Mercurial > repos > sauria > hifive
changeset 0:0a9c76d80e33 draft
planemo upload for repository https://github.com/bxlab/galaxy_tools/suites/suite_hifive commit abaefa638db82abe90f335d783c9503dce28944f-dirty
| author | sauria |
|---|---|
| date | Fri, 05 Jun 2015 14:09:00 -0400 |
| parents | |
| children | cb4f92e6fd4e |
| files | hifive.xml hifive_macros.xml readme.rst tool_dependencies.xml |
| diffstat | 4 files changed, 1292 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hifive.xml Fri Jun 05 14:09:00 2015 -0400 @@ -0,0 +1,390 @@ +<?xml version="1.0"?> +<tool id="hifive" name="hifive" version="@WRAPPER_VERSION@.0"> + <description>manipulate, analyze, and plot HiC and 5C chromatin interaction data</description> + <macros> + <import>hifive_macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <command><![CDATA[ +hifive + +$command.command_select + +#if str( $command.command_select ) == "hic-complete": + @HIC_NORMALIZE@ + @HIC_FEND@ + @HIC_SEQUENCE@ + @HIC_CHROMOSOMES@ + @HIC_PROJECT@ + @HIC_RANGE@ + -o $hic_comp_fends $hic_comp_data $hic_comp_project +#end if +#if str( $command.command_select ) == "fends": + @HIC_FEND@ + $hic_fend_output +#end if +#if str( $command.command_select ) == "hic-data": + @HIC_SEQUENCE@ + $fends $hic_data_output +#end if +#if str( $command.command_select ) == "hic-project": + @HIC_CHROMOSOMES@ + @HIC_PROJECT@ + @HIC_RANGE@ + $hic_data $hic_project_output +#end if +#if str( $command.command_select ) == "hic-normalize": + @HIC_NORMALIZE@ + @HIC_CHROMOSOMES@ + @HIC_RANGE@ + -o $hic_norm_output + $hic_project +#end if +#if str( $command.command_select ) == "hic-heatmap": + @HIC_CHROMOSOMES@ + $command.trans1 + @BINSIZE@ + @HIC_DATATYPE@ + @HIC_DYNAMIC@ + #if str( $command.image.generate ) == "yes": + @IMAGE@ + -i $hic_hm_image + #end if + $hic_project $hic_hm_output +#end if +#if str( $command.command_select ) == "hic-interval": + -c $command.chrom + #if $command.start: + -s $command.start + #end if + #if $command.stop: + -e $command.stop + #end if + #if $command.maxdist: + -m $command.maxdist + #end if + @BINSIZE@ + @HIC_DATATYPE@ + @HIC_DYNAMIC@ + #if str( $command.image.generate ) == "yes": + @IMAGE@ + @ROTATE@ + -i $hic_int_image + #end if + $hic_project $hic_int_output +#end if +#if str( $command.command_select ) == "5c-complete": + @5C_NORMALIZE@ + @5C_SEQUENCE@ + @5C_REGIONS@ + @5C_PROJECT@ + @5C_RANGE@ + -o $fivec_comp_frags $fivec_comp_data $fivec_comp_project + @5C_FRAGMENT@ +#end if +#if str( $command.command_select ) == "fragments": + @5C_FRAGMENT@ + $fivec_frag_output +#end if +#if str( $command.command_select ) == "5c-data": + @5C_SEQUENCE@ + $fragments $fivec_data_output +#end if +#if str( $command.command_select ) == "5c-project": + @5C_REGIONS@ + @5C_PROJECT@ + @5C_RANGE@ + $fivec_data $fivec_project_output +#end if +#if str( $command.command_select ) == "5c-normalize": + @5C_NORMALIZE@ + @5C_REGIONS@ + @5C_RANGE@ + -o $fivec_norm_output + $fivec_project +#end if +#if str( $command.command_select ) == "5c-heatmap": + @5C_REGIONS@ + $command.trans2 + @BINSIZE@ + @5C_DATATYPE@ + @5C_DYNAMIC@ + #if str( $command.image.generate ) == "yes": + @IMAGE@ + -i $fivec_hm_image + #end if + $fivec_project $fivec_hm_output +#end if +#if str( $command.command_select ) == "5c-interval": + -c $command.region + #if $command.start: + -s $command.start + #end if + #if $command.stop: + -e $command.stop + #end if + @BINSIZE@ + @5C_DATATYPE@ + @5C_DYNAMIC@ + #if str( $command.image.generate ) == "yes": + @IMAGE@ + @ROTATE@ + -i $fivec_int_image + #end if + $fivec_project $fivec_int_output +#end if + -q + + ]]></command> + <inputs> + <conditional name="command"> + <param name="command_select" type="select" label="Select action to perform"> + <option value="hic-complete">Complete HiC analysis</option> + <option value="5c-complete">Complete 5C analysis</option> + <option value="fends">Create HiC fend set</option> + <option value="hic-data">Create HiC data set</option> + <option value="hic-project">Create HiC project</option> + <option value="hic-normalize">Normalize HiC project</option> + <option value="hic-heatmap">Create HiC heatmap set</option> + <option value="hic-interval">Extract HiC interval</option> + <option value="fragments">Create 5C fragment set</option> + <option value="5c-data">Create 5C data set</option> + <option value="5c-project">Create 5C project</option> + <option value="5c-normalize">Normalize 5C project</option> + <option value="5c-heatmap">Create 5C heatmap set</option> + <option value="5c-interval">Extract 5C interval</option> + </param> + <when value="hic-complete"> + <expand macro="hic_fend_xml"/> + <expand macro="hic_sequence_xml"/> + <expand macro="hic_chromosomes_xml"/> + <expand macro="hic_project_xml"/> + <expand macro="hic_range_xml"/> + <expand macro="hic_normalize_xml"/> + </when> + <when value="fends"> + <expand macro="hic_fend_xml"/> + </when> + <when value="hic-data"> + <param format="h5" name="fends" type="data" label="HiFive fend file" optional="False"/> + <expand macro="hic_sequence_xml"/> + </when> + <when value="hic-project"> + <param format="h5" name="hic_data" type="data" label="HiFive HiC data file" optional="False"/> + <expand macro="hic_chromosomes_xml"/> + <expand macro="hic_project_xml"/> + <expand macro="hic_range_xml"/> + </when> + <when value="hic-normalize"> + <param format="h5" name="hic_project" type="data" label="HiFive HiC project file" optional="False"/> + <expand macro="hic_chromosomes_xml"/> + <expand macro="hic_range_xml"/> + <expand macro="hic_normalize_xml"/> + </when> + <when value="hic-heatmap"> + <param name="hic_project" type="data" format="h5" label="HiFive HiC project file" optional="False"/> + <expand macro="hic_chromosomes_xml"/> + <param type="select" name="trans1" label="Calculate and include trans interactions"> + <option value="-t">yes</option> + <option value="">no</option> + </param> + <expand macro="binsize_xml"/> + <expand macro="hic_datatype_xml"/> + <expand macro="dynamic_xml"/> + <conditional name="image"> + <param name="generate" type="select" label="Generate image"> + <option value="yes">yes</option> + <option value="no">no</option> + </param> + <when value="yes"> + <expand macro="image_xml"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="hic-interval"> + <param name="hic_project" type="data" format="h5" label="HiFive HiC project file" optional="False"/> + <param type="text" name="chrom" size="10" label="Chromosome" optional="False"> + <validator type="empty_field" /> + </param> + <param type="integer" name="start" value="0" label="Starting coordinate" optional="True"> + <validator type="in_range" min="0"/> + </param> + <param type="integer" name="stop" value="0" label="Stopping coordinate" optional="True"> + <validator type="in_range" min="0"/> + </param> + <expand macro="binsize_xml"/> + <param type="integer" name="maxdist" value="0" label="Maximum interaction distance" optional="True" help="A value of zero will include all interaction distances that fall between the start and stop coordinates."> + <validator type="in_range" min="0"/> + </param> + <expand macro="hic_datatype_xml"/> + <expand macro="dynamic_xml"/> + <conditional name="image"> + <param name="generate" type="select" label="Generate image"> + <option value="yes">yes</option> + <option value="no">no</option> + </param> + <when value="yes"> + <expand macro="image_xml"/> + <expand macro="rotate_xml"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="5c-complete"> + <expand macro="5c_fragment_xml"/> + <expand macro="5c_sequence_xml"/> + <expand macro="5c_regions_xml"/> + <expand macro="5c_project_xml"/> + <expand macro="5c_range_xml"/> + <expand macro="5c_normalize_xml"/> + </when> + <when value="fragments"> + <expand macro="5c_fragment_xml"/> + </when> + <when value="5c-data"> + <param format="h5" name="fragments" type="data" label="HiFive fragment file" optional="False"/> + <expand macro="5c_sequence_xml"/> + </when> + <when value="5c-project"> + <param format="h5" name="fivec_data" type="data" label="HiFive 5C data file" optional="False"/> + <expand macro="5c_regions_xml"/> + <expand macro="5c_project_xml"/> + <expand macro="5c_range_xml"/> + </when> + <when value="5c-normalize"> + <param format="h5" name="fivec_project" type="data" label="HiFive 5C project file" optional="False"/> + <expand macro="5c_regions_xml"/> + <expand macro="5c_range_xml"/> + <expand macro="5c_normalize_xml"/> + </when> + <when value="5c-heatmap"> + <param name="fivec_project" type="data" format="h5" label="HiFive 5C project file" optional="False"/> + <expand macro="5c_regions_xml"/> + <param type="select" name="trans2" label="Calculate and include trans interactions"> + <option value="-t">yes</option> + <option value="">no</option> + </param> + <expand macro="binsize_xml"/> + <expand macro="5c_datatype_xml"/> + <expand macro="dynamic_xml"/> + <conditional name="image"> + <param name="generate" type="select" label="Generate image"> + <option value="yes">yes</option> + <option value="no">no</option> + </param> + <when value="yes"> + <expand macro="image_xml"/> + </when> + <when value="no"/> + </conditional> + </when> + <when value="5c-interval"> + <param name="fivec_project" type="data" format="h5" label="HiFive 5C project file" optional="False"/> + <param type="integer" name="region" value="" label="Region" optional="False"> + <validator type="empty_field" /> + </param> + <param type="integer" name="start" value="0" label="Starting coordinate" optional="True"> + <validator type="in_range" min="0"/> + </param> + <param type="integer" name="stop" value="0" label="Stopping coordinate" optional="True"> + <validator type="in_range" min="0"/> + </param> + <expand macro="binsize_xml"/> + <expand macro="5c_datatype_xml"/> + <expand macro="dynamic_xml"/> + <conditional name="image"> + <param name="generate" type="select" label="Generate image"> + <option value="yes">yes</option> + <option value="no">no</option> + </param> + <when value="yes"> + <expand macro="image_xml"/> + <expand macro="rotate_xml"/> + </when> + <when value="no"/> + </conditional> + </when> + </conditional> + </inputs> + <outputs> + <data format="h5" name="hic_comp_fends" label="${tool.name} on ${on_string}: HiC fends"> + <filter>(command["command_select"] == "hic-complete")</filter> + </data> + <data format="h5" name="hic_comp_data" label="${tool.name} on ${on_string}: HiC data"> + <filter>(command["command_select"] == "hic-complete")</filter> + </data> + <data format="h5" name="hic_comp_project" label="${tool.name} on ${on_string}: HiC project ${command.analysis.algorithm}"> + <filter>(command["command_select"] == "hic-complete")</filter> + </data> + <data format="h5" name="hic_fend_output" label="${tool.name} on ${on_string}: HiC fends"> + <filter>(command["command_select"] == "fends")</filter> + </data> + <data format="h5" name="hic_data_output" label="${tool.name} on ${on_string}: HiC data"> + <filter>(command["command_select"] == "hic-data")</filter> + </data> + <data format="h5" name="hic_project_output" label="${tool.name} on ${on_string}: HiC project"> + <filter>(command["command_select"] == "hic-project")</filter> + </data> + <data format="h5" name="hic_norm_output" label="${tool.name} on ${on_string}: HiC project ${command.analysis.algorithm}"> + <filter>(command["command_select"] == "hic-normalize")</filter> + </data> + <data format="h5" name="hic_hm_output" label="${tool.name} on ${on_string}: HiC heatmap HDF5"> + <filter>(command["command_select"] == "hic-heatmap")</filter> + </data> + <data format="png" name="hic_hm_image" label="${tool.name} on ${on_string}: HiC heatmap PNG"> + <filter>(command["command_select"] == "hic-heatmap")</filter> + <filter>(command["image"]["generate"] == "yes")</filter> + </data> + <data format="chrint" name="hic_int_output" label="${tool.name} on ${on_string}: HiC interval"> + <filter>(command["command_select"] == "hic-interval")</filter> + </data> + <data format="png" name="hic_int_image" label="${tool.name} on ${on_string}: HiC interval PNG"> + <filter>(command["command_select"] == "hic-interval")</filter> + <filter>(command["image"]["generate"] == "yes")</filter> + </data> + <data format="h5" name="fivec_comp_frags" label="${tool.name} on ${on_string}: 5C frags"> + <filter>(command["command_select"] == "5c-complete")</filter> + </data> + <data format="h5" name="fivec_comp_data" label="${tool.name} on ${on_string}: 5C data"> + <filter>(command["command_select"] == "5c-complete")</filter> + </data> + <data format="h5" name="fivec_comp_project" label="${tool.name} on ${on_string}: 5C project ${command.analysis.algorithm}"> + <filter>(command["command_select"] == "5c-complete")</filter> + </data> + <data format="h5" name="fivec_frag_output" label="${tool.name} on ${on_string}: 5C frags"> + <filter>(command["command_select"] == "fragments")</filter> + </data> + <data format="h5" name="fivec_data_output" label="${tool.name} on ${on_string}: 5C data"> + <filter>(command["command_select"] == "5c-data")</filter> + </data> + <data format="h5" name="fivec_project_output" label="${tool.name} on ${on_string}: 5C project"> + <filter>(command["command_select"] == "5c-project")</filter> + </data> + <data format="h5" name="fivec_norm_output" label="${tool.name} on ${on_string}: 5C project ${command.analysis.algorithm}"> + <filter>(command["command_select"] == "5c-normalize")</filter> + </data> + <data format="h5" name="fivec_hm_output" label="${tool.name} on ${on_string}: 5C heatmap HDF5"> + <filter>(command["command_select"] == "5c-heatmap")</filter> + </data> + <data format="png" name="fivec_hm_image" label="${tool.name} on ${on_string}: 5C heatmap PNG"> + <filter>(command["command_select"] == "5c-heatmap")</filter> + <filter>(command["image"]["generate"] == "yes")</filter> + </data> + <data format="chrint" name="fivec_int_output" label="${tool.name} on ${on_string}: 5C interval"> + <filter>(command["command_select"] == "5c-interval")</filter> + </data> + <data format="png" name="fivec_int_image" label="${tool.name} on ${on_string}: 5C interval PNG"> + <filter>(command["command_select"] == "5c-interval")</filter> + <filter>(command["image"]["generate"] == "yes")</filter> + </data> + </outputs> + <tests> + </tests> + <help><![CDATA[ +@COMMAND_HELP@ +@HIC_HELP@ +@5C_HELP@ +]]></help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hifive_macros.xml Fri Jun 05 14:09:00 2015 -0400 @@ -0,0 +1,816 @@ +<?xml version="1.0"?> +<macros> + <xml name="requirements"> + <requirements> + <requirement type='package' version="1.0.3">hifive</requirement> + <yield/> + </requirements> + </xml> + <token name="@WRAPPER_VERSION@">0.1</token> + <xml name="stdio"> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:"/> + <exit_code range=":-1"/> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:"/> + <regex match="Exception:"/> + </stdio> + </xml> + <token name="@HIC_FEND@"> +-B $command.bed + </token> + <xml name="hic_fend_xml"> + <!-- Options controlling fend file creation --> + <param format="bed" name="bed" type="data" label="RE Cutsite BED File" optional="False"/> + </xml> + <token name="@HIC_SEQUENCE@"> +-i $command.insert +#if str( $command.datafile.format ) == "bam": + #for $bam_file in $command.datafile.paired_bam: + --bam ${bam_file.readend1} ${bam_file.readend2} + #end for +#elif str( $command.datafile.format ) == "mat": + --mat ${command.datafile.mat} +#else: + #for raw_file in $command.datafile.raw_files: + --raw ${raw_file.raw} + #end for +#end if + </token> + <xml name="hic_sequence_xml"> + <!-- Options controlling hic sequence data input --> + <conditional name="datafile"> + <param name="format" type="select" label="Data Format"> + <option value="bam">bam</option> + <option value="mat">mat</option> + <option value="raw">raw</option> + </param> + <when value="bam"> + <repeat name="paired_bam" title="Sequencing lane" min="1"> + <param format="bam" name="readend1" label="First read end" type="data"/> + <param format="bam" name="readend2" label="Second read end" type="data"/> + </repeat> + </when> + <when value="mat"> + <param format="tabular" name="mat" type="data" label="Mat file" optional="False"/> + </when> + <when value="raw"> + <repeat name="raw_files" title="Raw file" min="1"> + <param format="tabular" name="raw" type="data" label="Raw file" optional="False"/> + </repeat> + </when> + </conditional> + <param type="integer" name="insert" value="500" label="Maximum insert size" optional="False"> + <validator type="in_range" min="1"/> + </param> + </xml> + <token name="@HIC_PROJECT@"> +-f $command.minint +-j $command.minbin +-n $command.numbin + </token> + <xml name="hic_project_xml"> + <!-- Options controlling hic project creation --> + <param type="integer" name="minint" value="20" label="Minimum interactions per fend" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="integer" name="minbin" value="1000" label="Minimum distance bin cutoff" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="integer" name="numbin" value="100" label="Number of distance bins" optional="False" help="A value of zero indicates that finding the distance dependence function should be skipped."> + <validator type="in_range" min="0"/> + </param> + </xml> + <token name="@HIC_RANGE@"> +-m $command.filtermin +-x $command.filtermax + </token> + <xml name="hic_range_xml"> + <!-- Options controlling hic interaction size range limits --> + <param type="integer" name="filtermin" value="1000000" label="Minimum interaction distance" optional="False" help="The minimum interaction distance included for filtering fends and learning correction values."> + <validator type="in_range" min="0"/> + </param> + <param type="integer" name="filtermax" value="0" label="Maximum interaction distance" optional="False" help="The maximum interaction distance included for filtering fends and learning correction values."> + <validator type="in_range" min="0"/> + </param> + </xml> + <token name="@HIC_CHROMOSOMES@"> +#if str( $command.chroms ) != "": + -c $command.chroms +#end if + </token> + <xml name="hic_chromosomes_xml"> + <!-- Options controlling hic subset selection of chromosomes --> + <param type="text" size="60" name="chroms" value="" label="Included chromosomes" optional="False" help="If a subset of chromosomes are to be used, enter a comma-separated list of chromosome names."/> + </xml> + <token name="@HIC_NORMALIZE@"> +$command.analysis.algorithm +#if str( $command.analysis.algorithm ) == "probability" or str( $command.analysis.algorithm ) == "binning-probability": + -b $command.analysis.probiter + -l $command.analysis.step + -g $command.analysis.change + $command.analysis.precalc +#end if +#if str( $command.analysis.algorithm ) == "express" or str( $command.analysis.algorithm ) == "binning-express" : + $command.analysis.removedist + -w $command.analysis.expreads + $command.analysis.binary + -g $command.analysis.change + #if str( $command.analysis.subalgorithm.kr ) == "yes": + -z + #else + -e $command.analysis.expiter + #end if +#end if +#if str( $command.analysis.algorithm ) == "binning" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "binning-probability": + -r $command.analysis.biniter + -t $command.analysis.threshold + -y $command.analysis.binreads + -v $command.analysis.model + -s $command.analysis.modelbins + -u $command.analysis.modeltypes + --pseudocounts $command.analysis.pseudo +#end if + </token> + <xml name="hic_normalize_xml"> + <!-- Options controlling hic algorithm selection and normalization parameters --> + <conditional name='analysis'> + <param name="algorithm" type="select" label="Learning Algorithm"> + <option value="probability">Probability</option> + <option value="express">Express</option> + <option value="binning">Binning</option> + <option value="binning-probability">Binning-Probability</option> + <option value="binning-express">Binning-Express</option> + </param> + + <when value="probability"> + <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold."> + <validator type="in_range" min="0.00000001"/> + </param> + <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False"> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="precalc" label="Precalculate probability corrections from fragment means"> + <option value="-p">yes</option> + <option value="">no</option> + </param> + </when> + + <when value="express"> + <conditional name="subalgorithm"> + <param type="select" name="kr" label="Use Knight-Ruiz algorithm." help="This performs an unweighted matrix balancing for learning express corrections."> + <option value="yes">yes</option> + <option value="no">no</option> + </param> + <when value="yes"/> + <when value="no"> + <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + </when> + </conditional> + <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections."> + <option value="-d">yes</option> + <option value="">no</option> + </param> + <param type="select" name="expreads" label="Reads to use for learning express corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The minimum mean change in fend correction parameter values needed to keep running past 'iterations' number of iterations. If using the Knight-Ruiz algorithm this is the residual cutoff."> + <validator type="in_range" min="0.00000000000001"/> + </param> + <param type="select" name="binary" label="Use binary indicator instead of counts."> + <option value="">no</option> + <option value="-k">yes</option> + </param> + </when> + + <when value="binning"> + <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False" + help="The minimum change needed in the log-likelihood to continue learning binning corrections."> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="binreads" label="Reads to use for learning binning corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="text" size="60" name="model" value="len,distance" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modelbins" value="20,20" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modeltypes" value="even,even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'."> + <validator type="empty_field" /> + </param> + <param type="integer" name="pseudo" value="0" label="Number of pseudo-counts" optional="True"> + <validator type="in_range" min="0"/> + </param> + </when> + + <when value="binning-probability"> + <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False" + help="The minimum change needed in the log-likelihood to continue learning binning corrections."> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="binreads" label="Reads to use for learning binning corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="text" size="60" name="model" value="len,distance" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modelbins" value="20,20" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modeltypes" value="even,even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'."> + <validator type="empty_field" /> + </param> + <param type="integer" name="pseudo" value="0" label="Number of pseudo-counts" optional="True"> + <validator type="in_range" min="0"/> + </param> + <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold."> + <validator type="in_range" min="0.00000001"/> + </param> + <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False"> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="precalc" label="Precalculate probability corrections from fragment means"> + <option value="-p">yes</option> + <option value="">no</option> + </param> + </when> + + <when value="binning-express"> + <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False" + help="The minimum change needed in the log-likelihood to continue learning binning corrections."> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="binreads" label="Reads to use for learning binning corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="text" size="60" name="model" value="len,distance" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modelbins" value="20,20" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modeltypes" value="even,even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'."> + <validator type="empty_field" /> + </param> + <param type="integer" name="pseudo" value="0" label="Number of pseudo-counts" optional="True"> + <validator type="in_range" min="0"/> + </param> + <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections."> + <option value="-d">yes</option> + <option value="">no</option> + </param> + <param type="select" name="expreads" label="Reads to use for learning express corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + </when> + </conditional> + </xml> + <token name="@HIC_DATATYPE@"> +-d $command.datatype + </token> + <xml name="hic_datatype_xml"> + <!-- Options controlling type of hic data to return --> + <param name="datatype" type="select" label="Datatype"> + <option value="raw">raw</option> + <option value="fend">fend-corrected</option> + <option value="distance">distance-corrected</option> + <option value="enrichment">enrichment</option> + </param> + </xml> + <token name="@5C_FRAGMENT@"> +$command.bed + </token> + <xml name="5c_fragment_xml"> + <!-- Options controlling fragment file creation --> + <param format="bed" name="bed" type="data" label="Probed RE fragment boundary BED File" optional="False"/> + </xml> + <token name="@5C_SEQUENCE@"> +#if str( $command.datafile.format ) == "bam": + #for $bam_file in $command.datafile.paired_bam: + -B ${bam_file.readend1} ${bam_file.readend2} + #end for +#else: + #for $count_file in $command.datafile.count_files: + -C ${count_file.count} + #end for +#end if + </token> + <xml name="5c_sequence_xml"> + <!-- Options controlling 5c sequence data input --> + <conditional name="datafile"> + <param name="format" type="select" label="Data Format"> + <option value="bam">bam</option> + <option value="count">count</option> + </param> + <when value="bam"> + <repeat name="paired_bam" title="Sequencing lane" min="1"> + <param format="bam" name="readend1" label="First read end" type="data"/> + <param format="bam" name="readend2" label="Second read end" type="data"/> + </repeat> + </when> + <when value="count"> + <repeat name="count_files" title="Counts file" min="1"> + <param format="tabular" name="count" type="data" label="Counts file" optional="False"/> + </repeat> + </when> + </conditional> + </xml> + <token name="@5C_PROJECT@"> +-f $command.minint + </token> + <xml name="5c_project_xml"> + <!-- Options controlling 5c project creation --> + <param type="integer" name="minint" value="20" label="Minimum interactions per fragment" optional="False"> + <validator type="in_range" min="1"/> + </param> + </xml> + <token name="@5C_RANGE@"> +-m $command.mindist +-x $command.maxdist + </token> + <xml name="5c_range_xml"> + <!-- Options controlling 5c interaction size range limits --> + <param type="integer" name="mindist" value="0" label="Minimum interaction distance" optional="False" help="The minimum interaction distance included for filtering fragments and learning correction values."> + <validator type="in_range" min="0"/> + </param> + <param type="integer" name="maxdist" value="0" label="Maximum interaction distance" optional="False" help="The maximum interaction distance included for filtering fragments and learning correction values. A value of zero indicates no upper limit."> + <validator type="in_range" min="0"/> + </param> + </xml> + <token name="@5C_REGIONS@"> +#if str( $command.regions ) != "": + -r $command.regions +#end if + </token> + <xml name="5c_regions_xml"> + <!-- Options controlling 5c subset selection of regions --> + <param type="text" size="60" name="regions" value="" label="Included regions" optional="False" help="If a subset of regions are to be used, enter a comma-separated list of region indices."/> + </xml> + <token name="@5C_NORMALIZE@"> +$command.analysis.algorithm +#if str( $command.analysis.algorithm ) == "probability" or str( $command.analysis.algorithm ) == "binning-probability" or str( $command.analysis.algorithm ) == "probability-binning": + -b $command.analysis.probiter + -l $command.analysis.step + -g $command.analysis.change + $command.analysis.precalc +#end if +#if str( $command.analysis.algorithm ) == "express" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "probability-express": + $command.analysis.removedist + -w $command.analysis.expreads + #if str( $command.analysis.subalgorithm.kr ) == "yes": + -z + #else: + -e $command.analysis.expiter + $command.analysis.logged + #end if +#end if +#if str( $command.analysis.algorithm ) == "binning" or str( $command.analysis.algorithm ) == "binning-express" or str( $command.analysis.algorithm ) == "binning-probability" or str( $command.analysis.algorithm ) == "express-binning" or str( $command.analysis.algorithm ) == "probability-binning": + -i $command.analysis.biniter + -t $command.analysis.threshold + -y $command.analysis.binreads + -v $command.analysis.model + -n $command.analysis.modelbins + -u $command.analysis.modeltypes +#end if + </token> + <xml name="5c_normalize_xml"> + <!-- Options controlling 5c algorithm selection and normalization parameters --> + <conditional name='analysis'> + <param name="algorithm" type="select" label="Learning Algorithm"> + <option value="probability">Probability</option> + <option value="express">Express</option> + <option value="binning">Binning</option> + <option value="binning-probability">Binning-Probability</option> + <option value="binning-express">Binning-Express</option> + <option value="probability-binning">Probability-Binning</option> + <option value="express-binning">Express-Binning</option> + </param> + + <when value="probability"> + <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold."> + <validator type="in_range" min="0.00000001"/> + </param> + <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False"> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="precalc" label="Precalculate probability corrections from fragment means"> + <option value="-p">yes</option> + <option value="">no</option> + </param> + </when> + + <when value="express"> + <conditional name="subalgorithm"> + <param type="select" name="kr" label="Use Knight-Ruiz algorithm." help="This performs an unweighted matrix balancing for learning express corrections."> + <option value="yes">yes</option> + <option value="no">no</option> + </param> + <when value="yes"/> + <when value="no"> + <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="select" name="logged" label="Use logged-reads instead of reads."> + <option value="-k">yes</option> + <option value="">no</option> + </param> + </when> + </conditional> + <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections."> + <option value="-d">yes</option> + <option value="">no</option> + </param> + <param type="select" name="expreads" label="Reads to use for learning express corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + </when> + + <when value="binning"> + <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False" + help="The minimum change needed in the log-likelihood to continue learning binning corrections."> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="binreads" label="Reads to use for learning binning corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'."> + <validator type="empty_field" /> + </param> + </when> + + <when value="binning-probability"> + <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False" + help="The minimum change needed in the log-likelihood to continue learning binning corrections."> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="binreads" label="Reads to use for learning binning corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'."> + <validator type="empty_field" /> + </param> + <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold."> + <validator type="in_range" min="0.00000001"/> + </param> + <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False"> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="precalc" label="Precalculate probability corrections from fragment means"> + <option value="-p">yes</option> + <option value="">no</option> + </param> + </when> + + <when value="binning-express"> + <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False" + help="The minimum change needed in the log-likelihood to continue learning binning corrections."> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="binreads" label="Reads to use for learning binning corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'."> + <validator type="empty_field" /> + </param> + <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections."> + <option value="-d">yes</option> + <option value="">no</option> + </param> + <param type="select" name="expreads" label="Reads to use for learning express corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + </when> + + <when value="probability-binning"> + <param type="integer" name="probiter" value="1000" label="Maximum number of iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="change" value="0.0005" label="Parameter change cutoff" optional="False" help="The cutoff for the absolute gradient values such that learning will cease if all values fall below this threshold."> + <validator type="in_range" min="0.00000001"/> + </param> + <param type="float" name="step" value="0.5" label="Learning rate scaling factor" optional="False"> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="precalc" label="Precalculate probability corrections from fragment means"> + <option value="-p">yes</option> + <option value="">no</option> + </param> + <param type="select" name="precalc" label="Precalculate probability corrections from fragment means"> + <option value="-p">yes</option> + <option value="">no</option> + </param> + <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False" + help="The minimum change needed in the log-likelihood to continue learning binning corrections."> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="binreads" label="Reads to use for learning binning corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'."> + <validator type="empty_field" /> + </param> + </when> + + <when value="express-binning"> + <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="select" name="removedist" label="Remove estimated distance-dependence prior to learning express corrections."> + <option value="-d">yes</option> + <option value="">no</option> + </param> + <param type="select" name="expreads" label="Reads to use for learning express corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="integer" name="biniter" value="1000" label="Maximum number of binning iterations" optional="False"> + <validator type="in_range" min="1"/> + </param> + <param type="float" name="threshold" value="1.0" label="Learning threshold" optional="False" + help="The minimum change needed in the log-likelihood to continue learning binning corrections."> + <validator type="in_range" min="0.000001" max="1.0"/> + </param> + <param type="select" name="binreads" label="Reads to use for learning binning corrections."> + <option value="cis">cis</option> + <option value="trans">trans</option> + <option value="all">all</option> + </param> + <param type="text" size="60" name="model" value="len" label="Model parameters" optional="False" help="A comma-separated list of fragment characteristics to learn corrections for. These can include 'len' and any characteristics included in the fragment bed file."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modelbins" value="10" label="Number of parameter bins" optional="False" help="A comma-separated list of bins to divide each model parameter into."> + <validator type="empty_field" /> + </param> + <param type="text" size="60" name="modeltypes" value="even" label="Parameter types" optional="False" help="A comma-separated list of model parameter types. These can be 'even', 'fixed', 'even-const', and 'fixed-const'."> + <validator type="empty_field" /> + </param> + </when> + </conditional> + </xml> + <token name="@5C_DATATYPE@"> +-d $command.datatype + </token> + <xml name="5c_datatype_xml"> + <!-- Options controlling type of 5c data to return --> + <param name="datatype" type="select" label="Datatype"> + <option value="raw">raw</option> + <option value="fragment">fragment-corrected</option> + <option value="distance">distance-corrected</option> + <option value="enrichment">enrichment</option> + </param> + </xml> + <token name="@BINSIZE@"> +-b $command.binsize + </token> + <xml name="binsize_xml"> + <!-- 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 + -a $command.dynamic.search + $command.dynamic.failed +#end if + </token> + <token name="@5C_DYNAMIC@"> +#if str( $command.dynamic.binning ) == "yes": + -y + -x $command.dynamic.expbinsize + -f $command.dynamic.minobs + -g $command.dynamic.search + $command.dynamic.failed +#end if + </token> + <xml name="dynamic_xml"> + <!-- Options controlling dynamic binning of data --> + <conditional name="dynamic"> + <param name="binning" type="select" label="Dynamically bin data"> + <option value="no">no</option> + <option value="yes">yes</option> + </param> + <when value="yes"> + <param name="expbinsize" type="integer" label="Expansion binning size (bp)" value="10000" help="The size of bins to use when expanding heatmap bins. A zero indicates unbinned expansion." > + <validator type="in_range" min="0"/> + </param> + <param name="minobs" type="integer" label="Minimum observations" value="20" help="The number of observations needed to stop expanding a bin." > + <validator type="in_range" min="1"/> + </param> + <param name="search" type="integer" label="Maximum search distance" value="0" help="The maximum distance a bin can be expanded. A value of zero indicates no maximum." > + <validator type="in_range" min="0"/> + </param> + <param name="failed" type="select" label="Remove failed bins"> + <option value="">no</option> + <option value="-v">yes</option> + </param> + </when> + <when value="no"/> + </conditional> + </xml> + <token name="@IMAGE@"> +-k min_color=$command.image.mincolor +-k mid_color=$command.image.midcolor +-k max_color=$command.image.maxcolor +-k logged=$command.image.logged +#if $command.image.minscore: + -k minscore=$command.image.minscore +#end if +#if $command.image.maxscore: + -k maxscore=$command.image.maxscore +#end if + </token> + <xml name="image_xml"> + <!-- Options controlling hic image options --> + <param name="mincolor" type="color" value="#0000ff" label="Minimum value color"/> + <param name="midcolor" type="color" value="#ffffff" label="Middle value color"/> + <param name="maxcolor" type="color" value="#ff0000" label="Maximum value color"/> + <param name="logged" type="select" label="Logged values"> + <option value="true">yes</option> + <option value="false">no</option> + </param> + <param name="minscore" type="float" optional="True" label="Minimum score limit"/> + <param name="maxscore" type="float" optional="True" label="Maximum score limit"/> + </xml> + <token name="@ROTATE@"> +$command.image.rotate + </token> + <xml name="rotate_xml"> + <!-- Options controlling hic image rotation --> + <param name="rotate" type="select" label="Rotate image 45 degrees (horizontal axis)"> + <option value="">no</option> + <option value="-r">yes</option> + </param> + </xml> + <token name="@COMMAND_HELP@"><![CDATA[ +HiFive is a tool for handling, normalizing, and plotting HiC and 5C chromatin interaction data. It has numerous normalization approaches built in with a variety of options, allowing for fine-scale control and data processing. HiFive is broken down into a series of selectable commands, each with a HiC or 5C version. + +COMMANDS +-------- + +Complete HiC analysis / Complete 5C analysis - this command creates a genome partion file, loads data into a dataset, creates a project file and performs data normalization on that project file. + +Create HiC fend set / Create 5C fragment set - this command takes a bed file containing restriction fragment information and creates a HiFive partition file that will be used for downstream data processing. + +Create HiC data set / Create 5C data set - this command loads data from BAM file pairs or a variety of other file formats, partitions reads according to the information in the HiFive genome partition file and creates a HiFive data file. + +Create HiC project / Create 5C project - this command creates a HiFive project, associates a specific data set with it, constructs a distance-dependence function and filters fragments based on coverage. + +Normalize HiC project / Normalize 5C project - this command provides a selection of normalization algorithms and finds correction values for data normalization. + +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 +---------------------------------------- + +A bed file containing either restriction enzyme cutopoints or fragment bounds is converted into an hdf5-type fragment file of fragment characteristics. In addition to coordinates, strand, and chromosome information, additional columns can be included containing other fragment characteristics, such as GC content. If additional columns are included, they must be labeled in the header with a label containing no spaces or commas. These names can be used with the binning algorithm to include the fragment characteristic in the model to be learned. Additional characteristics should be comma-separated pairs of values corresponding to the upstream and downstream sides of the cutsite or ends of the fragment, depending on the whether the bed file contains cutsites or fragment coordinates, respectively. + +HiC data +-------- + +Reads are paired with the specified fend file, creating a HiFive dataset object. Data can be a series of paired-end bam files, a tabular format list of paired genomic positions (chromosome1 coordinate1 strand1 chromosome2 coordinate2 strand2), or a HiCPipe-style mat-formatted list of fend-pairs and observed read counts. + +HiC project +----------- + +Fends are filtered in an iterative manner using the minimum interaction cutoff and interaction size parameters specified to ensure that all valid fends have at least the minimum number of interactions with other valid fends. Subsequently, a distance dependence approximation curve is calculated piecewise using the number of bins specified. The first bin encompasses all interactions less than or equal to the minimum bin cutoff value. The remaining bins are evenly sized between log(minimum cutoff) and log(max possible interaction size). + +HiC normalization +----------------- + +Corrections values are learned for either each valid fend, ranges of fend characteristics, or both. The 'probability' and 'express' algorithms learn correction values associated with each fend while the 'binning' algorithm learns fend characteristic corrections. These can be chained together in either order to produce more robust corrections. + +Using the probability algorithm, observation of counts are assumed to be distributed according to a binomial distribution with an observation probability for each interaction equal to the product of the distance-dependence signal and the two fend correction parameters. Using the probability algorithm, learning is done using a backtracking line gradient descent approach. Learning proceeds for up to the maximum number of iterations but is terminated early if all of the absolute gradient values fall below the cutoff threshold. At each step, the learning rate is scaled down by the step value if the current learning rate does not produce sufficient improvement as measured by the Arjimo criterion. + +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 +--------------------------------------- + +A bed file containing targeted restriction enzyme fragment boundaries is converted into an hdf5-type fragment file of fragment characteristics. In addition to coordinates, strand, and chromosome information, additional columns can be included containing other fragment characteristics, such as GC content. If additional columns are included, they must be labeled in the header with a label containing no spaces or commas. These names can be used with the binning algorithm to include the fragment characteristic in the model to be learned. + +5C data +------- + +Reads are loaded and paired with the specified fragment file, creating a HiFive dataset object. Data can be a series of paired-end bam files or a tabular format list of paired fragments and their observed read count (fragment1 fragment2 count). + +5C project +---------- + +Fragments are filtered in an iterative manner using the minimum interaction cutoff and interaction size parameters specified to ensure that all valid fragments have at least the minimum number of interactions with other valid fragments. Subsequently, a distance dependence approximation line is calculated using a regression line to approximate the linear relationship between log(# reads) and log(distance). + +5C normalization +---------------- + +Corrections values are learned for either each valid fragment, ranges of fragment characteristics, or both. The 'probability' and 'express' algorithms learn correction values associated with each fragment while the 'binning' algorithm learns fragment characteristic corrections. These can be chained together in either order to produce more robust corrections. + +The probability algorithm assumes non-zero counts to distributed according to a log-normal distribution with each interaction having a mean equal to the distance-depedence predicted signal times each of the interaction fragment correction parameters and a universal sigma value. Using the probability algorithm, learning is done using a backtracking line gradient descent approach. Learning proceeds for up to the maximum number of iterations but is terminated early if all of the absolute gradient values fall below the cutoff threshold. At each step, the learning rate is scaled down by the step value if the current learning rate does not produce sufficient improvement as measured by the Arjimo criterion. + +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 predicted signal 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 log-normal distribution, correction values for each bin are learned, maximizing the log-likelihood of the data. Model parameters can be the fragment lengths ('len') and any other characteristics passed as additional columns (with header labels) in the bed file used to create the HiFive fragment 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 fragments ('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> +</macros>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri Jun 05 14:09:00 2015 -0400 @@ -0,0 +1,68 @@ +============================= +Galaxy wrapper for HiFive +============================= + +This wrapper allows use of the hifive package, a set of tools for handling HiC +and 5C data, on Galaxy. This includes managing data from mapped reads, either +in bam, mat, or raw formats. All stages use hdf5 dictionaries for fast access +and minimal memory and storage usage. + +This toolset includes methods for normalizing data from either HiC or 5C +experiments at the fragment-end, or fragment level resolution, respectively. +Once normalized, data can be used for plotting, binning, or other statistical +tests within the package very quickly. + +Original documentation can be found `here <http://hifive.docs.taylorlab.org/en/latest/>`_. + +Automated Installation +====================== + +Galaxy should be able to automatically install the dependencies, i.e. the +``h5py`` and ``hifive`` tool depedency packages. + +Manual Installation +=================== + +For those not using Galaxy's automated installation from the Tool Shed, put +the XML and Python files in the ``tools/hifive/`` folder and add the +XML files to your ``tool_conf.xml`` as normal. For example, use:: + + <section name="HiFive" id="hifive_tools"> + <tool file="hifive/complete_hic_project.xml" /> + <tool file="hifive/create_hic_fendset.xml" /> + <tool file="hifive/create_hic_dataset.xml" /> + <tool file="hifive/create_hic_project.xml" /> + <tool file="hifive/learn_hic_normalization.xml" /> + <tool file="hifive/create_hic_heatmap.xml" /> + <tool file="hifive/get_interval_hic_data.xml" /> + <tool file="hifive/complete_fivec_project.xml" /> + <tool file="hifive/create_fivec_fragmentset.xml" /> + <tool file="hifive/create_fivec_dataset.xml" /> + <tool file="hifive/create_fivec_project.xml" /> + <tool file="hifive/learn_fivec_normalization.xml" /> + <tool file="hifive/create_fivec_heatmap.xml" /> + <tool file="hifive/get_interval_fivec_data.xml" /> + </section> + + +================ +Wrapper Licence +================ + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 05 14:09:00 2015 -0400 @@ -0,0 +1,18 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="scipy" version="0.12.0"> + <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="numpy" version="1.7.1"> + <repository changeset_revision="8b3a5c7061d8" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="cython" version="0.20.1"> + <repository changeset_revision="c3a8c46fcb97" name="package_cython_0_20_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="h5py" version="2.5.0"> + <repository changeset_revision="cc1a2aae5057" name="package_h5py_2_5_0" owner="sauria" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="hifive" version="1.0.3"> + <repository changeset_revision="8cecdadaf46e" name="package_hifive_1_0_3" owner="sauria" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>