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annotate histogram2.xml @ 2:4d2c30376614 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram commit 5666c97386c843c109e45acce462243392285b84"
author devteam
date Mon, 27 Jul 2020 07:25:28 +0000
parents a629ef17ee46
children 7bd40c4d7df7
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4d2c30376614 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram commit 5666c97386c843c109e45acce462243392285b84"
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1 <tool id="histogram_rpy" name="Histogram" version="1.0.4">
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2 <description>of a numeric column</description>
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3 <requirements>
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4 <requirement type="package" version="3.3.2">rpy2</requirement>
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5 <requirement type="package" version="3.6.0">R</requirement>
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6 </requirements>
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7 <command>
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8 python '$__tool_directory__/histogram.py'
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9 '$input'
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10 '$out_file1'
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11 $numerical_column
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12 '$title'
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13 '$xlab'
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14 $breaks
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15 $density
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16 $frequency
4d2c30376614 "planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/histogram commit 5666c97386c843c109e45acce462243392285b84"
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17 </command>
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18 <inputs>
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19 <param name="input" type="data" format="tabular" label="Dataset" help="Dataset missing? See TIP below"/>
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20 <param name="numerical_column" type="data_column" data_ref="input" numerical="True" label="Numerical column for x axis" />
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21 <param name="breaks" type="integer" value="0" label="Number of breaks (bars)"/>
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22 <param name="title" type="text" value="Histogram" label="Plot title"/>
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23 <param name="xlab" type="text" value="V1" label="Label for x axis"/>
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24 <param name="density" type="boolean" checked="yes" label="Include smoothed density"/>
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25 <param name="frequency" type="boolean" checked="no" label="Plot as frequency (counts)"/>
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26 </inputs>
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27 <outputs>
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28 <data format="pdf" name="out_file1" />
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="input" value="histogram_in1.tabular" ftype="tabular"/>
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33 <param name="numerical_column" value="2"/>
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34 <param name="breaks" value="0"/>
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35 <param name="title" value="Histogram"/>
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36 <param name="xlab" value="V1"/>
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37 <param name="density" value="true"/>
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38 <param name="frequency" value="false"/>
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39 <output name="out_file1" file="histogram_out1.pdf" compare="sim_size"/>
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40 </test>
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41 </tests>
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42 <help>
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43
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44 .. class:: infomark
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45
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46 **TIP:** To remove comment lines that do not begin with a *#* character, use *Text Manipulation-&gt;Remove beginning*
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47
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48 .. class:: infomark
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49
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50 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
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51
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52 -----
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53
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54 **Syntax**
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55
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56 This tool computes a histogram of the numerical values in a column of a dataset.
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57
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58 - All invalid, blank and comment lines in the dataset are skipped. The number of skipped lines is displayed in the resulting history item.
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59 - **Column for x axis** - only numerical columns are possible.
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60 - **Number of breaks(bars)** - breakpoints between histogram cells. Value of '0' will determine breaks automatically.
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61 - **Plot title** - the histogram title.
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62 - **Label for x axis** - the label of the x axis for the histogram.
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63 - **Include smoothed density** - if checked, the resulting graph will join the given corresponding points with line segments.
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64
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65 -----
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66
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67 **Example**
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68
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69 - Input file::
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70
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71 1 68 4.1
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72 2 71 4.6
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73 3 62 3.8
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74 4 75 4.4
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75 5 58 3.2
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76 6 60 3.1
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77 7 67 3.8
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78 8 68 4.1
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79 9 71 4.3
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80 10 69 3.7
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81
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82 - Create a histogram on column 2 of the above dataset.
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83
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84 .. image:: histogram2.png
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85
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86 </help>
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87 </tool>