Mercurial > repos > iuc > macs2
diff macs2_bdgcmp.xml @ 5:beb902da6e5f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/macs2 commit e10f301c7f8c54a7d12df4e631527197baccf70b
| author | iuc |
|---|---|
| date | Sat, 08 Apr 2017 08:28:57 -0400 |
| parents | bfe57d6e0c4c |
| children | acbd3fb47f90 |
line wrap: on
line diff
--- a/macs2_bdgcmp.xml Mon Feb 06 02:30:37 2017 -0500 +++ b/macs2_bdgcmp.xml Sat Apr 08 08:28:57 2017 -0400 @@ -7,23 +7,24 @@ <expand macro="stdio" /> <expand macro="version_command" /> <command> + <![CDATA[ macs2 bdgcmp - -t "${ infile_treatment }" - -c "${ infile_control }" + -t '${ infile_treatment }' + -c '${ infile_control }' - -m "${ bdgcmp_options.bdgcmp_options_selector }" + -m '${ bdgcmp_options.bdgcmp_options_selector }' #if str($bdgcmp_options.bdgcmp_options_selector) in ['FE', 'logFE', 'logLR']: - -p "${ bdgcmp_options.pseudocount }" + -p '${ bdgcmp_options.pseudocount }' #end if - -o "${ outfile }" - + -o '${ outfile }' + ]]> </command> <inputs> <param name="infile_treatment" type="data" format="bedgraph" label="Treatment bedGraph file" /> <param name="infile_control" type="data" format="bedgraph" label="Control bedGraph file" /> <conditional name="bdgcmp_options"> - <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"> + <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" help="Available choices are: ppois, qpois, subtract, logFE, logLR, and slogLR. They represent Poisson Pvalue (-log10(pvalue) form) using control as lambda and treatment as observation, q-value through a BH process for poisson pvalues, subtraction from treatment, linear scale fold enrichment, log10 fold enrichment(need to set pseudocount), log10 likelihood between ChIP-enriched model and open chromatin model(need to set pseudocount), symmetric log10 likelihood between two ChIP-enrichment models, or maximum value between the two tracks. Default=ppois (--method)."> <option value="ppois" selected="true">Poisson pvalue (-log10) using control as lambda and treatment as observation (ppois)</option> <option value="qpois">q-value through a BH process for poisson pvalues (qpois)</option> <option value="subtract">subtraction from treatment (subtract)</option> @@ -33,13 +34,13 @@ <option value="slogLR">symmetric log10 likelihood between two ChIP-enrichment models (slogLR)</option> </param> <when value="FE"> - <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."/> + <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)."/> </when> <when value="logLR"> - <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."/> + <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)."/> </when> <when value="logFE"> - <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."/> + <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)."/> </when> <when value="ppois"/> <when value="qpois"/> @@ -52,30 +53,22 @@ </outputs> <tests> <test> - <param name="infile_control" value="callpeak_control_part.bdg" ftype="bedgraph"/> - <param name="infile_treatment" value="callpeak_treatment_part.bdg" ftype="bedgraph"/> - <param name="bdgcmp_options_selector" value="slogLR"/> - <output name="outfile" file="bdgcmp_on_Control_and_ChIP_slogLR.bdg"/> + <param name="infile_control" value="bdgcmp_input_control.bdg" ftype="bedgraph"/> + <param name="infile_treatment" value="bdgcmp_input_treatment.bdg" ftype="bedgraph"/> + <param name="bdgcmp_options_selector" value="ppois"/> + <output name="outfile" file="bdgcmp_output.bdg"/> </test> </tests> <help> + <![CDATA[ **What it does** -With the improvement of sequencing techniques, chromatin immunoprecipitation followed by high throughput sequencing (ChIP-Seq) -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 -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 -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. - -View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README +This is **bdgcmp** utility from the MACS2_ Package. It is designed to deduct noise by comparing two signal tracks in bedGraph. ------- - -**Usage** - -**Compare .bdg files**: Deduct noise by comparing two signal tracks in bedGraph. - +.. _MACS2: https://github.com/taoliu/MACS @citation@ +]]> </help> <expand macro="citations" /> </tool>