--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/heatmap.xml	Tue Aug 28 10:37:03 2018 -0400
@@ -0,0 +1,79 @@
+<tool id="heatmap" name="heatmap visualization from uto table (heatmaply)" version="0.1.0">
+    <requirements>
+        <requirement type="package" version="4.7.1">r-plotly</requirement>
+        <requirement type="package" version="0.14.1">r-heatmaply</requirement>
+        <requirement type="package" version="2.1.1">phantomjs</requirement>
+        <requirement type="package" version="2.2.1">pandoc</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        Rscript $__tool_directory__/heatmap_viz.R --input='$file' --output="$file.name"  --type='$output_type' --cols='$cols' 
+            --row_names=$rownames --header='$header' --col_text_angle='$angle_col'
+    ]]></command>
+    <inputs>
+        <param name="file" type="data" format="txt,tabular" label="Select a file (uto table)" help="" />
+        <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your input file contain header?" />
+        <param name="cols" type="text" value="" label="Enter columns to use from the first to the last separated by ':'" help='example : 3:8'/>
+        <param name="rownames" type="integer" value="1" label="Enter the column to use for row labels" help="for example : 1"/>
+        <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" />
+        <param name="output_type" type="select" label="Choose the output format">
+            <option value="html">html</option>
+            <option value="pdf">pdf</option>
+            <option value="jpeg">jpeg</option>
+            <option value="png">png</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output" format="html">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.html" ext="html" visible="true" assign_primary_output="true"/>
+                <filter>output_type=="html"</filter>
+        </data>
+        <data name="pdf" format="pdf">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.pdf" ext="pdf" visible="true" assign_primary_output="true"/>
+                <filter>output_type=="pdf"</filter>
+        </data>
+        <data name="jpeg" format="jpg">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.jpg" ext="jpg" visible="true" assign_primary_output="true"/>
+                <filter>output_type=="jpeg"</filter>
+        </data>
+        <data name="png" format="png">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.png" ext="png" visible="true" assign_primary_output="true"/>
+                <filter>output_type=="png"</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <output name="output" file="heatmap.html"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        Pathview R script
+        Arguments:
+        --help                  Print this test
+        --input                 path of the input  file (must contains a colum of uniprot and/or geneID accession number)
+        --output                Output name of file, could be .png, .jpeg, .pdf or .html
+        --cols                  Columns to use for heatmap, exemple : '3:8' to use columns from the third to the 8th
+        --row_names             Column which contains row names
+        --header                True or False
+        --col_text_angle        Angle of columns label ; from -90 to 90 degres
+
+        Example:
+        ./heatmap_viz.R --input='dat.nucl.norm.imputed.tsv' --output='heatmap.html' --cols='3:8' --row_names='2' --header=TRUE --col_text_angle=0 
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{renameTODO,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {TODO},
+  url = {https://plot.ly/r/},
+}</citation>
+        <citation type="bibtex">
+@misc{renameTODO,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {TODO},
+  url = {https://cran.r-project.org/package=heatmaply},
+}</citation>
+    </citations>
+</tool>
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