Mercurial > repos > iuc > macs2
comparison macs2_bdgcmp.xml @ 0:fe62ba547975 draft
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| author | iuc |
|---|---|
| date | Wed, 11 Feb 2015 10:18:02 -0500 |
| parents | |
| children | bfe57d6e0c4c |
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| -1:000000000000 | 0:fe62ba547975 |
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| 1 <tool id="macs2_bdgcmp" name="MACS2 bdgcmp" version="@VERSION_STRING@.0"> | |
| 2 <description>Deduct noise by comparing two signal tracks in bedGraph</description> | |
| 3 <expand macro="requirements" /> | |
| 4 <expand macro="version_command" /> | |
| 5 <macros> | |
| 6 <import>macs2_macros.xml</import> | |
| 7 </macros> | |
| 8 <command> | |
| 9 macs2 bdgcmp | |
| 10 -t "${ infile_treatment }" | |
| 11 -c "${ infile_control }" | |
| 12 | |
| 13 -m "${ bdgcmp_options.bdgcmp_options_selector }" | |
| 14 #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']: | |
| 15 -p "${ bdgcmp_options.pseudocount }" | |
| 16 #end if | |
| 17 -o "${ outfile }" | |
| 18 | |
| 19 </command> | |
| 20 <expand macro="stdio" /> | |
| 21 <inputs> | |
| 22 <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" /> | |
| 23 <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" /> | |
| 24 | |
| 25 <conditional name="bdgcmp_options"> | |
| 26 <param name="bdgcmp_options_selector" type="select" label="Method to use while calculating a score in any bin by comparing treatment value and control value"> | |
| 27 <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option> | |
| 28 <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option> | |
| 29 <option value="subtract">subtraction from treatment (subtract)</option> | |
| 30 <option value="logFE">log10 fold enrichment (logFE)</option> | |
| 31 <option value="FE">linear scale fold enrichment (FE)</option> | |
| 32 <option value="logLR">log10 likelihood between ChIP-enriched model and open chromatin model (logLR)</option> | |
| 33 <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option> | |
| 34 </param> | |
| 35 <when value="FE"> | |
| 36 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/> | |
| 37 </when> | |
| 38 <when value="logLR"> | |
| 39 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/> | |
| 40 </when> | |
| 41 <when value="logFE"> | |
| 42 <param name="pseudocount" type="float" label="Set pseudocount" value="0.0" help="The count will be applied after normalization of sequencing depth. default: 0.0, no pseudocount is applied."/> | |
| 43 </when> | |
| 44 <when value="ppois"/> | |
| 45 <when value="qpois"/> | |
| 46 <when value="subtract"/> | |
| 47 <when value="slogLR"/> | |
| 48 </conditional> | |
| 49 </inputs> | |
| 50 <outputs> | |
| 51 <data name="outfile" format="bedgraph" label="${tool.name} on ${on_string}" /> | |
| 52 </outputs> | |
| 53 <tests> | |
| 54 <test> | |
| 55 <param name="infile_control" value="callpeak_control_part.bdg" ftype="bedgraph"/> | |
| 56 <param name="infile_treatment" value="callpeak_treatment_part.bdg" ftype="bedgraph"/> | |
| 57 <param name="bdgcmp_options_selector" value="slogLR"/> | |
| 58 <output name="outfile" file="bdgcmp_on_Control_and_ChIP_slogLR.bdg"/> | |
| 59 </test> | |
| 60 </tests> | |
| 61 <help> | |
| 62 **What it does** | |
| 63 | |
| 64 With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) | |
| 65 is getting popular to study genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq analysis method, we present a novel algorithm, named Model-based Analysis of ChIP-Seq (MACS), for | |
| 66 identifying transcript factor binding sites. MACS captures the influence of genome complexity to evaluate the significance of enriched ChIP regions, and MACS improves the spatial resolution of | |
| 67 binding sites through combining the information of both sequencing tag position and orientation. MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity. | |
| 68 | |
| 69 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README | |
| 70 | |
| 71 ------ | |
| 72 | |
| 73 **Usage** | |
| 74 | |
| 75 **Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. | |
| 76 | |
| 77 | |
| 78 @citation@ | |
| 79 </help> | |
| 80 <expand macro="citations" /> | |
| 81 </tool> |