diff extract_aln_ends.xml @ 0:119fccb59597 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_aln_ends.xml	Thu Oct 22 09:52:51 2015 -0400
@@ -0,0 +1,52 @@
+<tool id="extract_aln_ends.py" name="extract_aln_ends.py" version="0.1.0">
+  <description>Extract alignment ends from sam file.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <version_command>python extract_aln_ends.py --version</version_command>
+  <command interpreter="python"><![CDATA[
+extract_aln_ends.py
+#if $positional_1 and $positional_1 is not None:
+$positional_1
+#end if
+
+> $default]]></command>
+  <inputs>
+    <param area="false" label="Sam input." name="positional_1" type="data" format="sam"/>
+  </inputs>
+  <outputs>
+    <data format="bed" hidden="false" name="default"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="positional_1" value="twomates.sam"/>
+      <output name="default" file="tworeads_aln_ends.bed"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+Extract alignment ends from sam file.
+
+The resulting bed file contains the outer coordinates of the alignments. The
+bed name field is set to the read id and the score field is set to the edit
+distance of the alignment. The crosslinked nucleotide is one nt upstream of the
+5'-end of the bed entries.
+
+This tool only reports results for alignments that are properly aligned in FR
+("forward-reverse") direction.
+
+Input:
+* sam file containing alignments (paired-end sequencing)
+
+Output:
+* bed6 file containing outer coordinates (sorted by read id)
+
+Author: Daniel Maticzka
+Copyright: 2015
+License: Apache
+Email: [e-mail]
+Status: Development
+]]></help>
+  <expand macro="citations" />
+</tool>