comparison hifive_macros.xml @ 1:cb4f92e6fd4e draft

planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit ded5555ebf85f4807cbe4f1bf1945a757bdc724d

0:0a9c76d80e33

        <!-- Options controlling binning size-->
        <param type="integer" name="binsize" value="10000" label="Binsize" optional="False" help="A value of zero will return unbinned data.">
            <validator type="in_range" min="0"/>
        </param>
    </xml>
    <token name="@HIC_DYNAMIC@">
#if str( $command.dynamic.binning ) == "yes":
    -y
    -x $command.dynamic.expbinsize
    -f $command.dynamic.minobs

Create HiC heatmap set / Create 5C heatmap set - this command creates a set of heatmaps, one per chromosome and, if selected, one per chromosome pair (trans), in a compact HDF5 format. Heatmaps can also be plotted at the time of creation.

Extract HiC interval / Extract 5C interval - this command returns a genomic interval files with data from a specified region. This data may also be plotted at the tie of extraction.

]]></token>
    <token name="@HIC_HELP@"><![CDATA[
HiC genomic partitioning - fend file
----------------------------------------

The express algorithm is a variant of matrix balancing and approximates the corrections through an iterative norm-2 adjustment to given all fragments a mean ratio of one for valid counts versus signal predicted from distance-dependence. This can be done using intra-regional interactions, inter-regional interactions, or all interactions.

The binning algorithm divides each model parameter into some number of bins and based on a binomial distribution, correction values for each bin are learned, maximizing the log-likelihood of the data. Model parameters can be the fend lengths ('len'), fend GC content ('gc'), and any other characteristics passed as additional columns (with header labels) in the bed file used to create the HiFive fend file. Each parameter has a number of bins specified to divide it into and can be partitioned according to its type to contain approximately equal numbers of fends ('even'), or to cover equal portions of the range of parameter values ('fixed'). In addition, parameter types can include the '-const' suffix to denote a parameter that should not be optimized after seeding.

]]></token>
    <token name="@5C_HELP@"><![CDATA[
5C genomic partitioning - fragment file
---------------------------------------

1:cb4f92e6fd4e

        <!-- Options controlling binning size-->
        <param type="integer" name="binsize" value="10000" label="Binsize" optional="False" help="A value of zero will return unbinned data.">
            <validator type="in_range" min="0"/>
        </param>
    </xml>
    <token name="@MRH_OPTIONS@">
-f $command.mrhminobs
-b $command.mrhminbinsize
-B $command.mrhmaxbinsize
#if str( $command.mrhtransminbinsize ) != "":
    -r $command.mrhtransminbinsize
#end if
#if str( $command.mrhtransmaxbinsize ) != "":
    -R $command.mrhtransmaxbinsize
#end if
    </token>
    <xml name="mrh_options_xml">
        <param name="mrhminobs" type="integer" label="Minimum observations" value="20" help="The number of observations needed to include a bin." >
            <validator type="in_range" min="1"/>
        </param>
        <!-- Options controlling binning sizes-->
        <param type="integer" name="mrhminbinsize" label="Cis minimum binsize (bp)" value="5000" >
            <validator type="in_range" min="1"/>
        </param>
        <param type="integer" name="mrhmaxbinsize" label="Cis maximum binsize (bp)" value="1280000" help="Must be a multiple of an integer power of two times the minimum binsize (i.e. minbin * 2^N = maxbin for an integer N). ">
            <validator type="in_range" min="1"/>
        </param>
        <param type="integer" name="mrhtransminbinsize" label="Trans minimum binsize (bp)" value='' help="If not specified, this will be set to the cis minimum binsize." />
        <param type="integer" name="mrhtransmaxbinsize" label="Trans maximum binsize (bp)" value='' help="If not specified, this will be set to the cis maximum binsize." />
    </xml>
    <token name="@HIC_DYNAMIC@">
#if str( $command.dynamic.binning ) == "yes":
    -y
    -x $command.dynamic.expbinsize
    -f $command.dynamic.minobs

Create HiC heatmap set / Create 5C heatmap set - this command creates a set of heatmaps, one per chromosome and, if selected, one per chromosome pair (trans), in a compact HDF5 format. Heatmaps can also be plotted at the time of creation.

Extract HiC interval / Extract 5C interval - this command returns a genomic interval files with data from a specified region. This data may also be plotted at the tie of extraction.

Create HiC multi-resolution heatmap - this command returns a multi-resolution heatmap file with data heatmapped across resolutions from the smallest to largest specified binsizes in 2X steps.

]]></token>
    <token name="@HIC_HELP@"><![CDATA[
HiC genomic partitioning - fend file
----------------------------------------

The express algorithm is a variant of matrix balancing and approximates the corrections through an iterative norm-2 adjustment to given all fragments a mean ratio of one for valid counts versus signal predicted from distance-dependence. This can be done using intra-regional interactions, inter-regional interactions, or all interactions.

The binning algorithm divides each model parameter into some number of bins and based on a binomial distribution, correction values for each bin are learned, maximizing the log-likelihood of the data. Model parameters can be the fend lengths ('len'), fend GC content ('gc'), and any other characteristics passed as additional columns (with header labels) in the bed file used to create the HiFive fend file. Each parameter has a number of bins specified to divide it into and can be partitioned according to its type to contain approximately equal numbers of fends ('even'), or to cover equal portions of the range of parameter values ('fixed'). In addition, parameter types can include the '-const' suffix to denote a parameter that should not be optimized after seeding.

HiC multi-resolution heatmapping
--------------------------------

Multi-resolution heatmapping (MRH) allows multiple levels of resolution to be stored and accessed simultaneously using an intelligent binning scheme that only accepts bin with a number of observed reads meeting the minimum observation threshold. MRH files can be interactively explored through the MRH plugin in Galaxy.

]]></token>
    <token name="@5C_HELP@"><![CDATA[
5C genomic partitioning - fragment file
---------------------------------------