diff pe_sync.xml @ 0:751f4938cf0d

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pe_sync.xml	Tue Feb 05 15:23:18 2013 -0500
@@ -0,0 +1,32 @@
+<tool id="pe_sync" name="pe-sync: Paired-end synchronization check" version="1.0">
+  <description>The Paired-end synchronization check program determines if the reads in paired-end fastq files are in the proper order (synchronized).</description>
+  <command interpreter="perl">
+    pe_sync_2_files.pl $quickcheck $input1 $input2 2>&amp;1 | tee $output
+  </command>
+  <inputs>
+    <param name="input1" type="data" format="fastq" label="Input 1"/>
+    <param name="input2" type="data" format="fastq" label="Input 2"/>
+    <param name="quickcheck" type="boolean" truevalue="quick" falsevalue="" checked="false" label="Just check a sample of the sequences"
+           help=""/>
+  </inputs>
+  <stdio>
+    <exit_code range="1:"  level="fatal"   description="Bad input dataset" />
+  </stdio>
+  <outputs>
+    <data format="txt" name="output" label="pe-sync report for ${input1.name} and ${input2.name}"/>
+  </outputs>
+  <tests>
+    <test>
+    </test>
+  </tests>
+  <help>
+Paired-end read file synchronization checks if left and right reads are in the same order.
+
+The "quick" option will not report the percent of out-of-sync reads
+for many failed files, but will run much faster.
+
+This script can handle Casava 1.8.0 style read IDs, and pre 1.8.0 style ids.
+Other types of read ID formats may cause a terminal error. 
+
+  </help>
+</tool>