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comparison macs2_filterdup.xml @ 5:beb902da6e5f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
author iuc
date Sat, 08 Apr 2017 08:28:57 -0400
parents bfe57d6e0c4c
children acbd3fb47f90
comparison
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4:56e104999978 5:beb902da6e5f
4 <import>macs2_macros.xml</import> 4 <import>macs2_macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <expand macro="version_command" /> 8 <expand macro="version_command" />
9 <command> 9 <command><![CDATA[
10 macs2 filterdup 10 macs2 filterdup
11 -i "${ infile }" 11 -i '${ infile }'
12 -o temp_outfile 12 -o '${ outfile }'
13
14 --format '${ infile.extension.upper() }' 13 --format '${ infile.extension.upper() }'
15 @effective_genome_size@ 14 @effective_genome_size@
16 @tag_size@ 15 @tag_size@
17 --pvalue "${ pvalue }" 16 --pvalue '${ pvalue }'
18 #if str( $keep_dup_options.keep_dup_options_selector ) == "user": 17 #if str( $keep_dup_options.keep_dup_options_selector ) == "user":
19 --keep-dup "${ keep_dup_options.user_keepdup }" 18 --keep-dup '${ keep_dup_options.user_keepdup }'
20 #else 19 #else
21 --keep-dup "${ keep_dup_options.keep_dup_options_selector }" 20 --keep-dup '${ keep_dup_options.keep_dup_options_selector }'
22 #end if 21 #end if
23 ; 22 ]]>
24 mv temp_outfile "${ outfile }"
25 </command> 23 </command>
26 <inputs> 24 <inputs>
27 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> 25 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
28 <expand macro="conditional_effective_genome_size" /> 26 <expand macro="conditional_effective_genome_size" />
29 <expand macro="tag_size" /> 27 <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)" /> 28 <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" /> 29 <expand macro="keep_duplicates" />
33 30
34 </inputs> 31 </inputs>
35 <outputs> 32 <outputs>
36 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> 33 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
44 <param name="gsize" value="3300000000" /> 41 <param name="gsize" value="3300000000" />
45 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/> 42 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/>
46 </test> 43 </test>
47 </tests> 44 </tests>
48 <help> 45 <help>
46 <![CDATA[
49 **What it does** 47 **What it does**
50 48
51 Remove duplicate reads at the same position, then convert acceptable format to BED format. 49 This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format.
52 filterdup tool from macs2 50
51 .. _MACS2: https://github.com/taoliu/MACS
53 52
54 @citation@ 53 @citation@
54 ]]>
55 </help> 55 </help>
56 <expand macro="citations" /> 56 <expand macro="citations" />
57 </tool> 57 </tool>