--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicDifferentialTAD.xml	Tue Mar 16 15:26:17 2021 +0000
@@ -0,0 +1,81 @@
+<tool id="hicexplorer_hicdifferentialtad" name="@BINARY@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
+    <description>searches for differential TADs</description>
+    <macros>
+        <token name="@BINARY@">hicDifferentialTAD</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$matrix_h5_cooler_target' 'matrix_target.$matrix_h5_cooler_target.ext' &&
+        ln -s '$matrix_h5_cooler_control' 'matrix_control.$matrix_h5_cooler_control.ext' &&
+
+        @BINARY@
+
+            --targetMatrix  'matrix_target.$matrix_h5_cooler_target.ext'
+            --controlMatrix  'matrix_control.$matrix_h5_cooler_control.ext'
+
+            #if $tadDomains:
+                --tadDomains '$tadDomains'
+            #end if
+
+            #if $pValue:
+                --pValue $pValue
+            #end if
+       
+            --mode $mode_selector
+            --modeReject $modeReject
+            --outFileNamePrefix galaxy_differential_tad
+            --threads @THREADS@
+
+]]>
+    </command>
+    <inputs>
+        <param name='matrix_h5_cooler_target' type="data" format="h5,cool" label="Target matrix to compute on" />
+        <param name='matrix_h5_cooler_control' type="data" format="h5,cool" label="Control matrix to compute on" />
+
+        <param argument="--tadDomains" type="data" format='bed' optional='false' label="TAD domains file" help= "The TADs domain file computed by hicFindTADs." />
+        <param argument="--pValue" type="float" label="P-value" min='0.0' max='1.0' help= "H0 is considered as \'two regions are identical.\' i.e. all regions with a test result of smaller p-value are rejected and considered as differential." value='0.05' />
+        <param name="mode_selector" type="select" label="Method to compute the differentail TAD expression">
+            <option value="intra-TAD">intra-TAD</option>
+            <option value="left-inter-TAD">left-inter-TAD</option>
+            <option value="right-inter-TAD">right-inter-TAD</option>
+            <option value="all" selected="True">all</option>
+        </param>
+
+        <param name="modeReject" type="select" label="Method to compute the differentail TAD expression">
+            <option value="one" selected="True">one</option>
+            <option value="all">all</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name='acceptedTADs' from_work_dir='galaxy_differential_tad_accepted.diff_tad' format='txt' label='Accepted TADs' />
+        <data name='rejectedTADs' from_work_dir='galaxy_differential_tad_rejected.diff_tad' format='txt' label='Rejected TADs' />
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler_target" value="small_test_matrix.cool" />
+            <param name="matrix_h5_cooler_control" value="small_test_matrix.cool" />
+
+            <param name="tadDomains" ftype='bed' value="hicDifferentialTAD/multiNone_domains.bed" />
+            <param name="pValue" value="1.0" />
+            <param name="mode_selector" value="all" />
+            <param name="modeReject" value="one" />
+            <output name="acceptedTADs" file="hicDifferentialTAD/accepted.txt" ftype="txt" />
+            <output name="rejectedTADs" file="hicDifferentialTAD/rejected.txt" ftype="txt" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Differential TAD detection
+==========================
+
+Computes if precomputed TADs are differentially expressed between two samples.
+
+
+For more information about HiCExplorer please consider our documentation on readthedocs.io_.
+
+.. _readthedocs.io: http://hicexplorer.readthedocs.io/en/latest/index.html
+
+]]>    </help>
+    <expand macro="citations" />
+</tool>