diff merge_pcr_duplicates.xml @ 2:de4ea3aa1090 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge_pcr_duplicates.xml	Thu Oct 22 10:26:45 2015 -0400
@@ -0,0 +1,52 @@
+<tool id="merge_pcr_duplicates.py" name="merge_pcr_duplicates.py" version="1.0">
+  <description>Merge PCR duplicates according to random barcode library.</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <version_command>python merge_pcr_duplicates.py --version</version_command>
+  <command interpreter="python"><![CDATA[merge_pcr_duplicates.py
+#if $positional_1 and $positional_1 is not None:
+$positional_1
+#end if
+
+#if $positional_2 and $positional_2 is not None:
+$positional_2
+#end if
+
+> $default]]></command>
+  <inputs>
+    <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
+    <param area="false" label="fasta barcode library." name="positional_2" type="data" format="fasta"/>
+  </inputs>
+  <outputs>
+    <data format="bed" hidden="false" name="default"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="positional_1" value="pcr_dupes_sorted_2.bed"/>
+      <param name="positional_2" value="pcr_dupes_randomdict.fa"/>
+      <output name="default" file="merged_pcr_dupes.bed"/>
+    </test>
+  </tests>
+  <help><![CDATA[
+Merge PCR duplicates according to random barcode library.
+
+Barcodes containing uncalled base 'N' are removed.
+
+Input:
+* bed6 file containing alignments with fastq read-id in name field
+* fasta library with fastq read-id as sequence ids
+
+Output:
+* bed6 file with random barcode in name field and number of PCR duplicates as score, sorted by fields chrom, start, stop, strand, name
+
+Author: Daniel Maticzka
+Copyright: 2015
+License: Apache
+Email: [e-mail]
+Status: Testing
+]]></help>
+  <expand macro="citations" />
+</tool>