# HG changeset patch
# User bgruening
# Date 1390935274 18000
# Node ID 2e5b92e7f3cbca6eae1927c0d4d2d915211e29c0
# Parent  60788be7b3464b5c32b6efe38d1187a6dfaef4cf
Uploaded

diff -r 60788be7b346 -r 2e5b92e7f3cb bamCorrelate.xml
--- a/bamCorrelate.xml	Sat Dec 21 17:30:26 2013 -0500
+++ b/bamCorrelate.xml	Tue Jan 28 13:54:34 2014 -0500
@@ -39,12 +39,12 @@
             --BED $mode.region_file
         #end if
 
-        ## options available in both modes
-        #if $mode.advancedOpt.showAdvancedOpt == "yes":
+        #### options available in both modes
+        #if str($mode.region.value) != '':
+            --region '$mode.region'
+        #end if
 
-            #if str($mode.advancedOpt.region.value) != '':
-            --region '$mode.advancedOpt.region'
-            #end if
+        #if $mode.advancedOpt.showAdvancedOpt == "yes":
 
             $mode.advancedOpt.doNotExtendPairedEnds
             $mode.advancedOpt.ignoreDuplicates
diff -r 60788be7b346 -r 2e5b92e7f3cb computeMatrix.xml
--- a/computeMatrix.xml	Sat Dec 21 17:30:26 2013 -0500
+++ b/computeMatrix.xml	Tue Jan 28 13:54:34 2014 -0500
@@ -51,8 +51,8 @@
     --afterRegionStartLength $mode.afterRegionStartLength
   #else
     --regionBodyLength $mode.regionBodyLength
-    --startLabel $mode.startLabel
-    --endLabel $mode.endLabel
+    --startLabel "$mode.startLabel"
+    --endLabel "$mode.endLabel"
     #if $mode.regionStartLength.regionStartLength_select == "yes":
       --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
       --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
@@ -100,18 +100,17 @@
         <param name="regionBodyLength" type="integer" value="500" label="Distance in bp to which all regions are going to be fitted"/>
         <param name="startLabel" type="text" value="TSS" size="10" label="Label for the region start" help ="Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
         <param name="endLabel" type="text" value="TES" size="10" label="Label for the region end" help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
-        <conditional name="regionStartLength">
-        <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
-          <option value="no" selected="true">no</option>
-          <option value="yes">yes</option>
-        </param>
-        <when value="no" />
-        <when value="yes">
-          <param name="beforeRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
-        
-          <param name="afterRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
-        </when>
-        </conditional>
+            <conditional name="regionStartLength">
+                <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
+                    <option value="no" selected="true">no</option>
+                    <option value="yes">yes</option>
+                </param>
+                <when value="no" />
+                <when value="yes">
+                    <param name="beforeRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
+                    <param name="afterRegionStartLength" type="integer" value="1000" min="1" optional="true" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
+                </when>
+            </conditional>
       </when>
       
       <when value="reference-point">
diff -r 60788be7b346 -r 2e5b92e7f3cb deepTools_macros.xml
--- a/deepTools_macros.xml	Sat Dec 21 17:30:26 2013 -0500
+++ b/deepTools_macros.xml	Tue Jan 28 13:54:34 2014 -0500
@@ -1,5 +1,9 @@
 <macros>
     <xml name="bamCorrelate_mode_actions">
+        <param name="region" type="text" value=""
+            label="Region of the genome to limit the operation to"
+            help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
+
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                 <option value="no" selected="true">no</option>
@@ -7,10 +11,6 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="region" type="text" value=""
-                    label="Region of the genome to limit the operation to"
-                    help="This is useful when testing parameters to reduce the computing time. The format is chr:start:end, for example &quot;chr10&quot; or &quot;chr10:456700:891000&quot;" />
-
                 <param name="doNotExtendPairedEnds" type="boolean" truevalue="--doNotExtendPairedEnds" falsevalue=""
                     label="Do not extend paired ends"
                     help="If set, reads are not extended to match the fragment length reported in the BAM file, instead they will be extended to match the fragment length. Default is to extend the reads if paired end information is available."/>
@@ -43,7 +43,7 @@
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.4_e5c75f3e967be0fa1d6dbcbb63a0f992e1cdcd61">deepTools</requirement>
+            <requirement type="package" version="1.5.4_eabc1c3842f4b6367fb41904061a3b95c9a0ce0c">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>
diff -r 60788be7b346 -r 2e5b92e7f3cb heatmapper.xml
--- a/heatmapper.xml	Sat Dec 21 17:30:26 2013 -0500
+++ b/heatmapper.xml	Tue Jan 28 13:54:34 2014 -0500
@@ -147,7 +147,6 @@
 
                 <param name="whatToShow" type="select" label="What to show" help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
                     <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
-                    <option value="plot only">summary plot only</option>
                     <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
                     <option value="heatmap only">heatmap only</option>
                     <option value="heatmap and colorbar">heatmap and colorbar</option>
@@ -174,11 +173,11 @@
                 <conditional name="used_multiple_regions">
                     <param name="used_multiple_regions_options" type="select" 
                         label="Did you used multiple regions in ComputeMatrix?"
-                        help="That option is only relevant if you want to cluster the results. Clustering is only available with one selected region in ComputeMatrix.">
-                        <option value="no">No, I used only one region.</option>
+                        help="Would you like to cluster the regions according to the similarity of the signal distribution? This is only possible if you used computeMatrix on only one group of regions.">
                         <option value="yes">Yes, I used multiple regions.</option>
+                        <option value="no">No, I used only one region.</option>
                     </param>
-                    <when value="yes">
+                    <when value="no">
                         <conditional name="clustering">
                             <param name="clustering_options" type="select" label="Clustering algorithm">
                                 <option value="none">No clustering</option>
@@ -191,7 +190,7 @@
                             <when value="none" />
                         </conditional>
                     </when>
-                    <when value="no" />
+                    <when value="yes" />
                 </conditional>
             </when>
         </conditional>
diff -r 60788be7b346 -r 2e5b92e7f3cb profiler.xml
--- a/profiler.xml	Sat Dec 21 17:30:26 2013 -0500
+++ b/profiler.xml	Tue Jan 28 13:54:34 2014 -0500
@@ -46,6 +46,10 @@
                 --plotTitle '$advancedOpt.plotTitle'
             #end if
 
+            #if str($advancedOpt.colors.value) != "None":
+                --colors '$advancedOpt.colors'
+            #end if
+
             $advancedOpt.onePlotPerGroup
 
             #if $advancedOpt.yMin:
@@ -101,14 +105,24 @@
                     label="Plot width" 
                     help="Width in cm. The default value is 8 centimeters. The minimum value is 1 cm." />
                 <param name="plotType" type="select" label="Plot type"
-                    help="For the summary plot (profile) only. The &quot;lines&quot; option will plot the profile line based on the average type selected. The &quot;fill&quot; option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The &quot;std&quot; option colors the region between the profile and the standard deviation of the data. As in the case of fill, a semi-transparent color is used. The option &quot;overlapped_lines&quot; plots each region values, one on top of the other; this option only works if &quot;one plot per proup&quot; is set.">
+                    help="For the summary plot (profile) only. The &quot;lines&quot; option will plot the profile line based on the average type selected. The &quot;fill&quot; option fills the region between zero and the profile curve. The fill in color is semi transparent to distinguish different profiles. The &quot;add standard error&quot; option colors the region between the profile and the standard error of the data. As in the case of fill, a semi-transparent color is used. The option &quot;overlapped_lines&quot; plots each region values, one on top of the other; this option only works if &quot;one plot per proup&quot; is set.">
                     <option value="lines" selected="true">lines</option>
                     <option value="fill">fill</option>
-                    <option value="std">std</option>
+                    <option value="se">add standard error</option>
                     <option value="overlapped_lines">overlapped lines</option>
                 </param>
                 <param name="regionsLabel" type="text" value="genes" size="30" label="Labels for the regions plotted in the heatmap" help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, &quot;label1, label2&quot;."/>
                 <param name="plotTitle" type="text" value="" size="30" label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title." />
+                <param name="colors" type="text" value="" size="40" label="List of colors to use for the plotted lines" help="Color names and html hex strings (e.g. #eeff22) are accepted. The color names should be given separated by spaces. (--colors red blue green)" >
+                    <sanitizer invalid_char=",">
+                        <valid initial="string.letters,string.digits">
+                            <add value=" " /> 
+                            <add value="#" />
+                        </valid>
+                    </sanitizer>
+                </param>
+
+
                 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
                 <param name="yMin" type="float" value="" size="3" label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
                 <param name="yMax" type="float" value="" size="3" label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values" optional="true"/>
diff -r 60788be7b346 -r 2e5b92e7f3cb tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Dec 21 17:30:26 2013 -0500
+++ b/tool_dependencies.xml	Tue Jan 28 13:54:34 2014 -0500
@@ -10,7 +10,7 @@
         <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="pysam" version="0.7.7">
         <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
@@ -57,7 +57,7 @@
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-    <package name="deepTools" version="1.5.4_e5c75f3e967be0fa1d6dbcbb63a0f992e1cdcd61">
+    <package name="deepTools" version="1.5.4_eabc1c3842f4b6367fb41904061a3b95c9a0ce0c">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
@@ -75,11 +75,11 @@
                     <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="matplotlib" version="1.2.1" />
                     </repository>
-                    <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="4b2ef8519550" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard e5c75f3e967be0fa1d6dbcbb63a0f992e1cdcd61</action>
+                <action type="shell_command">git reset --hard eabc1c3842f4b6367fb41904061a3b95c9a0ce0c</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;