--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/quast-select.xml	Wed Feb 07 16:37:42 2018 -0500
@@ -0,0 +1,45 @@
+<tool id="quast-select" name="Select Best" version="0.1.0" profile="16.10">
+    <description>assembly based on a combined QUAST table</description>
+    <requirements>
+        <requirement type="package">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        #for $asm in $coll
+        ln -s $asm ./$asm.element_identifier &&
+        #end for
+        cp ./\$(python $__tool_directory__/quast_select.py $table $criterion) $output
+    ]]></command>
+    <inputs>
+        <param type="data" format="tsv" name="table" label="Combined QUAST output (from table_union)"/>
+        <param type="select" label="Select best assembly by..." name="criterion">
+            <option value="N50">Longest N50</option>
+            <option value="Largest contig">Longest single contig</option>
+            <option value="# contigs">Fewest contigs</option>
+            <option value="# contigs (>= 1000 bp)">Fewest contigs of length 1kbp or longer</option>
+            <option value="Total length">Total assembly length</option>
+            <option value="Total length (>= 1000 bp)">Total assembly length of contigs longer than 1kbp</option>
+        </param>
+        <param type="data_collection" collection_type="list" format="fasta" name="coll" label="Collection of FASTA assemblies" />
+    </inputs>
+    <outputs>
+        <data format="fasta" name="output" label="Best assembly by ${criterion}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="table" value="combined_table.tsv" />
+            <param name="coll" >
+                <collection type="list">
+                    <element name="sample1" value="sample1.fasta" />
+                    <element name="sample2" value="sample2.fasta" />
+                    <element name="sample3" value="sample3.fasta" />
+                    <element name="sample4" value="sample4.fasta" />
+                </collection>
+            </param>
+            <param name="criterion" value="N50"/>
+            <output name="output" value="sample1.fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+        Pick the best assembly from a collection of assemblies and a combined QUAST report.
+    ]]></help>
+</tool>
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