diff hicPlotSVL.xml @ 0:450605e43e25 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/hicPlotSVL.xml	Mon Dec 16 15:50:36 2019 -0500
@@ -0,0 +1,102 @@
+<tool id="hicexplorer_hicplotsvl" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>plots the relation of short vs long range contacts</description>
+    <macros>
+        <token name="@BINARY@">hicPlotSVL</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+
+        #for $counter, $m in enumerate($matrix_h5_cooler_multiple):
+            #set identifier = @ESCAPE_IDENTIFIER_M@
+            ln -s '$m' '${counter}_$identifier' &&
+        #end for
+        #set $m = ' '.join([ '\'%s_%s\'' % ($counter, @ESCAPE_IDENTIFIER_MATRIX@) for $counter, $matrix in enumerate($matrix_h5_cooler_multiple) ])
+       
+        @BINARY@
+            --matrices $m
+            #if $distance:
+                --distance $distance
+            #end if
+
+            @CHROMOSOME_LIST@
+
+            #if $colorList:
+                #set $colorList_new = ' '.join([ '\'%s\'' % $color for $color in str($colorList).split(' ') ])
+                --colorList $colorList_new
+            #end if
+
+            #if $dpi:
+                --dpi $dpi
+            #end if 
+            --plotFileName plot.$image_file_format
+            --outFileName p_values.txt
+            --outFileNameData ratios.txt 
+            --threads @THREADS@
+
+            && mv plot.$image_file_format plot
+]]>
+    </command>
+    <inputs>
+        <expand macro='matrix_h5_cooler_multiple_macro'/>
+        <param argument="--distance" optional='true'  type="integer" label="Short range distance"
+            help="Distance which should be considered as short range. Default 2MB." value='2000000'/>
+        <expand macro="chromosome_list" />
+        <param argument="--colorList" optional='true' type="text" label="Colorlist" help="Colorlist for the boxplots." />
+        <param name='dpi' type='integer' label='DPI for image' help='Change the default resolution of the plot.' optional='true'/>
+        <param name="image_file_format" type="select" label="Image output format">
+            <option value="png" selected="True">png</option>
+            <option value="svg">svg</option>
+            <option value="pdf">pdf</option>
+        </param>
+    </inputs>
+    <outputs> 
+        <data name='output_plot' from_work_dir='plot' format='png' label='Plot SVL'>
+            <change_format>
+                <when input="image_file_format" value="svg" format="svg" />
+                <when input="image_file_format" value="pdf" format="pdf" />
+            </change_format>
+        </data>
+        <data name='output_p_values' from_work_dir='p_values.txt' format='txt' label='P values svl'/>
+        <data name='output_ratios' from_work_dir='ratios.txt' format='txt' label='Ratios svl'/>
+
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix_h5_cooler_multiple" value="small_test_matrix.h5,small_test_matrix.h5"/>
+            <param name="distance" value="2000000"/>
+            <param name="dpi" value="10"/>
+            <param name="color" value="y m c"/>
+            <repeat name="chromosome_list">
+                <param name="chromosomes" value="chr2L"/>
+            </repeat>
+            <repeat name="chromosome_list">
+                <param name="chromosomes" value="chr3L"/>
+            </repeat>
+            <repeat name="chromosome_list">
+                <param name="chromosomes" value="chr4"/>
+            </repeat>
+
+            <param name="image_file_format" value="png" />
+
+            <output name="output_plot" file="hicPlotSVL/plot.png" ftype="png" compare="sim_size"/>
+            <output name="output_p_values" file="hicPlotSVL/p_values.txt" ftype="txt" compare="sim_size"/>
+            <output name="output_ratios" file="hicPlotSVL/ratios.txt" ftype="txt" compare="sim_size"/>
+       
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Short vs long range contacts
+============================
+
+Computes the ratio of short vs. long range contacts on the given matrices and makes, if two or more matrices are present a differential test between the matrices.
+
+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>