# HG changeset patch
# User charles
# Date 1479117205 18000
# Node ID b3f6f58f454cb212fc6eb2b110ac5e8dbb0359b6

Uploaded

diff -r 000000000000 -r b3f6f58f454c cytosine_report_to_bedgraph.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/cytosine_report_to_bedgraph.xml	Mon Nov 14 04:53:25 2016 -0500
@@ -0,0 +1,112 @@
+<tool id="cytosine_report_to_bedgraph" name="Cytosine Report To Bedgraphs" version="0.0.0">
+
+  <description>Converts genome-wide cytosine methylation report to Bedgraphs</description>
+
+  <requirements>
+  	<requirement type="package" version="2.3.32">igvtools</requirement>
+  </requirements>
+
+  <command interpreter="python">
+<![CDATA[
+        cytosine_report_to_bedgraph_wrapper.py
+
+        --tool_dir "$__tool_directory__"
+
+        --cytosine_report "$cytosine_report"
+
+        --coverage_bedgraph "$coverage_bedgraph"
+        #if $tdf['tdf_selector']:
+          --tdf
+          --igv_genome "${tdf.built_in_igv_genomes_chr_sizes.fields.path}"
+          --coverage_tdf "$coverage_tdf"
+        #end if
+
+        #if $context:
+          --context
+          --CpG_bedgraph "$CpG_bedgraph"
+          --CHG_bedgraph "$CHG_bedgraph"
+          --CHH_bedgraph "$CHH_bedgraph"
+          #if $tdf['tdf_selector']:
+            --CpG_tdf "$CpG_tdf"
+            --CHG_tdf "$CHG_tdf"
+            --CHH_tdf "$CHH_tdf"
+          #end if
+        #else
+          --CXX "$CXX_bedgraph"
+          #if $tdf['tdf_selector']:
+            --CXX "$CXX_tdf"
+          #end if
+        #end if  
+
+        --log "$log_report"
+]]>
+  </command>
+  <inputs>
+    <param name="cytosine_report" type="data" format="txt" label="Submit a genome-wide cytosine methylation report" optional="False" />
+    <param name="context" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Create a bedGraph for each cytosine methylation context?" />
+    <conditional name="tdf">
+      <param name="tdf_selector" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Generate a tdf file from each resulting bedGraph?" />
+      <when value="true">
+        <param name="built_in_igv_genomes_chr_sizes" type="select" label="Select Reference Genome (igv genomes chr.sizes)" help="If your genome of interest is not listed, contact your Galaxy admin">
+          <options from_data_table="igv_genomes_chr_sizes">
+            <filter type="sort_by" column="name"/>
+            <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+          </options>
+        </param>
+      </when>
+      <when value="false"></when>
+    </conditional>
+  </inputs>
+
+  <outputs>
+    <data name="log_report" format="txt" label="${tool.name} on ${on_string}: Log Report" />
+    <data name="CpG_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CpG context">
+      <filter>context is True</filter>
+    </data>
+    <data name="CHG_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CHG context">
+      <filter>context is True</filter>
+    </data>
+    <data name="CHH_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CHH context">
+      <filter>context is True</filter>
+    </data>
+    <data name="CXX_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: CXX">
+      <filter>context is False</filter>
+    </data>
+    <data name="coverage_bedgraph" format="bedgraph" label="${tool.name} on ${on_string}: Coverage" />
+    <data name="CpG_tdf" format="tdf" label="${tool.name} on ${on_string}: CpG context (tdf)">
+      <filter>tdf['tdf_selector'] is True and context is True</filter>
+    </data>
+    <data name="CHG_tdf" format="tdf" label="${tool.name} on ${on_string}: CHG context (tdf)">
+          <filter>tdf['tdf_selector'] is True and context is True</filter>
+    </data>
+    <data name="CHH_tdf" format="tdf" label="${tool.name} on ${on_string}: CHH context (tdf)">
+          <filter>tdf['tdf_selector'] is True and context is True</filter>
+    </data>
+    <data name="CXX_tdf" format="tdf" label="${tool.name} on ${on_string}: CXX (tdf)">
+          <filter>context is False and tdf['tdf_selector'] is True</filter>
+    </data>
+    <data name="coverage_tdf" format="tdf" label="${tool.name} on ${on_string}: Coverage (tdf)" >
+      <filter>tdf['tdf_selector'] is True</filter>
+    </data>
+  </outputs>
+
+  <tests></tests>
+
+  <help>
+<![CDATA[
+
+**What it does**
+
+  | This tool takes as input a genome-wide cytosine methylation report (generated by the tool *Bismark Meth. Extractor*) and converts it into a bedGraph for each cytosine context (CpG, CHG and CHH). 
+  | These bedGraphs display, for a given context, the ratio of methylation of each covered cytosine in the genome.
+  |
+  | It also produces a bedGraph displaying the coverage count of each cytosine in the genome (non-covered cytosine are ignored).
+  | 
+
+  .. class:: infomark
+
+  | The tool outputs offer the possibility to vizualise the methylation signal of covered cytosines thanks to softwares like IGV (*Integrative Genomics Viewer*).
+  | In this respect, the tool can optionally generate a tdf binary file (*Tiled Data Format*) from each converted bedGraph. Tdf format is indeed better handled by IGV than bedGraph.
+]]>
+  </help>
+</tool>
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