diff hicCorrectMatrix.xml @ 0:d5bf8c60d661 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit 2f347b0756d720114f037ed1ff9ba4836e1b3b04

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicCorrectMatrix.xml	Thu Mar 30 02:21:47 2017 -0400
@@ -0,0 +1,163 @@
+<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>Runs Dekker's iterative correction over a hic matrix.</description>
+    <macros>
+        <token name="@BINARY@">hicCorrectMatrix</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+        ln -s '$matrix' temp_matrix.npz.h5 &&
+
+        hicCorrectMatrix
+            $mode.mode_selector
+            --matrix temp_matrix.npz.h5
+
+            ## special: --chromosomes is optional, but if given needs at least one argument
+            #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomes ])
+            #if chroms
+                --chromosomes "$chroms"
+            #end if
+
+            #if $mode.mode_selector == 'correct':
+
+                --iterNum $mode.iterNum
+                --outFileName corrected_matrix.npz.h5
+
+                #if $mode.filterThreshold_low and $mode.filterThreshold_large:
+                    --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
+                #end if
+
+                #if $mode.inflationCutoff:
+                    --inflationCutoff $mode.inflationCutoff
+                #end if
+
+                #if $mode.transCutoff:
+                    --transCutoff $mode.transCutoff
+                #end if
+
+                #if $mode.sequencedCountCutoff:
+                    --sequencedCountCutoff $mode.sequencedCountCutoff
+                #end if
+
+                $mode.skipDiagonal
+                $mode.perchr
+
+            #elif $mode.mode_selector == 'merge_failed':
+                --plotName diagnostic_plot.png
+                --outMatrixFile corrected_matrix.npz.h5
+                #if $mode.xMax:
+                    --xMax $mode.xMax
+                #end if
+                #if $mode.filterThreshold_low and $mode.filterThreshold_large:
+                    --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
+                #end if
+            #else:
+                --plotName diagnostic_plot.png
+                #if $mode.xMax:
+                    --xMax $mode.xMax
+                #end if
+            #end if
+
+]]>
+    </command>
+    <inputs>
+        <param argument="--matrix" name="matrix" type="data" format="h5"
+            label="Hi-C matrix" />
+
+        <conditional name="mode">
+            <param name="mode_selector" type="select" label="Range restriction (in bp)" argument="--range">
+                <option value="diagnostic_plot">Diagnostic plot</option>
+                <option value="correct">Correct matrix</option>
+            </param>
+            <when value="diagnostic_plot">
+                <expand macro="xMax" />
+            </when>
+            <when value="correct">
+                <param argument="--iterNum" name="iterNum" type="integer" optional="true" value="500"
+                    label="Number of iterations" />
+
+                <param argument="--inflationCutoff" name="inflationCutoff" type="float" optional="true"
+                    label="Inflation cutoff" value=""
+                    help="Value corresponding to the maximum number of times a bin can be scaled up during the iterative correction.
+                    For example, a inflationCutoff of 3 will filter out all bins that were expanded 3 times or more during the iterative correction."/>
+
+                <param argument="--transCutoff" name="transCutoff" type="float" optional="true"
+                    label="Trans region cutoff" value=""
+                    help="Clip high counts in the top -transcut trans regions (i.e. between chromosomes). A usual value is 0.05."/>
+
+                <param argument="--sequencedCountCutoff" name="sequencedCountCutoff" optional="true" type="float"
+                    label="Sequenced count cutoff"
+                    help="Each bin receives a value indicating the fraction that is covered by reads.
+                        A cutoff of 0.5 will discard all those bins that have less than half of the bin covered."/>
+
+                <param argument="--skipDiagonal" name="skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" checked="false"
+                    label="Skip diagonal counts"/>
+
+                <param argument="--perchr" name="perchr" type="boolean" truevalue="--perchr" falsevalue="" checked="false"
+                    label="Normalize each chromosome separately" />
+                <expand macro="filterThreshold" />
+
+            </when>
+        </conditional>
+
+        <repeat name="chromosomes" min="1"
+            title="Include chromosomes" help="List of chromosomes to be included in the iterative correction.
+                    The order of the given chromosomes will be kept for the resulting corrected matrix">
+            <param name="chromosome" type="text" value="" />
+        </repeat>
+
+    </inputs>
+    <outputs>
+        <data name="outFileName"  from_work_dir="corrected_matrix.npz.h5" format="h5">
+            <filter>mode['mode_selector'] == "correct"</filter>
+        </data>
+        <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
+            <filter>mode['mode_selector'] == "diagnostic_plot"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" value="hicBuildMatrix_result1.h5" ftype="h5"/>
+            <param name="mode_selector" value="correct"/>
+            <repeat name="chromosomes">
+                <param name="chromosome" value="chrUextra"/>
+            </repeat>
+            <repeat name="chromosomes">
+                <param name="chromosome" value="chr3LHet"/>
+            </repeat> 
+            <output name="outFileName" file="hicCorrectMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="matrix" ftype="h5" value="hicBuildMatrix_result1.h5"/>
+            <param name="mode_selector" value="diagnostic_plot"/>
+            <repeat name="chromosomes">
+                <param name="chromosome" value="chrUextra"/>
+            </repeat>
+            <repeat name="chromosomes">
+                <param name="chromosome" value="chr3LHet"/>
+            </repeat> 
+            <output name="diagnostic_plot" file="diagnostic_plot.png" ftype="png" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Runs Dekker's iterative correction over a hic matrix.
+
+
+    correct        Run the iterative correction.
+    diagnostic_plot
+                   Plots a histogram of the coverage per bin together with the
+                   modified z-score based on the median absolute deviation
+                   method (see Boris Iglewicz and David Hoaglin 1993, Volume
+                   16: How to Detect and Handle Outliers The ASQC Basic
+                   References in Quality Control: Statistical Techniques,
+                   Edward F. Mykytka, Ph.D., Editor.
+
+
+]]></help>
+    <expand macro="citations" />
+</tool>
+