Mercurial > repos > iuc > macs2
annotate macs2_filterdup.xml @ 19:86e2413cf3f8 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 7bd4238efae0d755b6a0dfff8daa43a228f18d96
author | iuc |
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date | Mon, 16 Oct 2023 13:18:37 +0000 |
parents | 640d3af5d833 |
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rev | line source |
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640d3af5d833
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents:
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1 <tool id="macs2_filterdup" name="MACS2 filterdup" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> |
0 | 2 <description>Remove duplicate reads at the same position</description> |
3 <macros> | |
4 <import>macs2_macros.xml</import> | |
5 </macros> | |
19
86e2413cf3f8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 7bd4238efae0d755b6a0dfff8daa43a228f18d96
iuc
parents:
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6 <expand macro="bio_tools"/> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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7 <expand macro="requirements" /> |
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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8 <expand macro="stdio" /> |
bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
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0
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9 <expand macro="version_command" /> |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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10 <command><![CDATA[ |
9
acbd3fb47f90
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
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11 @home_dir@ |
0 | 12 macs2 filterdup |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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changeset
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13 -i '${ infile }' |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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14 -o '${ outfile }' |
0 | 15 --format '${ infile.extension.upper() }' |
16 @effective_genome_size@ | |
17 @tag_size@ | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
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changeset
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18 --pvalue '${ pvalue }' |
0 | 19 #if str( $keep_dup_options.keep_dup_options_selector ) == "user": |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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20 --keep-dup '${ keep_dup_options.user_keepdup }' |
0 | 21 #else |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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22 --keep-dup '${ keep_dup_options.keep_dup_options_selector }' |
0 | 23 #end if |
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640d3af5d833
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents:
17
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changeset
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24 @buffer_size@ |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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25 ]]> |
0 | 26 </command> |
27 <inputs> | |
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424aefbd7777
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e90e79e18362561d0060d2c162f1938feebdbc29
iuc
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28 <param name="infile" type="data" format="bam,bed" label="Sequencing alignment file" /> |
0 | 29 <expand macro="conditional_effective_genome_size" /> |
30 <expand macro="tag_size" /> | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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31 <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" /> |
0 | 32 <expand macro="keep_duplicates" /> |
18
640d3af5d833
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e8307adcc6ee9245fa2bb9ecb6de1cbe008dc2c3"
iuc
parents:
17
diff
changeset
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33 <expand macro="buffer_size"/> |
0 | 34 </inputs> |
35 <outputs> | |
36 <data name="outfile" format="bed" label="${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> | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
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49 <![CDATA[ |
0 | 50 **What it does** |
51 | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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52 This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format. |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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53 |
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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54 .. _MACS2: https://github.com/taoliu/MACS |
0 | 55 |
56 @citation@ | |
5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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57 ]]> |
0 | 58 </help> |
59 <expand macro="citations" /> | |
60 </tool> |