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comparison merge_pcr_duplicates.xml @ 0:119fccb59597 draft

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author rnateam
date Thu, 22 Oct 2015 09:52:51 -0400
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1 <tool id="merge_pcr_duplicates.py" name="merge_pcr_duplicates.py" version="1.0">
2 <description>
3 </description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="requirements" />
8 <expand macro="stdio" />
9 <version_command>python merge_pcr_duplicates.py --version</version_command>
10 <command interpreter="python"><![CDATA[merge_pcr_duplicates.py
11 #if $positional_1 and $positional_1 is not None:
12 $positional_1
13 #end if
14
15 #if $positional_2 and $positional_2 is not None:
16 $positional_2
17 #end if
18
19 > $default]]></command>
20 <inputs>
21 <param area="false" label="bed6 file containing alignments." name="positional_1" type="data" format="bed"/>
22 <param area="false" label="fasta barcode library." name="positional_2" type="data" format="fasta"/>
23 </inputs>
24 <outputs>
25 <data format="bed" hidden="false" name="default"/>
26 </outputs>
27 <tests>
28 <test>
29 <param name="positional_1" value="pcr_dupes_sorted_2.bed"/>
30 <param name="positional_2" value="pcr_dupes_randomdict.fa"/>
31 <output name="default" file="merged_pcr_dupes.bed"/>
32 </test>
33 </tests>
34 <help><![CDATA[
35 Merge PCR duplicates according to random barcode library.
36
37 Barcodes containing uncalled base 'N' are removed.
38
39 Input:
40 * bed6 file containing alignments with fastq read-id in name field
41 * fasta library with fastq read-id as sequence ids
42
43 Output:
44 * bed6 file with random barcode in name field and number of PCR duplicates as score, sorted by fields chrom, start, stop, strand, name
45
46 Author: Daniel Maticzka
47 Copyright: 2015
48 License: Apache
49 Email: maticzkd@informatik.uni-freiburg.de
50 Status: Testing
51 ]]></help>
52 <expand macro="citations" />
53 </tool>