diff tools/ilmn_pacbio/assembly_stats.xml @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/ilmn_pacbio/assembly_stats.xml	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,54 @@
+<tool id="assembly_stats" name="Assembly Statistics" version="1.0.0">
+    <description>Calculate common measures of assembly quality</description>
+    <command interpreter="python">
+        assembly_stats.py $input1 $output1 --minContigLength=${minLength}
+    </command>
+    <inputs>
+        <param name="input1" format="fasta" type="data" label="Select FASTA file containing contigs"/>
+        <param name="minLength" type="integer" value="0" label="Minimum length of contigs to consider"/>
+    </inputs>
+    <outputs>
+        <data name="output1" format="tabular" label="Assembly statistics for ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="3.fasta" ftype="fasta"/>
+            <param name="minLength" value="100"/>
+            <output name="output1" ftype="tabular" file="assembly_stats.tabular" />
+        </test>
+    </tests>
+    <help>
+
+**What it does**
+
+Reports standard measures of *de novo* assembly quality such as number of contigs, sum of contigs, mean contig length, and N50.
+
+**Parameter list**
+
+Minimum length
+    Only include contigs of this size or greater for calculating statistics.
+
+**Output**
+
+Num contigs
+    Total number of contigs in the assembly
+
+Sum of contig lengths
+    Total sum of contig lengths
+
+Maximum contig length
+    Maximum of the contig lengths
+
+Mean contig length
+    Average contig length
+
+N50
+    Contig length at which 50% of the assembly is contained in contigs of this size or greater.
+
+99%
+    Number of contigs accounting for 99% of the observed assembly.
+
+    </help>
+</tool>
+
+