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comparison macs2_filterdup.xml @ 0:fe62ba547975 draft

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author iuc
date Wed, 11 Feb 2015 10:18:02 -0500
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1 <tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.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
10 -i "${ infile }"
11 -o temp_outfile
12
13 --format '${ infile.extension.upper() }'
14 @effective_genome_size@
15 @tag_size@
16 --pvalue "${ pvalue }"
17 #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
18 --keep-dup "${ keep_dup_options.user_keepdup }"
19 #else
20 --keep-dup "${ keep_dup_options.keep_dup_options_selector }"
21 #end if
22 ;
23 mv temp_outfile "${ outfile }"
24 </command>
25 <expand macro="stdio" />
26 <inputs>
27 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
28 <expand macro="conditional_effective_genome_size" />
29 <expand macro="tag_size" />
30 <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="default: 1e-5 (--pvalue)" />
31
32 <expand macro="keep_duplicates" />
33
34 </inputs>
35 <outputs>
36 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
37 </outputs>
38 <tests>
39 <test>
40 <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/>
41 <param name="pvalue" value="1e-5"/>
42 <param name="keep_dup_options_selector" value="auto"/>
43 <param name="effective_genome_size_options_selector" value="user_defined" />
44 <param name="gsize" value="3300000000" />
45 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/>
46 </test>
47 </tests>
48 <help>
49 **What it does**
50
51 Remove duplicate reads at the same position, then convert acceptable format to BED format.
52 filterdup tool from macs2
53
54 @citation@
55 </help>
56 <expand macro="citations" />
57 </tool>