diff multiplicom_primer_trimming.xml @ 0:fadef644b886 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multiplicom_primer_trimming.xml	Fri May 22 08:27:03 2015 -0400
@@ -0,0 +1,45 @@
+<tool id="multiplicom_primer_trimming" name="Multiplicom Primer Trimmer" version="0.0.1">
+  <description></description>
+  <requirements>
+    <requirement type="package" version='latest'>twoBitToFa</requirement>
+  </requirements>
+  <command interpreter="perl">
+	multiplicom_primer_trimming.pl
+	## input files
+	-i $inputf
+	-I $inputr
+	-b $mastr
+	## read length
+	-r $readlength
+	## output files
+	-o $outf
+	-O $outr
+	-F $failed
+	-R $report
+	## reference genome
+	-t "${indexes.fields.path}"
+	
+  </command>
+  <inputs>
+	<param name='inputf' type='data' format='fastq,fastqsanger' label='Forward Sequences' help='Forward Reads in fastq format' />
+	<param name='inputr' type='data' format='fastq,fastqsanger' label='Reverse Sequences' help='Reverse Reads in fastq format' />
+	<param name='mastr' type='data' format='bed' label='MASTR file' help='Design file of the Multiplicom MASTR assay' />
+	<param name='readlength' type='integer' value='250' label='Read Length' help='Applied Readlength, per read' />
+	<param name="indexes" type="select" label="Reference Genome" help="Select the correct genome build" >
+		<options from_data_table="twobit" >
+			<filter type="sort_by" column="2" />
+			<validator type="no_options" message="No indexes are available" />
+		</options>
+	</param>
+   </inputs>
+   <outputs>
+	<data format_source="inputf" name="outf" label="${tool.name} on ${on_string}: Forward Reads"/>
+    	<data format_source="inputr" name="outr" label="${tool.name} on ${on_string}: Reverse Reads"/>
+    	<data format_source="inputf"	name="failed" label="${tool.name} on ${on_string}: Failed Pairs"/>
+    	<data format="txt" name="report" label="${tool.name} on ${on_string}: Runtime output"/>
+   </outputs>
+   <help>
+	This tools scans paired FASTQ files for the presence of Multiplicom MASTR PCR primers. If found, primers are clipped. 	
+   </help>
+</tool>
+