diff scHicClusterCompartments.xml @ 0:5426f006d7ed draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/schicexplorer commit c41cef1b9acefdbdbd52996458fdee743ca5c0a6"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scHicClusterCompartments.xml	Sat Jan 25 04:38:26 2020 -0500
@@ -0,0 +1,128 @@
+<tool id="schicexplorer_schicclustercompartments" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>clusters single-cell Hi-C interaction matrices with A/B compartments dimension reduction</description>
+    <macros>
+        <token name="@BINARY@">scHicClusterCompartments</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        @BINARY@
+
+        --matrix '$matrix_mcooler'
+
+        --numberOfClusters $numberOfClusters
+
+        --clusterMethod $clusterMethod_selector
+
+        #if $chromosomes:
+            #set $chromosome = ' '.join([ '\'%s\'' % $chrom for $chrom in str($chromosomes).split(' ') ])
+            --chromosomes $chromosome
+        #end if
+
+        #if $norm:
+            $norm
+        #end if
+        #if $binarization:
+            $binarization
+        #end if
+
+        #if $extra_track_conditional.extra_track_selection == 'gene_density':
+            --extraTrack '$extra_track_conditional.extraTrack'
+        #elif $extra_track_conditional.extra_track_selection == 'histon_mark':
+            --histonMarkType '$extra_track_conditional.histonMarkType'
+        #end if
+
+        --outFileName cluster_list.txt
+
+        --threads @THREADS@
+
+
+
+    ]]></command>
+    <inputs>
+        
+        <expand macro="matrix_mcooler_macro"/>
+        <param name="clusterMethod_selector" type="select" label="Cluster method:">
+                <option value="kmeans" selected="True">K-means</option>
+                <option value="spectral" >Spectral clustering</option>
+        </param>
+        <param name="numberOfClusters" type="integer" value="7"  label="Number of clusters" help='How many clusters should be computed by kmeans or spectral clustering' />   
+
+        <param name='norm' type='boolean' truevalue='--norm' label='Use different expected value computation'/>
+        <param name='binarization' type='boolean' truevalue='--binarization' label='Convert positive values to 1 and all negative to -1.'/>
+        
+
+        <param name='chromosomes' type='text' label='List of chromosomes to consider' help='Please separate the chromosomes by space'/>
+        <conditional name="extra_track_conditional">
+            <param name='extra_track_selection' label='Extra track type' type='select'>
+                <option value='' selected='true'>No track</option>
+                <option value='gene_density'>Gene density</option>
+                <option value='histon_mark'>Histone mark coverage</option>
+            </param>
+            <when value='gene_density' >
+                <param name='extraTrack' type='data' format='bed' label='Correlate PCA with e.g. gene density or histone marks to flip sign'/>
+            </when>
+            <when value='histon_mark'>
+                <param name='histonMarkType' type='data' format='bed' label='Correlate PCA with e.g. gene density or histone marks to flip sign'/>
+            </when>
+            <when value='' />
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="cluster_list.txt" format="txt" label="${tool.name} on ${on_string}: Cluster results"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='kmeans' />
+            <param name='numberOfClusters' value='3' />
+            <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='spectral' />
+            <param name='numberOfClusters' value='3' />
+            <output name="outFileName" file="scHicClusterCompartments/cluster_spectral.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+        <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='kmeans' />
+            <param name='numberOfClusters' value='3' />
+            <param name='binarization' value='True'/>
+            <param name='norm' value='True'/>
+            <conditional name="extra_track_conditional">
+                <param name="extra_track_selection" value="histon_mark"/>
+                <param name="histonMarkType" value="scHicClusterCompartments/mm9_H3K36me3.bed.gz" />
+            </conditional>
+            <output name="outFileName" file="scHicClusterCompartments/cluster_kmeans_binarization_norm_histone_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+       <test>
+            <param name='matrix_mcooler' value='test_matrix.mcool' />
+            <param name='clusterMethod_selector' value='kmeans' />
+            <param name='numberOfClusters' value='3' />
+            <param name='binarization' value='True'/>
+            <param name='norm' value='True'/>
+            <conditional name="extra_track_conditional">
+                <param name="extra_track_selection" value="gene_density"/>
+                <param name="extraTrack" value="scHicClusterCompartments/mm9_gene.bed.gz" />
+            </conditional>
+            <output name="outFileName" file="scHicClusterCompartments/cluster_spectral_binarization_norm_gene_track.txt" ftype="txt" compare="sim_size" delta="4000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Clustering with dimension reduction via A/B compartments
+========================================================
+
+scHicClusterCompartments uses kmeans or spectral clustering to associate each cell to a cluster and therefore to its cell cycle. 
+The clustering is applied on dimension reduced data based on the A/B compartments track. This approach reduces the number of dimensions from samples * (number of bins)^2 to samples * (number of bins). 
+Please consider also the other clustering and dimension reduction approaches of the scHicExplorer suite. They can give you better results, 
+can be faster or less memory demanding.
+
+For more information about scHiCExplorer please consider our documentation on readthedocs.io_
+
+.. _readthedocs.io: http://schicexplorer.readthedocs.io/
+]]></help>
+    <expand macro="citations" />
+
+</tool>