# HG changeset patch
# User dereeper
# Date 1641204408 0
# Node ID 1306b28be7c3a19352f0c7dfc0e4d941d4735f11
# Parent  3249d78ecfc2e149775e8f8429d382779c97f029
Uploaded

diff -r 3249d78ecfc2 -r 1306b28be7c3 uniqprimer.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniqprimer.xml	Mon Jan 03 10:06:48 2022 +0000
@@ -0,0 +1,63 @@
+<tool id="uniqprimer" name="Uniqprimer" version="0.5.0">
+	<description>Design specific primers of sequences</description>
+	<requirements>
+		<requirement type="package" version="6.6.0">emboss</requirement>
+		<requirement type="package" version="3.23">mummer</requirement>
+		<requirement type="package" version="2.5.0">primer3</requirement>
+	</requirements>
+	<command>$__tool_directory__/uniqprimer.sh $include $exclude $product_size_range $primer_size $min_size $max_size $crossvalidate $outfile $log $fasta
+#for $i in $inputs
+        -i ${i.input}
+#end for
+
+</command>
+	<inputs>
+		<param format="fasta" name="include" type="data" label="FASTA file to include" help="Sequences for which you want design specific primer"/>
+		<repeat name="inputs" title="Include FASTA file">
+			<param name="input" label="Add FASTA file to include" type="data" format="fasta" />
+		</repeat>
+		<param format="fasta" name="exclude" type="data" label="FASTA file to exclude" help="Primers will not match these sequences"/>
+                <param type="text" name="product_size_range" label="Product size range" value="100-300"/>
+                <param type="text" name="primer_size" label="Optimal primer size" value="20"/>
+                <param type="text" name="min_size" label="Min primer size" value="18"/>
+                <param type="text" name="max_size" label="Max primer size" value="27"/>
+		<param name="crossvalidate" type="select" label="Cross validate primers against exclude files for extra certainty">
+			<option value="Yes">Yes</option>
+			<option value="No">No</option>
+		</param>
+	</inputs>
+	<outputs>
+		<data format="txt" name="outfile" label="Primer list"/>
+		<data format="fasta" name="fasta" label="Fasta for Primer3"/>
+		<data format="txt" name="log" label="Logfile"/>
+	</outputs>
+	<help>
+	
+
+.. class:: infomark
+
+**Program encapsulated in Galaxy by IRRI (International Rice Reasearch Institute) and South Green bioinformatics platform**
+
+.. class:: infomark
+
+**UniqPrimer version 0.5.0**
+
+-----
+
+==============
+ Please cite:
+==============
+
+"".
+
+-----
+
+===========
+ Overview:
+===========
+
+Uniqprimer designs specific primers of sequences. The goal of this tool is to accept a number of "include" FASTA files of diagnostic target genomes (draft or complete) and "exclude" files of non-target genomes, and output a list of PCR primers that will amplify target genomes but not non-target genomes.
+
+	</help>
+
+</tool>