diff metilene.xml @ 0:793c5c7e6fa4 draft

planemo upload commit f14004d917b2be0c2f8678f14f069b1fd4ffa1a9-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metilene.xml	Thu Dec 10 11:15:10 2015 -0500
@@ -0,0 +1,159 @@
+<?xml version="1.0" encoding="utf-8"?>
+<tool id="metilene" name="metilene" version="0.2-4.1">
+    <description>
+        calling differentially methylated regions from
+        bisulfite sequencing data
+    </description>
+    
+    <requirements>
+        <requirement type="package" version="5.18" >perl</requirement>
+        <requirement type="package" version="3.2.1" >R</requirement>
+        <requirement type="package" version="3.2.1" >R-ggplot2</requirement>
+        <requirement type="package" version="v2.24.0" >bedtools</requirement>
+        <requirement type="package" version="0.2-4" >metilene</requirement>
+    </requirements>
+    
+    <stdio>
+        <exit_code range=":-1"/>
+        <exit_code range="1:" />
+    </stdio>
+
+    <version_command>echo "0.2-4"</version_command>
+
+    <command><![CDATA[
+    ## =============== preprocessing
+    ##   generate metilene_g1_g2.input from multiple bedgraph files
+    metilene_input.pl 
+    --in1 $opt_in1
+    ##echo ",".join(map(str,$opt_in1))
+    --in2 $opt_in2
+    ##echo ",".join(map(str,$opt_in2))
+    >/dev/null 2>/dev/null
+    ;
+    ## ===============  metilene main program
+    metilene 
+    -M $Options.opt_M -m $Options.opt_m -d $Options.opt_d -t 1 -f 1 -v $Options.opt_v
+    metilene_g1_g2.input
+    >$output_bedlike
+    2>$output_stderr
+    ;
+    ## =============== postprocessing
+    cut -f1-4 $output_bedlike > $output_bedgraph
+    ;
+    ## write to job directory ...
+    metilene_output.pl -q $output_bedlike -p 0.05 -o ./metilene >/dev/null 2>/dev/null
+    ;
+    ## ... and move to output files
+    mv metilene_qval.0.05.bedgraph $output_qval_bedgraph ;
+    mv metilene_qval.0.05.out $output_qval_out ;
+    mv metilene_qval.0.05.pdf $output_qval_pdf
+    ]]></command>
+    
+    <inputs>
+        <!-- input bedgraph files 1 -->
+        <param
+            name="opt_in1"
+            type="data" format="bed,bedgraph" multiple="true"
+            optional="false"
+            label="Input group 1"
+            help="set of sorted bedgraph input profiles of group 1" />
+        <!-- input bedgraph files 2 -->
+        <param
+            name="opt_in2"
+            type="data" format="bed,bedgraph" multiple="true"
+            optional="false"
+            label="Input group 2"
+            help="set of sorted bedgraph input profiles of group 2" />
+        
+        <!-- Advanced parameters (folded) -->
+        <section name="Options" title="Advanced Options" expanded="False">
+	    <param
+                name="opt_M" 
+                label="The allowed nt distance between two CpGs within a DMR"
+                type="integer"
+	        optional="false"
+                value="300"
+	        help="-M, --maxdist"/>
+
+            <param
+                name="opt_m" 
+                label="The minimum # of CpGs in a DMR"
+                type="integer"
+	        optional="false"
+                value="10"
+	        help="-m, --mincpgs"/>
+            
+            <param
+                name="opt_d" 
+                label="The minimum mean methylation difference for calling DMRs"
+                type="float"
+	        optional="false"
+                value="0.1"
+	        help="-d, --minMethDiff"/>
+
+            <param
+                name="opt_v" 
+                label="Stringency of the valley filter (0.0 - 1.0)"
+                type="float"
+	        optional="false"
+                value="0.7"
+	        help="-v, --valley">
+                <validator type="in_range" min="0.0" max="1.0" 
+                           message="Valley filter value must be in [0,1]." />
+            </param>    
+	</section>
+    </inputs>
+    
+    <outputs>
+        <!-- finally: for bed-like use format=tabular -->
+        <data format="tabular" name="output_bedlike" 
+              label="${tool.name} on ${on_string}" />
+        <data format="bedgraph" name="output_bedgraph" 
+              label="${tool.name} on ${on_string}" />
+        <data format="txt" name="output_stderr" 
+              label="${tool.name} stderr ouptut on ${on_string}" />
+        <data format="bedgraph" name="output_qval_bedgraph" 
+              label="${tool.name} qval&lt;0.05 bedgraph on ${on_string}" />
+        <data format="pdf" name="output_qval_pdf" 
+              label="${tool.name} qval&lt;0.05 plots on ${on_string}" />
+        <data format="bedgraph" name="output_qval_out" 
+              label="${tool.name} qval&lt;0.05 out on ${on_string}" />
+    </outputs>
+    
+    <tests>
+        <test>
+	    <param name="opt_in1" value="example_S1.bedgraph,example_S2.bedgraph,example_S3.bedgraph,example_S4.bedgraph" />
+            <param name="opt_in2" value="example_S5.bedgraph,example_S6.bedgraph,example_S7.bedgraph,example_S8.bedgraph" />
+	    <output name="output_bedlike" file="metilene.out" />
+        </test>
+    </tests>
+    
+    
+    <help><![CDATA[
+**Fast and sensitive calling of differentially methylated regions
+from bisulfite sequencing data**
+
+Detailed documentation of the stand-alone tool metilene is available at
+.. __: http://www.bioinf.uni-leipzig.de/Software/metilene/manual.pdf
+
+The software metilene is available for download at
+.. __: http://www.bioinf.uni-leipzig.de/Software/metilene/
+    ]]></help>
+
+    <citations>
+        <citation type="bibtex">@Article{Juhling_Kretzmer_Bernhart-metil_Fast_and-2015,
+  author =	 {Juhling, Frank and Kretzmer, Helene and Bernhart, Stephan 
+                  H. and Otto, Christian and Stadler, Peter F. and Hoffmann, 
+                  Steve},
+  title =	 {metilene: {Fast} and sensitive calling of differentially 
+                  methylated regions from bisulfite sequencing data},
+  page =         {[Epub ahead of print]},
+  journal =	 {Genome Res},
+  year =	 {2015},
+  pmid =	 {26631489},
+  doi = 	 {10.1101/gr.196394.115},
+  issn = 	 {1088-9051},
+  issn = 	 {1549-5469}}</citation>
+    </citations>
+    
+</tool>