diff chicViewpoint.xml @ 0:6d76e532b669 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/chicViewpoint.xml	Mon Dec 16 14:28:22 2019 -0500
@@ -0,0 +1,99 @@
+<tool id="hicexplorer_chicviewpoint" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>computes viewpoints with the given reference points and a background model.</description>
+    <macros>
+        <token name="@BINARY@">chicViewpoint</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+
+        mkdir interactionFiles &&
+        #for $m in $matrix_h5_cooler_multiple:
+            #set identifier = @ESCAPE_IDENTIFIER_M@
+            ln -s '$m' '$identifier' &&
+        #end for
+        #set $m = ' '.join([ '\'%s\'' % @ESCAPE_IDENTIFIER_MATRIX@ for $matrix in $matrix_h5_cooler_multiple ])
+       
+        @BINARY@
+
+            --matrices $m
+            --range $rangeUpstream $rangeDownstream
+            --referencePoints '$referencePoints'
+            --averageContactBin $averageContactBin
+            --fixateRange $fixateRange
+            --threads @THREADS@
+            --backgroundModelFile '$backgroundModelFile'
+            --outputFolder interactionFiles
+            $writeFileNamesToFile
+
+    ]]></command>
+    <inputs>
+        <expand macro="matrix_h5_cooler_multiple_macro" />
+
+        <param argument="--referencePoints" type="data" format='interval'
+                        label="Reference points"
+                        help="Bed file contains all reference points which should be used to create viewpoints." />
+        <param name="rangeUpstream" type="integer" value="500000"  label="Upstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />
+        <param name="rangeDownstream" type="integer" value="500000"  label="Downstream range" help='Defines the region upstream of a reference point which should be considered in the analysis.' />   
+
+        <param argument="--backgroundModelFile" type="data" format='tabular'
+                        label="Background model"
+                        help="The background file computed by chicViewpointBackgroundModel" />
+        <param argument="--averageContactBin" type="integer" value="5"  label="Average contacts window size" help='Average the contacts of n bins via a sliding window approach.'/>    
+        <param argument="--fixateRange" type="integer" value="500000"  label="Clip background distance" help='Fixate score of background model starting at distance x. E.g. all values greater 500kb are set to the value of the 500kb bin.'/>    
+        <param name='writeFileNamesToFile' type='boolean' truevalue='--writeFileNamesToFile interactionFiles.txt'  falsevalue="" checked="false" label="Save interaction file names (batch processing)"
+                    help="Set this parameter if you want to use the batch processing mode for the further analysis."/>
+    </inputs>
+    <outputs>
+        <collection name="interactionFilesCollection" type="list" label="Interaction files">
+            <discover_datasets pattern="__name__" format="interval"  directory="interactionFiles" />
+        </collection>
+        <data name="interactionFileNames" from_work_dir="interactionFiles.txt" format="txt" label="${tool.name} interaction file names">
+            <filter>writeFileNamesToFile</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+           <param name="matrix_h5_cooler_multiple" value="cHi-C/FL-E13-5_chr1.cool,cHi-C/MB-E10-5_chr1.cool"/>
+            
+            <param name="referencePoints" value="cHi-C/referencePoints_chicViewpoint.bed"/>
+            <param name="backgroundModelFile" value="cHi-C/background.bed"/>
+            <param name="fixateRange" value="500000"/>
+            <param name="rangeUpstream" value="200000"/>
+            <param name="rangeDownstream" value="200000"/>
+            <param name="writeFileNamesToFile" value="True"/>
+
+           
+            <output_collection name="interactionFilesCollection" type="list" count="6">
+                <element name="FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/>
+                <element name="FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/>
+                <element name="FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/FL-E13-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/>
+
+                <element name="MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_19093103_19093103_Tfap2d.bed" ftype="interval" lines_diff="3"/>
+                <element name="MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_14300280_14300280_Eya1.bed" ftype="interval" lines_diff="3"/>
+                <element name="MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" file="cHi-C/chicViewpoint/output_3/MB-E10-5_chr1_chr1_4487435_4487435_Sox17.bed" ftype="interval" lines_diff="3"/>
+            </output_collection>
+            <output name="interactionFileNames" file="cHi-C/chicViewpoint/fileNames_two_matrices.txt" ftype="txt" lines_diff='0'/>
+            
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Compute viewpoints for all given reference points
+=================================================
+
+Computes per input matrix all viewpoints which are defined in the reference points file. All files are stored in the folder defined by `--outputFolder`, the files
+are named by the name of the reference point, the sample name and  the location of the reference point:
+
+gene_matrix_name_chr_start_end.bed
+
+If multiple reference points are used and the processing downstream should be automated via batch processing mode, please activate `--writeFileNamesToFile`. In this
+file all the file names will be written to; in the case of multiple samples two consecutive lines are consideres as treatment vs control in the differential analysis.
+
+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>