Mercurial > repos > sauria > hifive
changeset 8:5d96a89cd820 draft
Uploaded
| author | sauria |
|---|---|
| date | Thu, 23 Apr 2015 17:56:22 -0400 |
| parents | b17022a25879 |
| children | 5e3de32a8688 |
| files | hifive/hifive/complete_fivec_project.xml hifive/hifive/complete_hic_project.xml hifive/hifive/create_hic_project.xml hifive/hifive/learn_fivec_normalization.xml hifive/hifive/learn_hic_normalization.xml |
| diffstat | 5 files changed, 119 insertions(+), 23 deletions(-) [+] |
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--- a/hifive/hifive/complete_fivec_project.xml Thu Apr 16 16:35:12 2015 -0400 +++ b/hifive/hifive/complete_fivec_project.xml Thu Apr 23 17:56:22 2015 -0400 @@ -27,7 +27,12 @@ -b $analysis.probiter -l $analysis.step -g $analysis.change $analysis.precalc #end if #if str( $analysis.algorithm ) == "express" or str( $analysis.algorithm ) == "binning-express" or str( $analysis.algorithm ) == "probability-express": - -e $analysis.expiter $analysis.removedist -w $analysis.expreads + $analysis.removedist -w $analysis.expreads + #if str( $analysis.subalgorithm.kr ) == "yes": + -z + #else: + -e $analysis.expiter $analysis.logged + #end if #end if #if str( $analysis.algorithm ) == "binning" or str( $analysis.algorithm ) == "binning-express" or str( $analysis.algorithm ) == "binning-probability" or str( $analysis.algorithm ) == "express-binning" or str( $analysis.algorithm ) == "probability-binning": -i $analysis.biniter -t $analysis.threshold -y $analysis.binreads @@ -92,9 +97,22 @@ </when> <when value="express"> - <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> - <validator type="in_range" min="1"/> - </param> + <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>
--- a/hifive/hifive/complete_hic_project.xml Thu Apr 16 16:35:12 2015 -0400 +++ b/hifive/hifive/complete_hic_project.xml Thu Apr 23 17:56:22 2015 -0400 @@ -29,11 +29,16 @@ -b $analysis.probiter -l $analysis.step -g $analysis.change $analysis.precalc #end if #if str( $analysis.algorithm ) == "express" or str( $analysis.algorithm ) == "binning-express" : - -e $analysis.expiter $analysis.removedist -w $analysis.expreads + $analysis.removedist -w $analysis.expreads $analysis.binary -g $analysis.change + #if str( $analysis.subalgorithm.kr ) == "yes": + -z + #else + -e $analysis.expiter + #end if #end if #if str( $analysis.algorithm ) == "binning" or str( $analysis.algorithm ) == "binning-express" or str( $analysis.algorithm ) == "binning-probability": -r $analysis.biniter -t $analysis.threshold -y $analysis.binreads - -v $analysis.model -z $analysis.modelbins -u $analysis.modeltypes + -v $analysis.model -s $analysis.modelbins -u $analysis.modeltypes --pseudocounts $analysis.pseudo #end if -o $fends $data $project @@ -76,8 +81,8 @@ <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"> - <validator type="in_range" min="1"/> + <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> <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."/> <conditional name='analysis'> @@ -106,9 +111,18 @@ </when> <when value="express"> - <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> - <validator type="in_range" min="1"/> - </param> + <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> @@ -118,6 +132,13 @@ <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="-k">yes</option> + <option value="">no</option> + </param> </when> <when value="binning"> @@ -142,6 +163,9 @@ <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"> @@ -166,6 +190,9 @@ <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> @@ -203,6 +230,9 @@ <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>
--- a/hifive/hifive/create_hic_project.xml Thu Apr 16 16:35:12 2015 -0400 +++ b/hifive/hifive/create_hic_project.xml Thu Apr 23 17:56:22 2015 -0400 @@ -25,8 +25,8 @@ <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"> - <validator type="in_range" min="1"/> + <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> </inputs> <outputs>
--- a/hifive/hifive/learn_fivec_normalization.xml Thu Apr 16 16:35:12 2015 -0400 +++ b/hifive/hifive/learn_fivec_normalization.xml Thu Apr 23 17:56:22 2015 -0400 @@ -17,8 +17,13 @@ #if str( $analysis.algorithm ) == "probability" or str( $analysis.algorithm ) == "binning-probability" or str( $analysis.algorithm ) == "probability-binning": -b $analysis.probiter -l $analysis.step -g $analysis.change $analysis.precalc #end if - #if str( $analysis.algorithm ) == "express" or str( $analysis.algorithm ) == "binning-express" or str( $analysis.algorithm ) == "express-binning": - -e $analysis.expiter $analysis.removedist -w $analysis.expreads + #if str( $analysis.algorithm ) == "express" or str( $analysis.algorithm ) == "binning-express" or str( $analysis.algorithm ) == "probability-express": + $analysis.removedist -w $analysis.expreads + #if str( $analysis.subalgorithm.kr ) == "yes": + -z + #else: + -e $analysis.expiter $analysis.logged + #end if #end if #if str( $analysis.algorithm ) == "binning" or str( $analysis.algorithm ) == "binning-express" or str( $analysis.algorithm ) == "binning-probability" or str( $analysis.algorithm ) == "express-binning" or str( $analysis.algorithm ) == "probability-binning": -i $analysis.biniter -t $analysis.threshold -y $analysis.binreads @@ -63,9 +68,22 @@ </when> <when value="express"> - <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> - <validator type="in_range" min="1"/> - </param> + <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>
--- a/hifive/hifive/learn_hic_normalization.xml Thu Apr 16 16:35:12 2015 -0400 +++ b/hifive/hifive/learn_hic_normalization.xml Thu Apr 23 17:56:22 2015 -0400 @@ -18,11 +18,16 @@ -b $analysis.probiter -l $analysis.step -g $analysis.change $analysis.precalc #end if #if str( $analysis.algorithm ) == "express" or str( $analysis.algorithm ) == "binning-express" : - -e $analysis.expiter $analysis.removedist -w $analysis.expreads + $analysis.removedist -w $analysis.expreads $analysis.binary -g $analysis.change + #if str( $analysis.subalgorithm.kr ) == "yes": + -z + #else + -e $analysis.expiter + #end if #end if #if str( $analysis.algorithm ) == "binning" or str( $analysis.algorithm ) == "binning-express" or str( $analysis.algorithm ) == "binning-probability": -r $analysis.biniter -t $analysis.threshold -y $analysis.binreads - -v $analysis.model -z $analysis.modelbins -u $analysis.modeltypes + -v $analysis.model -s $analysis.modelbins -u $analysis.modeltypes --pseudocounts $analysis.pseudo #end if $data</command> @@ -61,9 +66,18 @@ </when> <when value="express"> - <param type="integer" name="expiter" value="1000" label="Number of express iterations" optional="False"> - <validator type="in_range" min="1"/> - </param> + <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> @@ -73,6 +87,13 @@ <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="-k">yes</option> + <option value="">no</option> + </param> </when> <when value="binning"> @@ -97,6 +118,9 @@ <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"> @@ -121,6 +145,9 @@ <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> @@ -158,6 +185,9 @@ <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>