Mercurial > repos > iuc > macs2
annotate macs2_filterdup.xml @ 46:a2689a440ff4 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit baa6a1ec8b3c440cdf73409ccaafcd303e9f4e72
| author | iuc |
|---|---|
| date | Mon, 30 Nov 2015 21:56:47 -0500 |
| parents | 8c8ae1e19b10 |
| children | 1b3f899ef044 |
| rev | line source |
|---|---|
| 33 | 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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8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
6 <expand macro="requirements" /> |
|
8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
7 <expand macro="stdio" /> |
|
8c8ae1e19b10
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit 344140b8df53b8b7024618bb04594607a045c03a
iuc
parents:
33
diff
changeset
|
8 <expand macro="version_command" /> |
| 33 | 9 <command> |
| 10 macs2 filterdup | |
| 11 -i "${ infile }" | |
| 12 -o temp_outfile | |
| 13 | |
| 14 --format '${ infile.extension.upper() }' | |
| 15 @effective_genome_size@ | |
| 16 @tag_size@ | |
| 17 --pvalue "${ pvalue }" | |
| 18 #if str( $keep_dup_options.keep_dup_options_selector ) == "user": | |
| 19 --keep-dup "${ keep_dup_options.user_keepdup }" | |
| 20 #else | |
| 21 --keep-dup "${ keep_dup_options.keep_dup_options_selector }" | |
| 22 #end if | |
| 23 ; | |
| 24 mv temp_outfile "${ outfile }" | |
| 25 </command> | |
| 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> |