--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/calculate_contrast_threshold.xml	Wed Sep 11 09:28:55 2019 -0400
@@ -0,0 +1,122 @@
+<tool id="calculate_contrast_threshold" name="Calculate Contrast threshold" version="1.0.0">
+    <description>from tag pileup CDT
+    </description>
+    <requirements>
+        <requirement type="package" version="1.15.4">numpy</requirement>
+        <requirement type="package" version="3.7.4">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code">
+        <![CDATA[
+      python '$__tool_directory__/calculate_contrast_threshold.py' -i '$input_file'
+
+      ## Setting the quantile values properly.
+      #if str($quantile_type.quantile_type_selector) == "b_option":
+        -q '${quantile_type.quantile}'
+        -m '${quantile_type.min_contrast}'
+      #else if str($quantile_type.quantile_type_selector) == "t_option":
+        -t '${quantile_type.quantile2}'
+      #end if
+      
+      -d '$header' -s '$start_col' -r '$row_num' -l '$col_num'
+    ]]>
+    </command>
+
+    <inputs>
+        <param name="input_file" argument="-i" type="data" format="txt" label="Pileup Data Matrix "/>
+        <param name="header" argument="-d" type="boolean" truevalue="T" falsevalue="F" checked="true" label="Does the input file have a Header ?" help="Standard CDT file have headers."/>
+        <param name="start_col" argument="-s" type="integer" value="2" label="Valid Data Start Column" help="Valid data values start from this column"/>
+        <param name="col_num" argument="-l" type="integer" value="300" label="Plot Width in pixels" help="Equal to the heatmap width you plan to create"/>
+        <param name="row_num" argument="-r" type="integer" value="600" label="Plot Height in pixels" help="Equal to the heatmap height you plan to create"/>
+
+
+        <conditional name="quantile_type">
+            <param name="quantile_type_selector" type="select" display="radio" label="Choose the Contrast paramter">
+                <option value="b_option" selected="true">Calculate thresholds from data (-b)</option>
+                <option value="t_option">Enforce absolute thresholds (-t)
+                </option>
+            </param>
+
+            <when value="b_option">
+                <param name="quantile" argument="-b" type="float" min="0" max="100" value="95" label="Quantile" help="Enter your quantile value above."/>
+                <param name="min_contrast" type="float" min="0" value="0" label="Minimum upper limit after Quantile calculation" help="This value will be used as the upper limit if the calculated quantile is below this value" argument="-m"/>
+            </when>
+
+            <when value="t_option">
+                <param name="quantile2" argument="-t" type="float" min="0" value="0.0" label="Absolute tag threshold" help="Enter your custom tag threshold value above. takes real values (>= 0)"/>
+            </when>
+        </conditional>
+
+    </inputs>
+
+    <outputs>
+        <data name="threshold_output" format="txt" from_work_dir="calcThreshold.txt"/>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_file" value="sample.tabular"/>
+            <param name="header" value="T"/>
+            <param name="start_col" value="2"/>
+            <param name="col_num" value="300"/>
+            <param name="row_num" value="600"/>
+            <conditional name="quantile_type">
+                <param name="quantile_type_selector" value="b_option"/>
+                <param name="quantile" value="95"/>
+                <param name="min_contrast" value="5"/>
+            </conditional>
+            <output name="threshold_output" file="calcThreshold_b.txt" />
+        </test>
+        <test>
+            <param name="input_file" value="sample.tabular"/>
+            <param name="header" value="T"/>
+            <param name="start_col" value="2"/>
+            <param name="col_num" value="300"/>
+            <param name="row_num" value="600"/>
+            <conditional name="quantile_type">
+                <param name="quantile_type_selector" value="t_option"/>
+                <param name="quantile2" value="10.0"/>
+            </conditional>
+            <output name="threshold_output" file="calcThreshold_t.txt" />
+        </test>
+    </tests>
+
+    <help>
+        <![CDATA[
+
+**What it does**
+
+----
+
+Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream.
+
+**Choosing Plot Width & Height**
+
+If your trying to create heatmaps with dimensions (Width x Height)px = (300 x 600)px. Use Plot width = 300, height = 600. This not only helps in generating unbiased heatmaps but also helps in reusing the calculated contrasts for heatmaps of same dimensions.
+
+**Understanding contrast parameters**
+
+`-b`
+
+    Calculates a percentile value (for example 95th percentile) from the input CDT data matrix to report upper-limit and lower-limit for setting heatmap contrasts.
+
+    Also can set a minimum upper-limit to fall-back, incase the calculated percentile is <= specified minimum.
+
+`-t`
+
+    Takes the absolute value entered and reports an upper_limit and lower_limit.
+
+    ]]>
+    </help>
+
+    <citations>
+        <citation type="bibtex">
+            @unpublished{None,
+            author = {Kuntala, Prashant Kumar and Lai, William KM },
+            title = {None},
+            year = {None},
+            eprint = {None},
+            url = {http://www.pughlab.psu.edu/}
+        }</citation>
+    </citations>
+
+</tool>