|
17
|
1 <tool id="macs2_filterdup" name="MACS2 filterdup" version="2.0.10.0">
|
|
|
2 <description>Remove duplicate reads at the same position</description>
|
|
|
3 <expand macro="requirements" />
|
|
|
4 <expand macro="version_command" />
|
|
|
5 <macros>
|
|
|
6 <import>macs2_macros.xml</import>
|
|
|
7 </macros>
|
|
|
8 <command>
|
|
|
9 macs2 filterdup
|
|
19
|
10 -i "${ infile }"
|
|
|
11 -o "${ outfile }"
|
|
17
|
12
|
|
19
|
13 --format '${ infile.extension.upper() }'
|
|
17
|
14 @effective_genome_size@
|
|
|
15 @tag_size@
|
|
19
|
16 --pvalue "${ pvalue }"
|
|
17
|
17 #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
|
|
19
|
18 --keep-dup "${ keep_dup_options.user_keepdup }"
|
|
17
|
19 #else
|
|
19
|
20 --keep-dup "${ keep_dup_options.keep_dup_options_selector }"
|
|
17
|
21 #end if
|
|
|
22 </command>
|
|
|
23 <expand macro="stdio" />
|
|
|
24 <inputs>
|
|
|
25 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
|
|
|
26 <expand macro="conditional_effective_genome_size" />
|
|
|
27 <expand macro="tag_size" />
|
|
|
28 <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="default: 1e-5 (--pvalue)" />
|
|
|
29
|
|
20
|
30 <expand macro="keep_duplicates" />
|
|
|
31
|
|
17
|
32 </inputs>
|
|
|
33 <outputs>
|
|
|
34 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
|
|
|
35 </outputs>
|
|
|
36 <tests>
|
|
|
37 <test>
|
|
|
38 <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/>
|
|
|
39 <param name="pvalue" value="1e-5"/>
|
|
|
40 <param name="keep_dup_options_selector" value="auto"/>
|
|
|
41 <param name="effective_genome_size_options_selector" value="3300000000"/>
|
|
|
42 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/>
|
|
|
43 </test>
|
|
|
44 </tests>
|
|
|
45 <help>
|
|
|
46 **What it does**
|
|
|
47
|
|
|
48 Remove duplicate reads at the same position, then convert acceptable format to BED format.
|
|
|
49 filterdup tool from macs2
|
|
|
50
|
|
|
51 @citation@
|
|
|
52 </help>
|
|
|
53 </tool>
|
