Mercurial > repos > nikos > hrf_seq

diff estimate_unique_counts.xml @ 2:14d6929f8aa1 draft default tip

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Tool tests or/and test-data are missing.
author nikos
date Thu, 11 Sep 2014 08:30:05 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/estimate_unique_counts.xml	Thu Sep 11 08:30:05 2014 -0400
@@ -0,0 +1,52 @@
+<tool id="hrf_euc" version="0.1" name="Estimate Unique Counts" force_history_refresh="True">
+    <description></description>
+    <requirements>
+        <requirement type="package" version="0.1.18">samtools</requirement>
+    </requirements>
+    <command interpreter="bash">
+	estimate_unique_counts.sh
+
+	## Inputs
+	-f $input1 -b $input2 
+	
+	##
+	#if str( $priming.flag ) == 'False':
+		-p -1
+	#else
+		-p $priming.position
+	#end if
+		
+    </command>
+
+    <inputs>
+        <param format="bam" name="input1" type="data" label="Aligned Reads" help="BAM format." />
+	<param format="tabular" name="input2" type="data" label="Barcodes" help="Produced by Debarcoding tool." />
+	<conditional name="priming"> 
+	    <param name="flag" type="boolean" checked="False" truevalue="True" falsevalue="False" label="Set priming position" help="Set all reads to have a specific priming position." />	
+	    <when value="True">
+	        <param name="position" type="integer" value="-1" label="Priming position" />
+	    </when>
+	</conditional>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="trimming_stats" label="${tool.name} on ${on_string}: Trimming stats" from_work_dir="output_dir/trimming_stats.txt" />
+        <data format="tabular" name="summary" label="${tool.name} on ${on_string}: Summary" from_work_dir="output_dir/summary.txt" />
+        <data format="tabular" name="unique_barcodes" label="${tool.name} on ${on_string}: Unique Barcodes" from_work_dir="output_dir/unique_barcodes.txt" />
+        <data format="tabular" name="read_counts" label="${tool.name} on ${on_string}: Read Counts" from_work_dir="output_dir/read_counts.txt" />
+    </outputs>
+    
+    <tests>
+	<test>
+	    <param name="input1" value="sample.bam" />
+	    <param name="input2" value="barcodes.txt" />
+	    <output name="trimming_stats" file="trimming_stats.txt" />
+	    <output name="summary" file="summary.txt" />
+	    <output name="unique_barcodes" file="unique_barcodes.txt" />
+	    <output name="read_counts" file="read_counts.txt" />
+	</test>
+    </tests>
+
+    <help>
+    </help>
+</tool>