# HG changeset patch
# User bgruening
# Date 1410336399 14400
# Node ID 1d802a322244a00ef2ba9c4d6d1057cc379fcfb3
# Parent  72d1d7c68bd37b00cdfb9761ad92c636c7ed67d9
Uploaded

diff -r 72d1d7c68bd3 -r 1d802a322244 bamCompare.xml
--- a/bamCompare.xml	Tue Aug 26 13:48:56 2014 -0400
+++ b/bamCompare.xml	Wed Sep 10 04:06:39 2014 -0400
@@ -172,9 +172,7 @@
                     label="Minimum mapping quality (e.g. BOWTIE2 measures)"
                     help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
 
-                <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
-                    label ="Treat missing data as zero"
-                    help  ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
+                <expand macro="missingDataAsZero" />
 
                 <param name="ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
diff -r 72d1d7c68bd3 -r 1d802a322244 bamCoverage.xml
--- a/bamCoverage.xml	Tue Aug 26 13:48:56 2014 -0400
+++ b/bamCoverage.xml	Wed Sep 10 04:06:39 2014 -0400
@@ -47,6 +47,8 @@
                 --minMappingQuality '$advancedOpt.minMappingQuality'
             #end if
 
+            --missingDataAsZero $advancedOpt.missingDataAsZero
+
             ##if str($advancedOpt.ignoreForNormalization).strip() != '':
             ##    --ignoreForNormalization $advancedOpt.ignoreForNormalization
             ##end if
@@ -114,6 +116,8 @@
                     label="Minimum mapping quality"
                     help= "If set, only reads that have a mapping quality score higher than the given value are considered. *Note* Bowtie's Mapping quality is related to uniqueness: the higher the score, the more unique is a read. A mapping quality defined by Bowtie of 10 or less indicates that there is at least a 1 in 10 chance that the read truly originated elsewhere."/>
 
+                <expand macro="missingDataAsZero" />
+
              <!--   <param name="ignoreForNormalization" type="text" value="" size="50"
                     label="regions that should be excluded for calculating the scaling factor"
                     help="Sometimes it makes sense to exclude certain regions when calculating the scaling factor. For example, if you know some regions that you suspect to be present more often in your sample's genome than in the reference genome that will therefore accumulate reads (CNV). Another typical example is the single X chromosome in male samples that should be scaled separately from the diploid autosomes. For example chrX,chrY,chr3. or chr10:12220-128932" />
diff -r 72d1d7c68bd3 -r 1d802a322244 bamPEFragmentSize.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bamPEFragmentSize.xml	Wed Sep 10 04:06:39 2014 -0400
@@ -0,0 +1,50 @@
+<tool id="deeptools_bamPEFragmentSize" name="bamPEFragmentSize" version="@WRAPPER_VERSION@.0">
+    <description>Given a BAM file it samples several regions to estimate the paird-end fragment length</description>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <macros>
+        <token name="@BINARY@">bamPEFragmentSize</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        bamPEFragmentSize
+
+        @THREADS@
+
+        --bam '$bamInput'
+        --bamIndex ${bamInput.metadata.bam_index}
+        #if $histogram:
+            --histogram $histogram_outfile
+        #end if
+        > $outfile
+
+]]>
+    </command>
+
+    <inputs>
+        <param name="bamInput" format="bam" type="data" label="BAM file"
+            help="The BAM file must be sorted."/>
+        <param name="histogram" type="boolean" truevalue="--histogram" falsevalue=""
+            label="Get the distribion of fragment length as histogram"
+            help="(--histogram)"/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="outfile" label="${tool.name} on ${on_string}" />
+        <data name="histogram_outfile" format="tabular" from_work_dir="quant_bias_corrected.sf" label="${tool.name} on ${on_string} (Bias corrected Quantification)">
+            <filter>histogram == '--histogram'</filter>
+        </data>
+    </outputs>
+    <help>
+
+**What it does**
+
+Given a BAM file it samples several regions to estimate the paird-end fragment length.
+
+-----
+
+@REFERENCES@
+
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r 72d1d7c68bd3 -r 1d802a322244 deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Aug 26 13:48:56 2014 -0400
+++ b/deepTools_macros.xml	Wed Sep 10 04:06:39 2014 -0400
@@ -44,14 +44,14 @@
     </xml>
     
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">1.5.8.2</token>
+    <token name="@WRAPPER_VERSION@">1.5.9.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="binary">@BINARY@</requirement>
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.8.2">deepTools</requirement>
+            <requirement type="package" version="1.5.9.1">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>
@@ -232,6 +232,12 @@
         </param>
     </xml>
 
+    <xml name="missingDataAsZero">
+                <param name="missingDataAsZero" type="boolean" truevalue="yes" falsevalue="no" checked="True"
+                    label ="Treat missing data as zero"
+                    help  ="This parameter determines if missing data should be treated as zeros. If unchecked, missing data will be ignored and not included in the output file. Missing data is defined as those regions for which both BAM files have 0 reads." />
+    </xml>
+
     <xml name="input_save_matrix_values">
         <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
     </xml>
diff -r 72d1d7c68bd3 -r 1d802a322244 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Aug 26 13:48:56 2014 -0400
+++ b/tool_dependencies.xml	Wed Sep 10 04:06:39 2014 -0400
@@ -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="1.5.8.2">
+    <package name="deepTools" version="1.5.9.1">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
@@ -79,7 +79,7 @@
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard ae9c18b3b7e79d0d1077f636168ac24baeb7b184</action>
+                <action type="shell_command">git reset --hard 351890e3db9a443484c5c349791b7247163cc94f</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;