# HG changeset patch
# User dktanwar
# Date 1508175895 14400
# Node ID 050a7438485a82e1b7f795158272ce77563c8148
# Parent  6376a1b6df655d65dbbcad67d380e25f38a15294
Uploaded

diff -r 6376a1b6df65 -r 050a7438485a RemoveSNPs.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/RemoveSNPs.xml	Mon Oct 16 13:44:55 2017 -0400
@@ -0,0 +1,34 @@
+<tool id="RemoveSNPs" name="Remove Mismatches (SNPs) from SAM Alignment file" version="0.1.0">
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        bash $__tool_directory__/RemoveSNPs "$input1" 3 > "$output1"
+    ]]></command>
+    <inputs>
+        <param type="data" name="SAM alignment files" format="sam" />
+	<param type="integer" name="SNPs/ mismatches allowed" value="3" />
+    </inputs>
+    <outputs>
+        <data name="output1" format="sam" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="input.sam"/>
+            <output name="output1" file="output.sam"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        This program will remove mismatches from sam file.\n Usage: RemoveSNPs test.sam 3
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{RemoveSNPs,
+  author = {Tanwar, Deepak},
+  year = {2017},
+  title = {RemoveSNPs},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/dktanwar/NGS_Sperm_H3K4me3_Planemo_tools/tree/master/01_RemoveSNPs},
+}</citation>
+    </citations>
+</tool>