diff hicDetectLoops.xml @ 0:2d1f9759fa0e draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 3b41d687ff30583540d055f6995de00530cca81d-dirty"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicDetectLoops.xml	Mon Dec 16 15:49:32 2019 -0500
@@ -0,0 +1,104 @@
+<tool id="hicexplorer_hicdetectloops" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>searches for enriched regions</description>
+    <macros>
+        <token name="@BINARY@">hicDetectLoops</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
+        @BINARY@
+
+            --matrix  'matrix.$matrix_h5_cooler.ext'
+
+            #if $peakWidth:
+                --peakWidth $peakWidth
+            #end if
+
+            #if $windowSize:
+                --windowSize $windowSize
+            #end if
+
+            #if $pValuePreselection:
+                --pValuePreselection $pValuePreselection
+            #end if
+
+            #if $peakInteractionsThreshold:
+                --peakInteractionsThreshold $peakInteractionsThreshold
+            #end if
+
+            #if $maximumInteractionPercentageThreshold:
+                --maximumInteractionPercentageThreshold $maximumInteractionPercentageThreshold
+            #end if
+            #if $pValue:
+                --pValue $pValue
+            #end if
+            #if $maxLoopDistance:
+                --maxLoopDistance $maxLoopDistance
+            #end if
+
+            #if $region:
+                --region '$region'
+            #end if
+
+            #if $chromosomes:
+                #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
+                --chromosomes $chromosome
+            #end if
+
+            --statisticalTest $statisticalTest_selector
+            
+            --outFileName output_loop.bedgraph
+
+            --threads @THREADS@
+]]>
+    </command>
+    <inputs>
+        <expand macro="matrix_h5_cooler_macro" />
+        <param argument="--peakWidth" type="integer" optional='true' label="Peak width" help= "The width of the peak region in bins. The square around the peak will include (2 * peakWidth)^2 bins." />
+        <param argument="--windowSize" type="integer" optional='true' label="Window size" help= "The window size for the neighborhood region the peak is located in. All values from this region (exclude the values from the peak
+                           region) are tested against the peak region for significant difference. The square will have the size of (2 * windowSize)^2 bins" />
+        <param argument="--pValuePreselection" type="float" label="P-value preselection" help= "Only candidates with p-values less the given threshold will be considered as candidates. 
+                                For each genomic distance a negative binomial distribution is fitted and for each pixel a p-value given by the cumulative density function is given. 
+                                This does NOT influence the p-value for the neighborhood testing." value='0.05'/>
+        <param argument="--peakInteractionsThreshold" type="integer" label="Minimum interaction number" help= "The minimum number of interactions a detected peaks needs to have to be considered." value='5' />
+        <param argument="--maximumInteractionPercentageThreshold" type="float" value='0.1' label="Maximum interaction share" help= "For each genomic distance the maximum value is considered and all candidates need to have at least \'max_value * maximumInteractionPercentageThreshold\' interactions." />
+        <param argument="--pValue" type="float" label="P-value" help= "Rejection level for the statistical test for H0. H0 is peak region and background have the same distribution." value='0.05'/>
+        <param argument="--maxLoopDistance" optional='true'  type="integer" label="Maximal loop distance" help= "Maximum genomic distance of a loop, usually loops are within a distance of ~2MB." value='2000000'/>
+        <param argument="--minLoopDistance" optional='true'  type="integer" label="Maximal loop distance" help= "Minimum genomic distance of a loop to be considered." value='100000'/>
+        <param argument="--chromosomes" optional='true'  type="text" label="Chromosomes to include" help= "Chromosomes to include in the analysis. If not set, all chromosomes are included." />
+        <param argument="--region" optional='true'  type="text" label="Chromosomes to include" help= "The format is chr:start-end." />
+        <param name="statisticalTest_selector" type="select" label="Stistical test">
+            <option value="wilcoxon-rank-sum" selected="True">Wilcoxon rank-sum'</option>
+            <option value="anderson-darling">Anderson-Darling</option>
+        </param>
+    </inputs>
+    <outputs> 
+        <data name='output_loops' from_work_dir='output_loop.bedgraph' format='bedgraph' label='Computed loops'/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler" value="small_test_matrix.cool"/>
+            <param name="maxLoopDistance" value="30000000"/>
+            <param name="windowSize" value="5"/>
+            <param name="peakWidth" value="2"/>
+            <param name="pValue" value="0.5"/>
+            <param name="pValuePreselection" value="0.55"/>
+            <!-- <param name="chromosomes" value="X"/> -->
+            <output name="output_loops" file="hicDetectLoops/loops.bedgraph" ftype="bedgraph" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Loop detection
+==============
+
+Computes enriched regions (peaks) or long range contacts on the given contact matrix.
+
+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>