# HG changeset patch
# User sauria
# Date 1429826182 14400
# Node ID 5d96a89cd82093272349bb43faaac79109a54b70
# Parent  b17022a25879b4aa3a579d9c7543742f9ddd2834
Uploaded

diff -r b17022a25879 -r 5d96a89cd820 hifive/hifive/complete_fivec_project.xml
--- 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>
diff -r b17022a25879 -r 5d96a89cd820 hifive/hifive/complete_hic_project.xml
--- 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>
diff -r b17022a25879 -r 5d96a89cd820 hifive/hifive/create_hic_project.xml
--- 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>
diff -r b17022a25879 -r 5d96a89cd820 hifive/hifive/learn_fivec_normalization.xml
--- 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>
diff -r b17022a25879 -r 5d96a89cd820 hifive/hifive/learn_hic_normalization.xml
--- 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>