diff extract_aln_ends.xml @ 0:0e70f9058b02 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit ae3b9baaf7040ed8b165d17466b8b2fe016d3d48

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extract_aln_ends.xml	Tue Nov 14 05:53:02 2017 -0500
@@ -0,0 +1,49 @@
+<tool id="bctools_extract_alignment_ends" name="Extract alignment ends" version="@VERSION@">
+    <description>from SAM or BAM</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        extract_aln_ends.py
+        '$alignments'
+        > '$alignment_ends'
+    ]]></command>
+    <inputs>
+        <param name="alignments" type="data" format="sam,bam" label="Alignments in SAM or BAM format"/>
+    </inputs>
+    <outputs>
+        <data name="alignment_ends" format="bed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="alignments" value="twomates.sam"/>
+            <output name="alignment_ends" file="tworeads_aln_ends.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+bctools - Extract alignment ends from from SAM or BAM alignments
+================================================================
+
+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:
+------
+
+* BAM file containing alignments (paired-end sequencing)
+
+Output:
+-------
+
+* BED file containing outer coordinates (sorted by read id)
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>