Mercurial > repos > iuc > macs2
annotate macs2_filterdup.xml @ 6:2119d851a53b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit df97bfd630719a2e1d4e11d67960753184afa238
| author | iuc |
|---|---|
| date | Tue, 11 Apr 2017 17:46:41 -0400 |
| parents | beb902da6e5f |
| children | acbd3fb47f90 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="macs2_filterdup" name="MACS2 filterdup" version="@VERSION_STRING@.0"> |
| 2 <description>Remove duplicate reads at the same position</description> | |
| 3 <macros> | |
| 4 <import>macs2_macros.xml</import> | |
| 5 </macros> | |
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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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6 <expand macro="requirements" /> |
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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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0
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changeset
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7 <expand macro="stdio" /> |
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bfe57d6e0c4c
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 63955994af5090ec444c03c221df0012d5ae4e74
iuc
parents:
0
diff
changeset
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8 <expand macro="version_command" /> |
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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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2
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changeset
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9 <command><![CDATA[ |
| 0 | 10 macs2 filterdup |
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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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11 -i '${ infile }' |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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12 -o '${ outfile }' |
| 0 | 13 --format '${ infile.extension.upper() }' |
| 14 @effective_genome_size@ | |
| 15 @tag_size@ | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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16 --pvalue '${ pvalue }' |
| 0 | 17 #if str( $keep_dup_options.keep_dup_options_selector ) == "user": |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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18 --keep-dup '${ keep_dup_options.user_keepdup }' |
| 0 | 19 #else |
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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 '${ keep_dup_options.keep_dup_options_selector }' |
| 0 | 21 #end if |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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22 ]]> |
| 0 | 23 </command> |
| 24 <inputs> | |
| 25 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> | |
| 26 <expand macro="conditional_effective_genome_size" /> | |
| 27 <expand macro="tag_size" /> | |
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5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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28 <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" /> |
| 0 | 29 <expand macro="keep_duplicates" /> |
| 30 | |
| 31 </inputs> | |
| 32 <outputs> | |
| 33 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" /> | |
| 34 </outputs> | |
| 35 <tests> | |
| 36 <test> | |
| 37 <param name="infile" value="ChIP_200K_w_dups.bed" ftype="bed"/> | |
| 38 <param name="pvalue" value="1e-5"/> | |
| 39 <param name="keep_dup_options_selector" value="auto"/> | |
| 40 <param name="effective_genome_size_options_selector" value="user_defined" /> | |
| 41 <param name="gsize" value="3300000000" /> | |
| 42 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/> | |
| 43 </test> | |
| 44 </tests> | |
| 45 <help> | |
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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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46 <![CDATA[ |
| 0 | 47 **What it does** |
| 48 | |
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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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49 This is **filterdup** utility from the MACS2_ Package. It removes duplicate reads and converts results to BED format. |
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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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50 |
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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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51 .. _MACS2: https://github.com/taoliu/MACS |
| 0 | 52 |
| 53 @citation@ | |
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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 ]]> |
| 0 | 55 </help> |
| 56 <expand macro="citations" /> | |
| 57 </tool> |