--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ccat_wrapper.xml	Mon Jan 27 09:27:03 2014 -0500
@@ -0,0 +1,148 @@
+<tool id="peakcalling_ccat" name="CCAT" version="0.0.1">
+  <description>Control-based ChIP-seq Analysis Tool</description>
+  <requirements>
+    <requirement type="package" version="3.0">CCAT</requirement>
+  </requirements>
+  <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' 
+  #if str( $options_type[ 'options_type_selector' ] ) == 'advanced':
+  '$input_advanced_config_file' 
+  #else:
+  '${ options_type.input_config_file.fields.path }'
+  #end if
+  'CCAT in Galaxy' 
+  '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command>
+  <inputs>
+    <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" >
+      <validator type="unspecified_build" />
+    </param>
+    <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" >
+      <validator type="unspecified_build" />
+    </param>
+    <conditional name="options_type">
+      <param name="options_type_selector" type="select" label="Advanced Options">
+        <option value="basic" selected="True">Hide Advanced Options</option>
+        <option value="advanced">Show Advanced Options</option>
+      </param>
+      <when value="basic">
+        <param name="input_config_file" type="select" label="Select a pre-defined configuration file">
+          <options from_data_table="ccat_configurations">
+            <validator type="no_options" message="No configurations are available"/>
+          </options>
+        </param>
+      </when>
+      <when value="advanced">
+        <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/>
+        <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/>
+        <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/>
+        <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" >
+          <option value="1">Transition from sense strand to anti-sense strand</option>
+          <option value="0" selected="True">Local maximum of read-enrichment profile</option>
+        </param>
+        <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/>
+        <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/>
+        <param name="random_seed" type="integer" label="Random Seed" value="123456"/>
+        <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/>
+        <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/>
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
+    <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
+    <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)">
+      <actions>
+        <action type="metadata" name="chromCol" default="1"/>
+        <action type="metadata" name="startCol" default="3"/>
+        <action type="metadata" name="endCol" default="4"/>
+      </actions>
+    </data>
+    <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/>
+  </outputs>
+  <configfiles>
+    <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced':
+fragmentSize	${options_type[ 'fragment_size' ]}
+slidingWinSize	${options_type[ 'sliding_window_size' ]}
+movingStep	${options_type[ 'moving_step' ]}
+isStrandSensitiveMode	${options_type[ 'is_strand_sensitive_mode' ]}
+minCount	${options_type[ 'min_count' ]}
+outputNum	${options_type[ 'output_num' ]}
+randomSeed	${options_type[ 'random_seed' ]}
+minScore	${options_type[ 'min_score' ]}	
+bootstrapPass	${options_type[ 'bootstrap_pass' ]}
+#end if</configfile>
+  </configfiles>
+  <tests>
+    <test>
+      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="options_type_selector" value="advanced" />
+      <param name="fragment_size" value="200" />
+      <param name="sliding_window_size" value="500" />
+      <param name="moving_step" value="50" />
+      <param name="is_strand_sensitive_mode" value="0" />
+      <param name="min_count" value="4" />
+      <param name="output_num" value="100000" />
+      <param name="random_seed" value="123456" />
+      <param name="min_score" value="5.0" />
+      <param name="bootstrap_pass" value="50" />
+      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
+      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
+      <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="True" />
+      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
+    </test>
+    <test>
+      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="options_type_selector" value="basic" />
+      <param name="input_config_file" value="ccat_3.0_histone_config" />
+      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_1.interval.re_match" compare="re_match" />
+      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_1.interval.re_match" compare="re_match" />
+      <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_1.interval.sorted.re_match" compare="re_match" sort="true" />
+      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_1.txt" />
+    </test>
+    <!-- Test below gives different answers on different architectures, 
+    e.g.: x86_64 GNU/Linux gave an extra line (additional peak called) when compared to the version running on 10.6.0 Darwin i386 
+    slidingWinSize was fixed to be 1000, default as per readme.txt
+    -->
+    <!--
+    <test>
+      <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" />
+      <param name="options_type_selector" value="basic" />
+      <param name="input_config_file" value="ccat_3.0_histone_config_readme" />
+      <output name="output_peak_file" file="peakcalling_ccat/3.0/ccat_test_peak_out_2.interval.re_match" compare="re_match" />
+      <output name="output_region_file" file="peakcalling_ccat/3.0/ccat_test_region_out_2.interval.re_match" compare="re_match" />
+      <output name="output_top_file" file="peakcalling_ccat/3.0/ccat_test_top_out_2.interval.sorted.re_match" compare="re_match" sort="true" />
+      <output name="output_log_file" file="peakcalling_ccat/3.0/ccat_test_log_out_2.txt" />
+    </test>
+  -->
+  </tests>
+  <help>
+**What it does**
+
+This tool allows ChIP-seq peak/region calling using CCAT.
+
+View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm.
+
+------
+
+**Citation**
+
+For the underlying tool, please cite `Xu H, Handoko L, Wei X, Ye C, Sheng J, Wei CL, Lin F, Sung WK. A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics. 2010 May 1;26(9):1199-204. &lt;http://www.ncbi.nlm.nih.gov/pubmed/20371496&gt;`_
+
+If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
+
+  </help>
+</tool>