--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicFindTADs.xml	Thu Mar 30 03:22:25 2017 -0400
@@ -0,0 +1,144 @@
+<tool id="hicexplorer_hicfindtads" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>find minimum cuts that correspond to boundaries</description>
+    <macros>
+        <token name="@BINARY@">hicFindTADs</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command><![CDATA[
+        #if $mode.mode_selector == 'TAD_score':
+            ln -s '$mode.matrix' matrix.npz.h5 &&
+        #end if
+
+        #if $mode.mode_selector == 'find_TADs':
+            ln -s '$tad_score_zscore_matrix' ./tadScoreFile.tabular_zscore_matrix.h5 &&
+        #end if
+
+        hicFindTADs
+            $mode.mode_selector
+
+            #if $mode.mode_selector == 'find_TADs':
+                --tadScoreFile '$tadScoreFile'
+                --outPrefix galaxy_tad_prefix
+                ##--maxThreshold $mode.maxThreshold
+                --delta $mode.delta
+                --pvalue $mode.pvalue
+                #if $mode.minBoundaryDistance:
+                    --minBoundaryDistance $mode.minBoundaryDistance
+                #end if
+
+            #else:
+                --matrix matrix.npz.h5
+                --maxDepth $mode.maxDepth
+                --minDepth $mode.minDepth
+                --outFileName ./tadScoreFile.tabular
+
+                --step $mode.step
+            #end if
+
+    ]]></command>
+    <inputs>
+
+        <conditional name="mode">
+            <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range">
+                <option value="find_TADs">find TADs</option>
+                <option value="TAD_score">TAD score</option>
+            </param>
+            <when value="find_TADs">
+                <param argument="--tadScoreFile" type="data" format="tabular" label="TAD score file"/>
+                <param name="tad_score_zscore_matrix" type="data" format="h5" label="TAD score Matrix file"/>
+
+                <param argument="--delta" type="float" value="0.001" optional="True"
+                       label="Minimum threshold of the difference between the TAD-separation score of a putative boundary and the mean of the TAD-sep. score of surrounding bins."
+                        help="The delta value reduces spurious boundaries that are shallow, which usually
+                              occur at the center of large TADs when the TAD-sep. score is flat. Higher
+                              delta threshold values produce more conservative boundary estimations. By
+                              default, multiple delta thresholds are saved for the following delta
+                              values: 0.001, 0.01, 0.03, 0.05, 0.1. Other single or multiple values
+                              can be given."/>                <param argument="--pvalue" type="float" value="0.01" 
+                    label="P-value threshold"
+                    help="The probability of a local minima to be a boundary is estimated by comparing the distribution (Wilcoxon ranksum) of the
+                            zscores between the left and right regions (diamond) at the local minimum with the matrix zscores for a diamond at
+                            --minDepth to the left and a diamond --minDepth to the right.
+                            The reported pvalue is the Bonferroni correction all pvalues."/>
+                <param argument="--minBoundaryDistance" type="integer" value="" optional="True"
+                    label="Minimum distance between boundaries (in bp)."
+                    help="This parameter can be used to reduce spurious boundaries caused by noise. "/>
+
+            </when>
+            <when value="TAD_score">
+
+                <param argument="--matrix" type="data" format="h5" label="Corrected Hi-C matrix to use for the computations"/>
+                <param argument="--minDepth" type="integer" value="30000"
+                    label="Minimum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
+                    help="This number should be at least 3 times as large as the bin size of the Hi-C matrix."/>
+                <param argument="--maxDepth" type="integer" value="100000"
+                    label="Maximum window length (in bp) to be considered to the left and to the right of each Hi-C bin."
+                    help="This number should around 6-10 times as large as the bin size of the Hi-C matrix."/>
+                <param argument="--step" type="integer" value="10000"
+                    label="Step size when moving from minDepth to maxDepth"
+                    help="The step size grows exponentially as `maxDeph + (step * int(x)**1.5) for x in [0, 1, ...]`
+                    until  it reaches `maxDepth`. For example, selecting step=10,000, minDepth=20,000
+                    and maxDepth=150,000 will compute TAD-scores for window sizes:
+                    20,000, 30,000, 40,000, 70,000 and 100,000"/>
+            </when>
+        </conditional>
+
+
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="tadScoreFile.tabular" format="tabular">
+            <filter>mode['mode_selector'] == "TAD_score"</filter>
+        </data>
+        <data name="tad_score_zscore_matrix" from_work_dir="tadScoreFile.tabular_zscore_matrix.h5" format="h5">
+            <filter>mode['mode_selector'] == "TAD_score"</filter>
+        </data>
+        <data name="boundaries" from_work_dir="galaxy_tad_prefix_boundaries.bed" format="bed"
+            label="${tool.name} on ${on_string}: Boundary positions">
+            <filter>mode['mode_selector'] == "find_TADs"</filter>
+        </data>
+        <data name="score" from_work_dir="galaxy_tad_prefix_score.bedgraph" format="bedgraph"
+            label="${tool.name} on ${on_string}: Matrix with multi-scale TAD scores">
+            <filter>mode['mode_selector'] == "find_TADs"</filter>
+        </data>
+        <data name="domains" from_work_dir="galaxy_tad_prefix_domains.bed" format="bed"
+            label="${tool.name} on ${on_string}: TAD domains">
+            <filter>mode['mode_selector'] == "find_TADs"</filter>
+        </data>
+        <data name="boundaries_bin" from_work_dir="galaxy_tad_prefix_boundaries.gff"
+            format="bed" label="${tool.name} on ${on_string}: Boundary information plus score">
+            <filter>mode['mode_selector'] == "find_TADs"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <!--test>
+            <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/>
+            <param name="mode_selector" value="TAD_score"/>
+            <param name="minDepth" value="20000"/>
+            <param name="maxDepth" value="60000"/>
+            <param name="step" value="100000"/>
+            <output name="outFileName" file="hicFindTADs_TAD_score.tabular" ftype="tabular"/>
+            <output name="tad_score_zscore_matrix" file="tadScoreFile.tabular_zscore_matrix.h5" ftype="h5" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="tadScoreFile" value="hicFindTADs_TAD_score.tabular" ftype="tabular"/>
+            <param name="tad_score_zscore_matrix" value="tadScoreFile.tabular_zscore_matrix.h5" ftype="h5"/>
+            <param name="mode_selector" value="find_TADs"/>
+            <param name="delta" value="0.002"/>
+            <param name="pvalue" value="0.01"/>
+
+            <output name="boundaries" file="hicFindTADs_find_boundaries.bed" ftype="bed"/>
+            <output name="score" file="hicFindTADs_find_score.bedgraph" ftype="bedgraph"/>
+            <output name="domains" file="hicFindTADs_find_domains.bed" ftype="bed"/>
+            <output name="boundaries_bin" file="hicFindTADs_find_boundaries.gff" ftype="gff"/>
+        </test-->
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Uses the graph clustering measure "conductance" to find minimum cuts that correspond to boundaries.
+
+]]></help>
+    <expand macro="citations" />
+</tool>