Add wordcloud

tools/wordcloud/.shed.yml

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+name: wordcloud
+owner: bgruening
+description: A little word cloud generator in Python.
+long_description: |
+  The wordcloud library allows you to create word clouds from text data.
+  It is highly customizable and can generate word clouds in various shapes and colors.
+  The wordcloud library is available as an open-source project on GitHub.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud
+homepage_url: https://github.com/amueller/word_cloud
+type:
+categories:
+  - Visualization

tools/wordcloud/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">1.9.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">23.0</token>
+    <xml name="requirements">
+        <requirement type="package" version="1.9.4">wordcloud</requirement>
+        <requirement type="package" version="2.7.0">codecov</requirement>
+        <requirement type="package" version="7.3.2">coverage</requirement>
+        <requirement type="package" version="3.8.0">flake8</requirement>
+        <requirement type="package" version="7.4.3">pytest</requirement>
+        <requirement type="package" version="4.1.0">pytest-cov</requirement>
+        <requirement type="package" version="0.9.7">pytest-sugar</requirement>
+        <requirement type="package" version="28.0.0">setuptools</requirement>
+        <requirement type="package" version="4.0.2">twine</requirement>
+        <requirement type="package" version="0.38.1">wheel</requirement>
+        <requirement type="package" version="1.5.1">numpydoc</requirement>
+        <requirement type="package" version="2.31.1">imageio</requirement>
+        <requirement type="package" version="7.2.3">sphinx</requirement>
+        <requirement type="package" version="1.2.2">sphinx_rtd_theme</requirement>
+        <requirement type="package" version="0.8.2">sphinx_gallery</requirement>
+        <requirement type="package" version="0.4.0">sphinx-argparse</requirement>
+        <requirement type="package" version="3.0.1">sphinx-issues</requirement>
+        <requirement type="package" version="3.8.0">matplotlib</requirement>
+        <requirement type="package" version="6.0.4">multidict</requirement>
+        <requirement type="package" version="0.42.1">jieba</requirement>
+        <requirement type="package" version="1.11.3">scipy</requirement>
+        <requirement type="package" version="2.0.2">python-bidi</requirement>
+        <requirement type="package" version="3.0.0">arabic_reshaper</requirement>
+    </xml>
+</macros>

tools/wordcloud/test-data/regxp.txt

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+\w[\w']+

tools/wordcloud/test-data/stopwords.txt

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+is
+an
+for
+the
+open
+source
+platform

tools/wordcloud/test-data/test.txt

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+Galaxy is an open source, web-based platform for data intensive biomedical research. Galaxy contains more than 800 different single analysis tools and ready-to-use pipelines for different applications.

tools/wordcloud/wordcloud.xml

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+<tool id="wordcloud" name="wordcloud" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT">
+    <description>A little word cloud generator in Python.</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <requirements>
+        <expand macro="requirements"/>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir -p 'output' &&
+        wordcloud_cli --text $text 
+            #if str($regexp) != '':
+                --regexp $regexp 
+            #end if
+            #if str($stopwords) != '':
+                --stopwords $stopwords 
+            #end if
+            #if str($fontfile) != '':
+                --fontfile $fontfile 
+            #end if
+            #if str($mask) != '':
+                --mask $mask 
+            #end if
+            #if str($colormask) != '':
+                --colormask $colormask 
+            #end if
+            --contour_width $contour_width 
+            --contour_color $contour_color 
+            --relative_scaling $relative_scaling 
+            --margin $margin 
+            --width $width 
+            --height $height 
+            --color $color 
+            --background $background 
+            #if $no_collocations:
+                --no_collocations 
+            #end if
+            #if $include_numbers:
+                --include_numbers 
+            #end if
+            #if str($min_word_length) != '':
+                --min_word_length $min_word_length 
+            #end if
+            #if str($prefer_horizontal) != '':
+                --prefer_horizontal $prefer_horizontal 
+            #end if
+            #if str($scale) != '':
+                --scale $scale 
+            #end if
+            #if str($colormap) != '':
+                --colormap $colormap 
+            #end if
+            #if str($mode) != '':
+                --mode $mode 
+            #end if
+            #if str($max_words) != '':
+                --max_words $max_words 
+            #end if
+            #if str($min_font_size) != '':
+                --min_font_size $min_font_size 
+            #end if
+            #if str($max_font_size) != '':
+                --max_font_size $max_font_size 
+            #end if
+            #if str($font_step) != '':
+                --font_step $font_step 
+            #end if
+            #if str($random_state) != '':
+                --random_state $random_state 
+            #end if
+            #if $no_normalize_plurals:
+                --no_normalize_plurals 
+            #end if
+            #if $repeat:
+                --repeat 
+            #end if
+            #if $version:
+                --version 
+            #end if
+    ]]></command>
+    <inputs>
+        <conditional name="input_source">
+            <param name="select_file" type="select" label="Input from txt file">
+                <option value="true" selected="true">Use txt</option>
+                <option value="false">Provide sequence as text-field</option>
+            </param>
+            <when value="true">
+                <param format="txt" name="txt_input" type="data" label=" Enter your text file (Txt file)"/>
+            </when>
+            <when value="false">
+                <param name="input_sequence" type="text" label="Type your text here" help="Enter your text here"/>
+            </when>
+        </conditional>
+        <param argument="--regexp" type="data" format="txt" optional="True" label="Regular expression to filter words" help="regular expression to filter words"/>
+        <param argument="--stopwords" type="data" format="txt" optional="True" label="Stopwords file" help="Specify file of stopwords (containing one word per line) to remove from the given text after parsing"/>
+        <param argument="--fontfile" type="data" format="ttf" label="Font file you wish to use " help=" The font file you want to use"/>
+        <param argument="--min_font_size" value="4" type="integer" label=" Smallest font size to use" optional="False"/>
+        <param argument="--max_font_size" type="integer" label="Maximum font size for the largest word" optional="False"/>
+        <param argument="--font_step" value="1" type="integer" label="Step size for the font" help="Font_step &gt; 1 might speed up computation but give a worse fit"/>
+        <param argument="--margin" value="2" type="integer" label="Spacing to leave around words"/>
+        <param argument="--color" type="color" label="Use given color as coloring for the image">
+            <validator type="regex" message="Please select a valid RGB color">[#][0-9A-Fa-f]{6}</validator>
+        </param>
+        <param argument="--background" type="color" label="Use given color as background color for the image" value="#000000">
+            <validator type="regex" message="Please select a valid RGB color">[#][0-9A-Fa-f]{6}</validator>
+        </param>
+        <param argument="--mask" type="data" format="png" optional="True" label="Mask to use for the image form"/>
+        <param argument="--colormask" type="data" format="png" optional="True" label="Color mask to use for image coloring"/>
+        <param argument="--contour_width" value="0" min="0" type="float" label="Contour width" help="Use given color as mask contour color"/>
+        <param argument="--contour_color" type="color" label="Contour color" value="#000000">
+            <validator type="regex" message="Please select a valid RGB color">[#][0-9A-Fa-f]{6}</validator>
+        </param>
+        <param argument="--relative_scaling" value="0.0" min="0.0" max="1.0" type="float" label="Scaling of words by frequency (0 - 1)"/>
+        <param argument="--no_collocations" type="boolean" truevalue="True" falsevalue="False" value="True" label="Do not add collocations (bigrams) to word cloud"/>
+        <param argument="--include_numbers" type="boolean" truevalue="True" falsevalue="False" value="False" label="Whether to include numbers as phrases or not"/>
+        <param argument="--min_word_length" value="0" type="integer" label="Minimum number of letters a word must have to be included"/>
+        <param argument="--prefer_horizontal" value="0.9" type="float" label="Ratio of times to try horizontal fitting as opposed to vertical" min="0" max="1"/>
+        <param argument="--scale" value="1.0" type="float" label="Scaling between computation and drawing"/>
+        <param argument="--colormap" type="select" label="Matplotlib colormap name" value="viridis">
+            <option value="viridis">viridis</option>
+            <option value="plasma">plasma</option>
+            <option value="inferno">inferno</option>
+            <option value="magma">magma</option>
+            <option value="cividis">cividis</option>
+            <option value="Greys">Greys</option>
+            <option value="Purples">Purples</option>
+            <option value="Blues">Blues</option>
+            <option value="Greens">Greens</option>
+            <option value="Oranges">Oranges</option>
+            <option value="Reds">Reds</option>
+            <option value="YlOrBr">YlOrBr</option>
+            <option value="YlOrRd">YlOrRd</option>
+            <option value="OrRd">OrRd</option>
+            <option value="PuRd">PuRd</option>
+            <option value="RdPu">RdPu</option>
+            <option value="BuPu">BuPu</option>
+            <option value="GnBu">GnBu</option>
+            <option value="PuBu">PuBu</option>
+            <option value="YlGnBu">YlGnBu</option>
+            <option value="PuBuGn">PuBuGn</option>
+            <option value="BuGn">BuGn</option>
+            <option value="YlGn">YlGn</option>
+        </param>
+        <param argument="--mode" type="select" label="Use RGB or RGBA for transparent background" value="RGB">
+            <option value="RGB">RGB</option>
+            <option value="RGBA">RGBA</option>
+        </param>
+        <param argument="--max_words" value="200" type="integer" label="Maximum number of words"/>
+        <param argument="--width" value="400" type="integer" label="Define output image width"/>
+        <param argument="--height" type="integer" value="200" label="Define output image height"/>
+        <param argument="--random_state" type="integer" label="Random seed"/>
+        <param argument="--no_normalize_plurals" value="True" type="boolean" optional="True" label="Whether to remove trailing s from words"/>
+        <param argument="--repeat" type="boolean" truevalue="True" falsevalue="False" value="False" label="Whether to repeat words and phrases until max_words or min_font_size is reached"/>
+        <param argument="--version" type="boolean" truevalue="True" falsevalue="False" value="False" label="Show program's version number"/>
+    </inputs>
+    <outputs>
+        <data name="output_image" format="png" from_work_dir="output/wordcloud.png" label="${tool.name} on ${on_string}.png">
+            <filter>'png' in output_format</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="select_file" value="true"/>
+            <param name="txt_input" value="test.txt"/>
+            <param name="regexp" value="regxp.txt"/>
+            <param name="stopwords" value="stopwords.txt"/>
+            <param name="fontfile" value="font.ttf"/>
+            <param name="mask" value="mask.png"/>
+            <param name="colormask" value="colormask.png"/>
+            <param name="contour_width" value="1"/>
+            <param name="contour_color" value="#000000"/>
+            <param name="relative_scaling" value="1"/>
+            <param name="margin" value="1"/>
+            <param name="width" value="400"/>
+            <param name="height" value="400"/>
+            <param name="color" value="#898989"/>
+            <param name="background" value="#116787"/>
+            <param name="no_collocations" value="False"/>
+            <param name="include_numbers" value="True"/>
+            <param name="min_word_length" value="1"/>
+            <param name="prefer_horizontal" value="0.5"/>
+            <param name="scale" value="1"/>
+            <param name="colormap" value="viridis"/>
+            <param name="mode" value="RGB"/>
+            <param name="max_words" value="100"/>
+            <param name="min_font_size" value="1"/>
+            <param name="max_font_size" value="100"/>
+            <param name="font_step" value="1"/>
+            <param name="random_state" value="10"/>
+            <param name="no_normalize_plurals" value="False"/>
+            <param name="repeat" value="False"/>
+            <param name="version" value="True"/>
+            <output name="output_image" file="output/wordcloud.png"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+A little word cloud generator in Python.
+A word cloud is a visual representation (image) of word data. In other words, it is a collection, or cluster, of words depicted in different sizes. The bigger and bolder the word appears, the more often it's mentioned within a given text and the more important it is.
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+            @misc{amueller2018wordcloud,
+                title={Word Clouds with Python},
+                author={Amueller, Sebastian},
+                year={2018},
+                url={https://amueller.github.io/word_cloud/}
+            }
+        </citation>
+    </citations>
+</tool>