Mercurial > repos > bgruening > wordcloud
changeset 0:54c2d8ebf0cf draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/wordcloud commit 6d08a14015698273ace1032aeefd2eb7bd404862
| author | bgruening |
|---|---|
| date | Fri, 13 Dec 2024 21:43:12 +0000 |
| parents | |
| children | |
| files | test-data/font.ttf test-data/mask.png test-data/output_1.png test-data/output_2.png test-data/stopwords.txt test-data/test.txt wordcloud.xml |
| diffstat | 7 files changed, 214 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/stopwords.txt Fri Dec 13 21:43:12 2024 +0000 @@ -0,0 +1,1 @@ +an
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.txt Fri Dec 13 21:43:12 2024 +0000 @@ -0,0 +1,1 @@ +Galaxy is an open source, web-based platform for data intensive biomedical research.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/wordcloud.xml Fri Dec 13 21:43:12 2024 +0000 @@ -0,0 +1,212 @@ +<tool id="wordcloud" name="Generate a word cloud" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description>with highly customizable appearance</description> + <macros> + <token name="@TOOL_VERSION@">1.9.4</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.0</token> + </macros> + <requirements> + <requirement type="package" version="1.9.4">wordcloud</requirement> + </requirements> + <version_command>wordcloud_cli --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + wordcloud_cli + --imagefile 'output.png' + --text $text + #if $stopwords + --stopwords $stopwords + #end if + #if $fontfile + --fontfile $fontfile + #end if + #if $min_font_size + --min_font_size $min_font_size + #end if + #if $max_font_size + --max_font_size $max_font_size + #end if + #if $font_step + --font_step $font_step + #end if + #if $min_word_length + --min_word_length $min_word_length + #end if + #if str($max_words): + --max_words $max_words + #end if + #if str($width): + --width $width + #end if + #if str($height): + --height $height + #end if + #if str($margin): + --margin $margin + #end if + #if $background + --background '$background' + #end if + #if $mask + --mask $mask + #end if + #if $color_choice == "color": + --color '$color' + #else if $color_choice == "colormask": + --colormask $colormask + #end if + #if $colormap + --colormap $colormap + #end if + #if $mode + --mode $mode + #end if + #if $contour_width + --contour_width $contour_width + #end if + #if $contour_color + --contour_color '$contour_color' + #end if + #if str($prefer_horizontal): + --prefer_horizontal $prefer_horizontal + #end if + #if str($scale): + --scale $scale + #end if + #if str($relative_scaling): + --relative_scaling $relative_scaling + #end if + $no_collocations + $include_numbers + $no_normalize_plurals + $repeat + #if $random_state + --random_state $random_state + #end if + ]]> + </command> + <inputs> + <param argument="--text" type="data" format="txt" label="Input file" help="Input file to process"/> + <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="binary" optional="true" label="Font file you wish to use " help="The font file you want to use"/> + <param argument="--min_font_size" type="integer" min="1" value="4" optional="true" label=" Smallest font size to use" /> + <param argument="--max_font_size" type="integer" min="1" optional="true" label="Maximum font size for the largest word" /> + <param argument="--font_step" type="integer" value="1" label="Step size for the font" help="Font_step > 1 might speed up computation but give a worse fit"/> + <param argument="--min_word_length" type="integer" value="0" optional ="True" label="Minimum number of letters a word must have to be included"/> + <param argument="--max_words" type="integer" min="1" value="200" optional="true" label="Maximum number of words"/> + <param argument="--width" type="integer" min="1" value="400" optional="true" label="Define output image width"/> + <param argument="--height" type="integer" min="1" value="200" optional="true" label="Define output image height"/> + <param argument="--margin" type="integer" value="2" label="Spacing to leave around words"/> + <param argument="--background" type="color" value="#000000" optional="true" label="Use given color as background color for the image"> + <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"/> + <conditional name="color_choice" label="Choose color option"> + <param name="color_option" type="select" label="Color option"> + <option value="color">Color</option> + <option value="colormask">Color Mask</option> + </param> + <when value="color"> + <param argument="--color" type="color" value="#00FF00" optional="true" 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> + </when> + <when value="colormask"> + <param argument="--colormask" type="data" format="png" optional="true" label="Color Mask" help="Upload a color mask image"/> + </when> + </conditional> + <param argument="--colormap" type="select" value="viridis" optional="true" label="Matplotlib colormap name"> + <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" value="RGB" optional="True" label="Use RGB or RGBA for transparent background"> + <option value="RGB">RGB</option> + <option value="RGBA">RGBA</option> + </param> + <param argument="--contour_width" type="float" min="0" value="0" optional="true" label="Contour width" help="Use given color as mask contour color"/> + <param argument="--contour_color" type="color" value="#000000" optional="true" label="Contour color"> + <validator type="regex" message="Please select a valid RGB color">[#][0-9A-Fa-f]{6}</validator> + </param> + <param argument="--prefer_horizontal" type="float" min="0" max="1" value="0.9" optional="true" label="Ratio of times to try horizontal fitting as opposed to vertical"/> + <param argument="--scale" type="float" value="1.0" optional="True" label="Scaling between computation and drawing"/> + <param argument="--relative_scaling" type="float" min="0.0" max="1.0" value="0.0" optional="true" label="Scaling of words by frequency (0 - 1)"/> + <param argument="--no_collocations" type="boolean" truevalue="--no_collocations" falsevalue="" value="True" label="Do not add collocations (bigrams) to word cloud"/> + <param argument="--include_numbers" type="boolean" truevalue="--include_numbers" falsevalue="" value="False" label="Whether to include numbers as phrases or not"/> + <param argument="--no_normalize_plurals" type="boolean" truevalue="--no_normalize_plurals" falsevalue="" label="Whether to remove trailing s from words"/> + <param argument="--repeat" type="boolean" truevalue="--repeat" falsevalue="" label="Whether to repeat words and phrases until max_words or min_font_size is reached"/> + <param argument="--random_state" type="integer" value="10" label="Random seed" /> + </inputs> + <outputs> + <data name="output" format="png" label="Word cloud image" from_work_dir="output.png"/> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="text" value="test.txt" ftype="txt"/> + <param name="random_state" value="10"/> + <output name="output" file="output_1.png" compare="image_diff" /> + </test> + <test expect_num_outputs="1"> + <param name="text" value="test.txt" ftype="txt"/> + <param name="stopwords" value="stopwords.txt"/> + <param name="fontfile" value="font.ttf"/> + <param name="min_font_size" value="4"/> + <param name="max_font_size" value="100"/> + <param name="font_step" value="1"/> + <param name="min_word_length" value="0"/> + <param name="max_words" value="200"/> + <param name="width" value="800"/> + <param name="height" value="600"/> + <param name="margin" value="0"/> + <param name="background" value="#FFFFFF"/> + <param name="mask" value="mask.png"/> + <param name="color" value="#1F4068"/> + <param name="colormap" value="viridis"/> + <param name="mode" value="RGB"/> + <param name="contour_width" value="8"/> + <param name="contour_color" value="#1F4068"/> + <param name="prefer_horizontal" value="0.9"/> + <param name="scale" value="1.0"/> + <param name="relative_scaling" value="0.0"/> + <param name="no_collocations" value="True"/> + <param name="include_numbers" value="False"/> + <param name="no_normalize_plurals" value="True"/> + <param name="repeat" value="True"/> + <param name="random_state" value="10"/> + <output name="output" file="output_2.png" compare="image_diff" /> + </test> + </tests> + <help><![CDATA[ +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>