Merge pull request #5750 from Delphine-L/merqury

Creation of wrapper for merqury histogram plot

tools/merqury/merqury_plot_CN.xml

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+<tool id="merquryplot" name="Merqury histogram plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
+    <description>evaluate the assembly quality</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="bio_tools"/>
+    <expand macro="requirements"/>
+    <version_command>merqury --version</version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p output_files/ &&
+        \$MERQURY/plot/plot_spectra_cn.R 
+        -f '$input1' 
+        -o output_files/merqury_plot
+        #if $z
+            --zero-hist '$z' 
+        #end if
+        #if $cutoff
+             --cutoff '$cutoff' 
+        #end if 
+        --xdim $xdim
+        --ydim $ydim
+        #if $xmax>0
+            --xmax $xmax
+        #end if 
+        #if $ymax>0
+            --ymax $ymax
+        #end if
+        --type $type
+        #if $output_selector=='pdf'
+            -p
+        #end if 
+
+    ]]>    </command>
+    <inputs>
+        <param argument="-f" type="data" name="input1" format="tabular" />
+        <param argument="--xdim" type="integer" label="Width of plot"  value="6" min="0" />
+        <param argument="--ydim" type="integer" label="Height of plot"  value="5" min="0" />
+        <param argument="--xmax" type="float" label="Maximum limit for k-mer multiplicity (leave 0 for default)"  value="0" min="0" help="default: (x where y=peak) * 2.1" />
+        <param argument="--ymax" type="float" label="Maximum limit for k-mer count (leave 0 for default)"  value="0" min="0"  help="default: (y where y=peak) * 1.1" />
+        <param argument="-z" type="data" label="Assembly only counts" format="tabular" help=".only.hist file " optional="true" />
+        <param argument="--cutoff" type="data" label="Solid k-mer cutoffs" format="txt" help="cutoff.txt file" optional="true" />
+        <param name="output_selector" type="select" label="Output format" argument="-p">
+            <option value="png" selected="true">PNG</option>
+            <option value="pdf">PDF</option>
+        </param>
+        <param argument="--type" type="select" label="Type of plot (default all)">
+            <option value="all" selected="true">All</option>
+            <option value="line">Line</option>
+            <option value="fill">Fill</option>
+            <option value="stack">Stack</option>
+        </param>
+    </inputs>
+    <outputs>
+        <collection name="png_files" type="list" label="${tool.name} on ${on_string}: png plots">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.png" format="png" directory="output_files"/>
+            <filter>"png" in output_selector</filter>
+        </collection>
+        <collection name="pdf_files" type="list" label="${tool.name} on ${on_string}: pdf plots">
+            <discover_datasets pattern="(?P&lt;name&gt;.+)\.pdf" format="pdf" directory="output_files"/>
+            <filter>"pdf" in output_selector</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test  expect_num_outputs="1">
+            <param name="input1" value="output_merqury.assembly_01.spectra-cn.tabular"/>
+            <param name="xdim"  value="6" />
+            <param name="ydim"  value="5" />
+            <param name="xmax"  value="0" />
+            <param name="ymax"  value="0" />
+            <param name="z" value="output_merqury.assembly_01.only.tabular"/>
+            <param name="type" value="all" />
+            <param name="output_selector"  value="png" />
+            <output_collection name="png_files" type="list" count="3">
+                <element name="merqury_plot.fl">
+                    <assert_contents>
+                        <has_size value="99000" delta="5000"/>
+                    </assert_contents>
+                </element>
+                <element name="merqury_plot.ln">
+                    <assert_contents>
+                        <has_size value="99000" delta="5000"/>
+                    </assert_contents>
+                </element>
+                <element name="merqury_plot.st">
+                    <assert_contents>
+                        <has_size value="124000" delta="20000"/>
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+
+   <help><![CDATA[
+
+.. class:: infomark
+
+**Purpose**
+Make spectra-cn plots. Line, filled, and stacked spectra-cn plots will be
+generated. Inputs : Histogram files generated by merqury.
+
+    ]]>    </help>
+    <expand macro="citations"/>
+</tool>
+

tools/merqury/test-data/output_merqury.assembly_01.only.tabular

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