diff plot_grouped_barplot.xml @ 0:6c9aac0d6ca2 draft default tip

planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_grouped_barplot commit c6ba903395dc6d41cb318c7d95a2d9cf3ca65313-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plot_grouped_barplot.xml	Mon Apr 18 10:08:25 2016 -0400
@@ -0,0 +1,145 @@
+<tool id="plot_grouped_barplot" name="Plot grouped 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_grouped_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
+
+            #set $column_with_data=""
+            #set $colors=""
+            #set $names=""
+            #set $sep=""
+            #for sample in $samples:
+                #set $column_with_data = $column_with_data + $sep + str($sample.column_id)
+                #set $colors = $colors + $sep + str($sample.color)
+                #set $names = $names + $sep +str($sample.name)
+                #set $sep=","
+            #end for
+            #set $column_with_data = $column_with_data
+            #set $colors = $colors
+            #set $names = $names
+
+            --data_column $column_with_data
+            --col "$colors"
+            --names "$names"
+            --replace_null $replace_null
+            --order $order
+            --names_column $names_column
+            --xlab "$xlab"
+            --log $log
+            --bottom_margin $bottom_margin
+            --left_margin $left_margin
+            --top_margin $top_margin
+            --right_margin $right_margin
+            --legend_pos $legend_pos
+    ]]></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>
+
+        <repeat name="samples" title="Add sample information (column id, name, color)" >
+            <param name="name" type="text" label="Name of the data" help="(--sample_name)"/>
+            <param name="column_id" type="data_column" data_ref="input_file" label="Column containing corresponding data" multiple="false" numerical="true" help="(after normalization, --charact_input_file)"/>
+            <param name="color" label="Bar color" type="text" value= "blue" help="R color (--col)"/>
+        </repeat>
+        <param name="replace_null" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Replace null values by NA?" help="(--replace_null)"/>
+        <param name="order" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Order given the first chosen data?" help="(--order)"/>
+
+        <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="log" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Log scale?" help="(--log)"/>
+
+        <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)"/>
+        <param name="legend_pos" label="Position of the legend" type="select" help="">
+            <option value="topright" selected="True">Top right</option>
+            <option value="topleft">Top left</option>
+            <option value="bottomright">Bottom right</option>
+            <option value="bottomleft">Bottom left</option>
+        </param>
+    </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="samples_0|name" value="A"/>
+            <param name="samples_0|column_id" value="2"/>
+            <param name="samples_0|color" value="blue"/>
+            <param name="samples_1|name" value="B"/>
+            <param name="samples_1|column_id" value="3"/>
+            <param name="samples_1|color" value="red"/>
+            <param name="replace_null" value="FALSE"/>
+            <param name="order" value="FALSE"/>
+            <param name="names_column" value="1"/>
+            <param name='xlab' value=""/>
+            <param name='log' value="FALSE"/>
+            <param name='bottom_margin' value="5"/>
+            <param name="left_margin" value="19"/>
+            <param name='top_margin' value="1"/>
+            <param name='right_margin' value="1"/>
+            <param name="legend_pos" value="topright"/>
+            <output name="output_pdf_file" file="output_file.pdf"/>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+**What it does**
+
+This tool plot a grouped barplot with multiple data:
+
+.. 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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