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changeset 1:bed2b67b46b7 draft

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Uploaded
author sauria
date Tue, 14 Apr 2015 16:27:21 -0400
parents b855fcdb534d
children bdb07d744116
files hifive/create_fivec_heatmap.xml hifive/create_hic_heatmap.xml hifive/get_interval_fivec_data.xml hifive/get_interval_hic_data.xml hifive/tool_dependencies.xml
diffstat 5 files changed, 104 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/hifive/create_fivec_heatmap.xml	Mon Apr 13 14:34:05 2015 -0400
+++ b/hifive/create_fivec_heatmap.xml	Tue Apr 14 16:27:21 2015 -0400
@@ -13,6 +13,9 @@
         #if str( $regions ) != "":
             -r $regions
         #end if
+        #if str( $dynamic.binning ) == "yes":
+            -y -x $dynamic.expbinsize -f $dynamic.minobs -g $dynamic.search $dynamic.failed
+        #end if
         #if str( $image.generate ) == "yes":
             -k min_color=$image.mincolor -k mid_color=$image.midcolor -k max_color=$image.maxcolor
             -i $image_file -k logged=$image.logged
@@ -55,6 +58,28 @@
             <option value="enrichment">enrichment</option>
         </param>
         <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 numbers."/>
+        <conditional name="dynamic">
+            <param name="binning" type="select" label="Dynamically bin data">
+                <option value="yes">yes</option>
+                <option value="no">no</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>
         <conditional name="image">
             <param name="generate" type="select" label="Generate image">
                 <option value="yes">yes</option>
--- a/hifive/create_hic_heatmap.xml	Mon Apr 13 14:34:05 2015 -0400
+++ b/hifive/create_hic_heatmap.xml	Tue Apr 14 16:27:21 2015 -0400
@@ -8,6 +8,9 @@
         #if str( $chroms ) != "":
             -c $chroms
         #end if
+        #if str( $dynamic.binning ) == "yes":
+            -y -x $dynamic.expbinsize -f $dynamic.minobs -a $dynamic.search $dynamic.failed
+        #end if
         #if str( $image.generate ) == "yes":
             -k min_color=$image.mincolor -k mid_color=$image.midcolor -k max_color=$image.maxcolor
             -i $image_file -k logged=$image.logged
@@ -36,6 +39,28 @@
             <option value="enrichment">enrichment</option>
         </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="dynamic">
+            <param name="binning" type="select" label="Dynamically bin data">
+                <option value="yes">yes</option>
+                <option value="no">no</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>
         <conditional name="image">
             <param name="generate" type="select" label="Generate image">
                 <option value="yes">yes</option>
--- a/hifive/get_interval_fivec_data.xml	Mon Apr 13 14:34:05 2015 -0400
+++ b/hifive/get_interval_fivec_data.xml	Tue Apr 14 16:27:21 2015 -0400
@@ -11,6 +11,9 @@
         #if $stop:
             -e $stop
         #end if
+        #if str( $dynamic.binning ) == "yes":
+            -y -x $dynamic.expbinsize -f $dynamic.minobs -g $dynamic.search $dynamic.failed
+        #end if
         #if str( $image.generate ) == "yes":
             -k min_color=$image.mincolor -k mid_color=$image.midcolor -k max_color=$image.maxcolor
             -i $image_file -k logged=$image.logged
@@ -46,6 +49,28 @@
             <option value="fragment">fragment-corrected</option>
             <option value="enrichment">enrichment</option>
         </param>
+        <conditional name="dynamic">
+            <param name="binning" type="select" label="Dynamically bin data">
+                <option value="yes">yes</option>
+                <option value="no">no</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>
         <conditional name="image">
             <param name="generate" type="select" label="Generate image">
                 <option value="yes">yes</option>
--- a/hifive/get_interval_hic_data.xml	Mon Apr 13 14:34:05 2015 -0400
+++ b/hifive/get_interval_hic_data.xml	Tue Apr 14 16:27:21 2015 -0400
@@ -14,6 +14,9 @@
         #if $maxdist:
             -m $maxdist
         #end if
+        #if str( $dynamic.binning ) == "yes":
+            -y -x $dynamic.expbinsize -f $dynamic.minobs -a $dynamic.search $dynamic.failed
+        #end if
         #if str( $image.generate ) == "yes":
             -k min_color=$image.mincolor -k mid_color=$image.midcolor -k max_color=$image.maxcolor
             -i $image_file -k logged=$image.logged $image.rotate
@@ -49,6 +52,28 @@
             <option value="fend">fend-corrected</option>
             <option value="enrichment">enrichment</option>
         </param>
+        <conditional name="dynamic">
+            <param name="binning" type="select" label="Dynamically bin data">
+                <option value="yes">yes</option>
+                <option value="no">no</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>
         <conditional name="image">
             <param name="generate" type="select" label="Generate image">
                 <option value="yes">yes</option>
--- a/hifive/tool_dependencies.xml	Mon Apr 13 14:34:05 2015 -0400
+++ b/hifive/tool_dependencies.xml	Tue Apr 14 16:27:21 2015 -0400
@@ -1,4 +1,4 @@
-<?xml version="1.0"?>
+<?xml version="1.1"?>
 <tool_dependency>
     <package name="scipy" version="0.14">
         <repository changeset_revision="2e3809844979" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
@@ -12,10 +12,10 @@
     <package name="h5py" version="2.4.0">
         <repository changeset_revision="79b31a4c757c" name="package_h5py_2_4_0" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="hifive" version="1.0">
-        <repository changeset_revision="8f35dfa26c62" name="package_hifive_1_0" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="hifive" version="1.0.1">
+        <repository changeset_revision="429c3c79840d" name="package_hifive_1_0_1" owner="sauria" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <set_environment version="1.0">
+    <set_environment version="1.1">
         <environment_variable action="set_to" name="HIFIVE_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
     </set_environment>
 </tool_dependency>