+        </test>
+        <test>
+            <param name="genome" value="genome.fa" />
+            <conditional name="reads">
+                <param name="type" value="long" />
+                <param name="single" value="fastq1.fq.gz" />
+            </conditional>
+            <output name="output" file="hapog_long.fasta"/>
+            <output name="changes" file="hapog_long.changes" />
+        </test>
+        <test>
+            <param name="genome" value="genome.fa" />
+            <conditional name="reads">
+                <param name="type" value="bam" />
+                <param name="bam" value="input.bam" />
+            </conditional>
+            <output name="output" file="hapog_bam.fasta"/>
+            <output name="changes" file="hapog_bam.changes" />
+        </test>
+    </tests>
+    <help><![CDATA[
+Hapo-G uses alignments produced by BWA (or any other aligner that produces SAM files) to polish the consensus of a genome assembly.
+]]></help>
+    <citations>
+        <citation type="doi">10.1093/nargab/lqab034</citation>
+    </citations>
+</tool>