Mercurial > repos > bebatut > plot_barplot

annotate plot_barplot.xml @ 1:7c1274bf54c6 draft

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planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/plot_barplot commit 135cee4f1bce44ba7124906fa4fb20fbb582ef3b-dirty
author bebatut
date Wed, 02 Mar 2016 05:40:17 -0500
parents de039abf9641
children f8cec112f5f9
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1 <tool id="plot_barplot" name="Plot barplot" version="0.1.0">
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2 <description>with R</description>
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4 <requirements>
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5 <requirement type="package" version="3.2.1">R</requirement>
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6 <requirement type="package" version="1.20.0">getopt</requirement>
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7 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 </stdio>
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14 <version_command></version_command>
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16 <command><![CDATA[
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17 Rscript $__tool_directory__/plot_barplot.R
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18 --input_file $input_file
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20 #if str($output_format)=="pdf"
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21 --output_pdf_file $output_pdf_file
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22 #else
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23 --output_svg_file $output_svg_file
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24 #end if
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27 --data_column $column_with_data
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28 --names_column $names_column
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29 --xlab "$xlab"
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30 --col $col
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31 --bottom_margin $bottom_margin
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32 --left_margin $left_margin
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33 --top_margin $top_margin
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34 --right_margin $right_margin
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35 ]]></command>
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37 <inputs>
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38 <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)"/>
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40 <param name="output_format" label="Format for output image" type="select" help="">
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41 <option value="pdf" selected="True">PDF</option>
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42 <option value="svg">SVG</option>
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43 </param>
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45 <param name="column_with_data" type="data_column" data_ref="input_file" multiple="false" numerical="true" label="Column containing data?" help="(--data_column)" />
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47 <param name="names_column" type="data_column" data_ref="input_file" multiple="false" numerical="false" label="Column containing data names?" help="(--names_column)" />
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49 <param name="xlab" type="text" value="" label="Label for x axis" help="(--xlab)"/>
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51 <param name="col" label="Bar color" type="text" value= "blue" help="R color (--col)"/>
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53 <param name="bottom_margin" type="integer" value="5" label="Bottom margin" help="(--bottom_margin)"/>
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54 <param name="left_margin" type="integer" value="19" label="Left margin" help="(--left_margin)"/>
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55 <param name="top_margin" type="integer" value="1" label="Top margin" help="(--top_margin)"/>
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56 <param name="right_margin" type="integer" value="1" label="Right margin" help="(--right_margin)"/>
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57 </inputs>
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59 <outputs>
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60 <data name="output_pdf_file" format="pdf"
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61 label="${tool.name} on ${on_string}: PDF barplot">
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62 <filter>output_format=="pdf"</filter>
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63 </data>
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64 <data name="output_png_file" format="png"
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65 label="${tool.name} on ${on_string}: PNG barplot">
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66 <filter>output_format=="png"</filter>
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67 </data>
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68 <data name="output_svg_file" format="svg"
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69 label="${tool.name} on ${on_string}: SVG barplot">
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70 <filter>output_format=="svg"</filter>
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71 </data>
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72 </outputs>
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74 <tests>
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75 </tests>
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77 <help><![CDATA[
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78 **What it does**
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80 This tool plot a barplot from a tabular file into different format files given different customizable parameters.
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82 This tool relies on R's barplot function.
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83
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84 ]]></help>
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86 <citations>
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87 </citations>
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88 </tool>