diff wiggle_correlation_union.xml @ 0:3d1097835b2f draft default tip

Imported from capsule None

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/wiggle_correlation_union.xml	Mon Sep 22 11:54:41 2014 -0400
@@ -0,0 +1,109 @@
+<tool name="Two wiggle file correlation in union regions" id="correlation_intervals" version="0.1.0">
+  <description>Calculate the correlation coefficient of two wiggle / bigwig files in the union regions from two bed files</description>
+  <macros>
+    <import>corr_macros.xml</import>
+  </macros>
+  <expand macro="requirements_union" />
+  <command>
+#if $wfile1.extension == "wig"
+    qc_chIP_peak.py -s $step -m $method -f bed
+#elif $wfile1.extension == "bigwig"
+    qc_chIP_peakBW.py 
+#end if
+  -x $wfile1 -y $wfile2 -p $bfile1 -q $bfile2 -r qc_chIP-output.txt &amp;> $log &amp;&amp;
+Rscript qc_chIP-output.txt
+  </command>
+  <inputs>
+    <!-- need pybedtools for qc_chIP_peakBW.py
+    <param format="wig,bigwig" name="wfile1" type="data" label="WIGGLE / bigwig file 1"/>
+    -->
+    <param format="wig" name="wfile1" type="data" label="WIGGLE / bigwig file 1"/>
+    <param format="bed" name="bfile1" type="data" label="BED file 1(100,000 lines max)"/>
+    <!-- need pybedtools for qc_chIP_peakBW.py
+    <param format="wig,bigwig" name="wfile2" type="data" label="WIGGLE / bigwig file 2"/>
+    -->
+    <param format="wig" name="wfile2" type="data" label="WIGGLE / bigwig file 2"/>
+    <param format="bed" name="bfile2" type="data" label="BED file 2(100,000 lines max)"/>
+    <param name="step" type="integer" label="Step" value="5" help="step in points. This option is only used for wig file.">
+      <validator type="in_range" max="100" min="1" message="Step is out of range, Step has to be between 1 to 100" />
+    </param>    
+    <param name="method" type="select" label="method:" help="method to process the paired two sets of data in the sampling step." >
+      <option value="mean" selected="true">mean</option>
+      <option value="median">median</option>
+      <option value="sum">sum</option>
+      <option value="sample">sample</option>
+    </param>
+    <param name="method" type="hidden" label="method:" help="method to process the paired two sets of data in the sampling step." >
+      <option value="mean">mean</option>
+    </param>
+  </inputs>
+  <outputs>
+    <data format="pdf" name="output" from_work_dir="qc_chIP-output.txt.pdf"/>
+    <data format="txt" name="log" label="job log" />
+    <data format="txt" name="rscript" label="job rscript" from_work_dir="qc_chIP-output.txt"/>
+  </outputs>
+  <expand macro="stdio"/>
+  <tests>
+    <test>
+      <param name="wfile1" value="control.wig" />
+      <param name="bfile1" value="peaks.bed" />
+      <param name="wfile2" value="treatment.wig" />
+      <param name="bfile2" value="peaks.bed" />
+      <param name="step" value="5" />
+      <output name="log">
+        <assert_contents>
+            <has_text_matching expression="centering pscore2" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+
+
+  <help>
+This tool calculates the correlation coefficient on two sets where the
+two sets intersect The tool is written by Tao Liu. It calls R for
+plotting.
+
+.. class:: infomark
+
+**TIP:** This can be used to evaluate the correlation between
+two biological replicates.
+
+.. class:: warningmark
+
+**NEED IMPROVEMENT**
+
+-----
+
+**Parameters**
+
+- **WIGGLE file 1 and 2** are the two wiggle files to be
+  included. These two are required.
+- **BED file 1 and 2** are the two BED files to be used to
+  extract scores from wiggle files.
+- **wiggle files** click *Add new wiggle file* to add more wiggle
+  files and labels. 
+- **Genome/Assembly** Genome assembly to be used. The tool will
+  download the chromosome information from UCSC database.
+- **Method** When scores are extracted for a region in BED file, a
+  method will be applied to calculate a value to represent this
+  region. Options are *median* to use the median value or *mean* to
+  use the average value.
+- **Step** Step in data points. The step is a window to extract the
+  scores from wiggle files along the whole genome. So that every step
+  number of points will have a value to represent it by using certain **Method** 
+- **Method** When scores are extracted for a step long window, a
+  method will be applied to calculate a value to represent this
+  window. Options are *median* to use the median value or *mean* to
+  use the average value, or *sample* to sample 1 point to represent
+  the region, or *sum* to use the sum of values in the region.
+
+-----
+
+**Outputs**
+
+- **PNG file** is the correlation plot
+
+  </help>
+
+</tool>