Mercurial > repos > iuc > macs2
annotate macs2_filterdup.xml @ 13:01cded2297b7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 1cf6ca65ca6bbf3553d830f13be1760dcd667cae
| author | iuc |
|---|---|
| date | Fri, 04 May 2018 21:39:56 -0400 |
| parents | acbd3fb47f90 |
| children | 424aefbd7777 |
| 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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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
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0
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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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9 <command><![CDATA[ |
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9
acbd3fb47f90
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 586ecaebf9e6020fac2674fbda368e293d1c9bc2
iuc
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5
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10 @home_dir@ |
| 0 | 11 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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12 -i '${ infile }' |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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13 -o '${ outfile }' |
| 0 | 14 --format '${ infile.extension.upper() }' |
| 15 @effective_genome_size@ | |
| 16 @tag_size@ | |
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beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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17 --pvalue '${ pvalue }' |
| 0 | 18 #if str( $keep_dup_options.keep_dup_options_selector ) == "user": |
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5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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19 --keep-dup '${ keep_dup_options.user_keepdup }' |
| 0 | 20 #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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21 --keep-dup '${ keep_dup_options.keep_dup_options_selector }' |
| 0 | 22 #end if |
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5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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23 ]]> |
| 0 | 24 </command> |
| 25 <inputs> | |
| 26 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" /> | |
| 27 <expand macro="conditional_effective_genome_size" /> | |
| 28 <expand macro="tag_size" /> | |
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5
beb902da6e5f
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
iuc
parents:
2
diff
changeset
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29 <param name="pvalue" type="text" value="1e-5" label="Pvalue cutoff for binomial distribution test" help="Default=1e-5 (--pvalue)" /> |
| 0 | 30 <expand macro="keep_duplicates" /> |
| 31 | |
| 32 </inputs> | |
| 33 <outputs> | |
| 34 <data name="outfile" format="bed" label="${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="user_defined" /> | |
| 42 <param name="gsize" value="3300000000" /> | |
| 43 <output name="outfile" file="filterdup_on_ChIP_200K_w_dups.bed"/> | |
| 44 </test> | |
| 45 </tests> | |
| 46 <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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47 <![CDATA[ |
| 0 | 48 **What it does** |
| 49 | |
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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 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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51 |
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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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52 .. _MACS2: https://github.com/taoliu/MACS |
| 0 | 53 |
| 54 @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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55 ]]> |
| 0 | 56 </help> |
| 57 <expand macro="citations" /> | |
| 58 </tool> |