diff merge_pcr_duplicates.xml @ 0:daad7189e48e 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/merge_pcr_duplicates.xml	Tue Nov 14 05:53:44 2017 -0500
@@ -0,0 +1,51 @@
+<tool id="bctools_merge_pcr_duplicates" name="Merge PCR duplicates" version="@VERSION@">
+    <description>according to UMIs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        merge_pcr_duplicates.py
+        '$alignments_bed'
+        '$barcode_library'
+        --outfile '$events'
+    ]]></command>
+    <inputs>
+        <param name="alignments_bed" type="data" format="bed" label="BED6 file containing alignments" />
+        <param name="barcode_library" type="data" format="fastq" label="FASTQ barcode library" />
+    </inputs>
+    <outputs>
+        <data name="events" format="bed"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="alignments_bed" value="pcr_dupes_sorted_2.bed"/>
+            <param name="barcode_library" value="pcr_dupes_randomdict.fastq"/>
+            <output name="events" file="merged_pcr_dupes.bed"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+bctools - Merge PCR duplicates according to UMIs
+================================================
+
+Merge PCR duplicates according to unique molecular identifier (UMI) library. All alignments with
+same outer coordinates and barcode will be merged into a single crosslinking
+event.
+
+Barcodes containing uncalled base 'N' are removed.
+
+Input:
+------
+
+* BED6 file containing alignments with FASTQ read-id in name field
+* FASTQ library of UMIs
+
+Output:
+-------
+
+* BED6 file with a read id from a representative alignment in the name field and number of PCR duplicates as score, sorted by fields chrom, start, stop, strand, name
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>