diff plot_barplot.xml @ 0:a8e03ffaaedc draft

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 74beefba9d138c892208b103b52e706ab4313a4a-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_barplot.xml	Mon Apr 18 10:35:54 2016 -0400
@@ -0,0 +1,121 @@
+<tool id="plot_barplot" name="Plot barplot" version="0.1.0">
+    <description>with R</description>
+
+    <requirements>
+        <requirement type="package" version="3.2.1">R</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+    </requirements>
+
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+    </stdio>
+
+    <version_command></version_command>
+
+    <command><![CDATA[
+        Rscript $__tool_directory__/plot_barplot.R
+            --input_file $input_file
+            --header $header
+
+            #if str($output_format)=="pdf"
+                --output_pdf_file $output_pdf_file
+            #else
+                --output_svg_file $output_svg_file
+            #end if
+
+
+            --data_column $column_with_data
+            --names_column $names_column
+            --xlab "$xlab"
+            --col $col
+            --bottom_margin $bottom_margin
+            --left_margin $left_margin
+            --top_margin $top_margin
+            --right_margin $right_margin
+    ]]></command>
+
+    <inputs>
+        <param name="input_file" type="data" format="tabular,tsv,csv" label="Input file" help="File in tabular format with tab-separated columns and header in first line (--input_file)"/>
+
+        <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="false" label="Header in first line?" help="(--header)"/>
+
+        <param name="output_format" label="Format for output image" type="select" help="">
+            <option value="pdf" selected="True">PDF</option>
+            <option value="svg">SVG</option>
+        </param>
+
+        <param name="column_with_data" type="data_column" data_ref="input_file" multiple="false" numerical="true" label="Column containing data?" help="(--data_column)" />
+
+        <param name="names_column" type="data_column" data_ref="input_file" multiple="false" numerical="false" label="Column containing data names?" help="(--names_column)" />
+
+        <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/>
+
+        <param name="col" label="Bar color" type="text" value= "blue" help="R color (--col)"/>
+
+        <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
+        <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/>
+        <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
+        <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
+    </inputs>
+
+    <outputs>
+        <data name="output_pdf_file" format="pdf"
+            label="${tool.name} on ${on_string}: PDF barplot">
+            <filter>output_format=="pdf"</filter>
+        </data>
+        <data name="output_png_file" format="png"
+            label="${tool.name} on ${on_string}: PNG barplot">
+            <filter>output_format=="png"</filter>
+        </data>
+        <data name="output_svg_file" format="svg"
+            label="${tool.name} on ${on_string}: SVG barplot">
+            <filter>output_format=="svg"</filter>
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_file" value="input_file.txt"/>
+            <param name="header" value="FALSE"/>
+            <param name="output_format" value="pdf"/>
+            <param name="column_with_data" value="2"/>
+            <param name="names_column" value="1"/>
+            <param name="xlab" value=""/>
+            <param name="col" value="blue"/>
+            <param name="bottom_margin" value="5"/>
+            <param name="left_margin" value="19"/>
+            <param name="top_margin" value="1"/>
+            <param name="right_margin" value="1"/>
+            <output name="output_pdf_file" file="output_test_col_2.pdf"/>
+        </test>
+        <test>
+            <param name="input_file" value="input_file.txt"/>
+            <param name="header" value="FALSE"/>
+            <param name="output_format" value="pdf"/>
+            <param name="column_with_data" value="3"/>
+            <param name="names_column" value="1"/>
+            <param name="xlab" value=""/>
+            <param name="col" value="red"/>
+            <param name="bottom_margin" value="5"/>
+            <param name="left_margin" value="19"/>
+            <param name="top_margin" value="1"/>
+            <param name="right_margin" value="1"/>
+            <output name="output_pdf_file" file="output_test_col_3.pdf"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool plot a barplot.
+
+.. image:: $PATH_TO_IMAGES/output.png
+   :scale: 50 %
+
+This tool relies on R's barplot function. The input file must be a tabular file with multiple columns: a column with row names (for bar names) and a least a column with data. The output image is customizable (margin, legend positions, ...) and can be export in different format. 
+    ]]></help>
+
+    <citations>
+    </citations>
+</tool>
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