Mercurial > repos > bgruening > deeptools

changeset 27:bf1b1dcdd67b draft

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Uploaded
author bgruening
date Mon, 17 Mar 2014 16:23:58 -0400
parents 2ad3b027dfcd
children f7712a057440
files bamCompare.xml bamCorrelate.xml bamCoverage.xml bamFingerprint.xml bigwigCompare.xml computeGCBias.xml computeMatrix.xml correctGCBias.xml deepTools_macros.xml heatmapper.xml profiler.xml tool_dependencies.xml
diffstat 12 files changed, 117 insertions(+), 15 deletions(-) [+]
line wrap: on
line diff
--- a/bamCompare.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/bamCompare.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.4">
+<tool id="deeptools_bamCompare" name="bamCompare" version="1.0.5">
     <description>normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
--- a/bamCorrelate.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/bamCorrelate.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.4">
+<tool id="deeptools_bamCorrelate" name="bamCorrelate" version="1.0.5">
     <description>correlates pairs of BAM files</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
--- a/bamCoverage.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/bamCoverage.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.4">
+<tool id="deeptools_bamCoverage" name="bamCoverage" version="1.0.5">
     <description> generates a coverage bigWig file from a given BAM file.  Multiple options are available to count reads and normalize coverage. (bam2bigwig)</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
@@ -60,7 +60,7 @@
 
         <param name="fragmentLength" type="integer" value="300" min="1"
             label="Length of the average fragment size"
-            help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). The formula to normalize using the sequencing depth is genomeSize/(number of mapped reads * fragment length). *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
+            help ="Reads will be extended to match this length unless they are paired-end, in which case they will be extended to match the fragment length. If this value is set to the read length or smaller, the read will not be extended. *Warning* the fragment length affects the normalization to 1x (see &quot;normalize coverage to 1x&quot;). Sequencing depth is defined as: (total number of mapped reads * fragment length) / effective genome size. *NOTE*: If the BAM files contain mated and unmated paired-end reads, unmated reads will be extended to match the fragment length."/>
 
         <param name="binSize" type="integer" value="50" min="1" 
             label="Bin size in bp"
--- a/bamFingerprint.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/bamFingerprint.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.4">
+<tool id="deeptools_bamFingerprint" name="bamFingerprint" version="1.0.5">
     <description>plots profiles of BAM files; useful for assesing ChIP signal strength</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwigCompare.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -0,0 +1,102 @@
+<tool id="deeptools_bigwigCompare" name="bigwigCompare" version="1.0.5">
+    <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
+    <macros>
+        <token name="@BINARY@">bigwigCompare</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <command>
+        bigwigCompare
+
+        @THREADS@
+
+        --bigwig1 '$bigwigFile1'
+        --bigwig2 '$bigwigFile2'
+
+        --outFileName '$outFileName'
+        --outFileFormat '$outFileFormat'
+
+        --ratio $comparison_type
+
+        #if str($region).strip() != '':
+            --region '$region'
+        #end if
+
+        #if $advancedOpt.showAdvancedOpt == "yes":
+
+          --missingDataAsZero $advancedOpt.missingDataAsZero
+          --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
+          --pseudocount '$advancedOpt.pseudocount'
+          --binSize $advancedOpt.binSize
+
+        #end if
+    </command>
+    <inputs>
+        <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
+        <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
+
+        <param name="comparison_type" type="select" 
+                label="How to compare the two files"
+                help="The reciprocal ratio returns the negative of the inverse of the ratio if the ratio is less than 0. The resulting values are interpreted as negative fold changes." >
+            <option value="log2" selected="true">log2 ratio</option>
+            <option value="ratio">simple ratio</option>
+            <option value="subtract">difference (subtract input from treatment)</option>
+            <option value="add">sum</option>
+            <option value="reciprocal_ratio">reciprocal ratio</option>
+        </param>
+
+        <param name="outFileFormat" type="select" label="Coverage file format">
+            <option value="bigwig" selected="true">bigwig</option>
+            <option value="bedgraph">bedgraph</option>
+        </param>
+
+        <expand macro="region_limit_operation" />
+
+        <conditional name="advancedOpt">
+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param name="binSize" type="integer" value="50" min="1" 
+                    label="Bin size in bp"
+                    help="Size of the bins in bp for the output of the bigwig/bedgraph file "/>
+
+                <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 replaced with a zero. If set to &quot;no&quot;, missing data will be ignored and will not be included in the output file at all. Missing data is defined as those regions for which no value exists in *any* of the bigwig files. The decision to include or exclude missing data depends on the interpretation of the data. Missing data in a bigwig file may mean that there is no information available for certain regions, for example a repetitive region that is not being considered. In the same file regions with low coverage may get zero read counts. If missing data is replaced by zero, this would convert the excluded repetitive regions into regions of low coverage." />
+
+                <param name="scaleFactor1" type="float" value="1" label="Scale factor for treatment"/>
+                <param name="scaleFactor2" type="float" value="1" label="Scale factor for input"/>
+                <param name="pseudocount" type="float" value="1" label="Pseudocount" help="Small number to avoid dividing by zero."/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="bigwig" name="outFileName">
+        <change_format>
+            <when input="outFileFormat" value="bigwig" format="bigwig" />
+            <when input="outFileFormat" value="bedgraph" format="bedgraph" />
+        </change_format>
+        </data>
+    </outputs>
+
+  <help>
+
+**What it does**
+
+This tool compares two bigwig files based on the number of mapped reads. To
+compare the bigwig files the genome is partitioned into bins of equal size,
+then the number of reads found in each BAM file are counted for such bins and
+finally a summarizing value is reported. This value can be the ratio of the
+number of reads per bin, the log2 of the ratio, the sum or the difference.
+
+
+-----
+
+@REFERENCES@
+
+    </help>
+</tool>
--- a/computeGCBias.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/computeGCBias.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.4">
+<tool id="deeptools_computeGCBias" name="computeGCBias" version="1.0.5">
     <description>to see whether your samples should be normalized for GC bias</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
--- a/computeMatrix.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/computeMatrix.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.4">
+<tool id="deeptools_computeMatrix" name="computeMatrix" version="1.0.5">
     <description>summarizes and prepares an intermediary file containing scores associated with genomic regions that can be used afterwards to plot a heatmap or a profile</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
--- a/correctGCBias.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/correctGCBias.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.4">
+<tool id="deeptools_correctGCBias" name="correctGCBias" version="1.0.5">
     <description>uses the output from computeGCBias to generate corrected BAM files</description>
     <expand macro="requirements" />
     <expand macro="stdio" />
--- a/deepTools_macros.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/deepTools_macros.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -50,7 +50,7 @@
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.4_3268f7e1458f3a520ab6fea3039971ee9d7a6d5b">deepTools</requirement>
+            <requirement type="package" version="1.5.4_43d3b51b3c3ab71dc07f31fefe6b3492226cc217">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>
--- a/heatmapper.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/heatmapper.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_heatmapper" name="heatmapper" version="1.0.4">
+<tool id="deeptools_heatmapper" name="heatmapper" version="1.0.5">
     <description>creates a heatmap for a score associated to genomic regions</description>
     <expand macro="requirements"/>
     <expand macro="stdio" />
--- a/profiler.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/profiler.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -1,4 +1,4 @@
-<tool id="deeptools_profiler" name="profiler" version="1.0.4">
+<tool id="deeptools_profiler" name="profiler" version="1.0.5">
     <description>
         creates a profile plot for a score associated to genomic regions
     </description>
--- a/tool_dependencies.xml	Thu Feb 06 06:40:05 2014 -0500
+++ b/tool_dependencies.xml	Mon Mar 17 16:23:58 2014 -0400
@@ -7,7 +7,7 @@
         <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="dceff6072512" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d639ff3d6b6e" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
         <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.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_3268f7e1458f3a520ab6fea3039971ee9d7a6d5b">
+    <package name="deepTools" version="1.5.4_43d3b51b3c3ab71dc07f31fefe6b3492226cc217">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
@@ -72,14 +72,14 @@
                     <repository changeset_revision="ef12a3a11d5b" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.7.1" />
                     </repository>
-                    <repository changeset_revision="dceff6072512" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="d639ff3d6b6e" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                         <package name="matplotlib" version="1.2.1" />
                     </repository>
                     <repository changeset_revision="984d208b0808" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                         <package name="scipy" version="0.12.0" />
                     </repository>
                 </action>
-                <action type="shell_command">git reset --hard 3268f7e1458f3a520ab6fea3039971ee9d7a6d5b</action>
+                <action type="shell_command">git reset --hard 43d3b51b3c3ab71dc07f31fefe6b3492226cc217</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;