--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/graphmap_align.xml	Thu Sep 27 15:26:47 2018 -0400
@@ -0,0 +1,63 @@
+<tool id="graphmap_align" name="Mapper" version="@VERSION@">
+    <description>for long, error-prone reads, like Nanopore ONT and PacBio</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code">
+    <![CDATA[
+        ln -s '$r' ref.${r.ext} && 
+        ln -s '$d' reads.${d.ext} && 
+
+        graphmap align  
+        -r ref.${r.ext} 
+        -d reads.${d.ext}
+        #if $preset:
+            -x $preset
+        #end if
+        -t \${GALAXY_SLOTS:-4} |
+        samtools view -b -u | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o output.bam -
+    ]]></command>
+    <inputs>
+        <param argument="-r" type="data"  format="fasta,fastq" label="reference sequence" />
+        <param argument="-d" type="data"  format="fasta,fastq" label="reads" />
+        <param name="preset" type="select" optional="True" label="Pre-set parameters to increase sensitivity for different sequencing technologies. (-x)">
+            <option value="illumina">illumina preset</option>
+            <option value="overlap">overlap preset</option>
+            <option value="sensitive">sensitive preset</option>
+        </param>
+<!-- 
+        <param type="data" name="reference" format="fasta,fastq" label="Sequences"/>
+        <param type="data" name="reads" format="fasta,fastq" label="Sequences"/>
+        <param type="data" name="overlaps" format="sam,tabular" label="Overlaps"/>
+        <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> -->
+
+    </inputs>
+    <outputs>
+        <data name="output" format="bam" from_work_dir="output.bam" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
+            <param name="d" value="E.coli_contigs.fasta"/>
+            <output name="output" ftype="bam" file="result1_map.bam"/>
+        </test>
+        <test>
+            <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
+            <param name="d" value="E.coli_contigs.fasta"/>
+            <param name="preset" value="illumina"/>
+            <output name="output" ftype="bam" file="result2_map.bam"/>
+        </test>
+        <test>
+            <param name="r" value="Loman_E.coli_MAP006-1_2D_50x_first_500_reads.fasta"/>
+            <param name="d" value="E.coli_contigs.fasta"/>
+            <param name="preset" value="sensitive"/>
+            <output name="output" ftype="bam" file="result3_map.bam"/>
+        </test></tests>
+    <help><![CDATA[
+        GraphMap - A very accurate and sensitive long-read, high error-rate sequence mapper
+        GraphMap (c) by Ivan Sovic, Mile Sikic and Niranjan Nagarajan
+        GraphMap is licensed under The MIT License.
+    ]]></help>
+    <expand macro="citations" />
+</tool>
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