Mercurial > repos > galaxyp > metaquantome
diff metaquantome_viz.xml @ 4:80ce9ca55697 draft
planemo upload commit d27827cf38d30b9c98923f73bc9cae4ffe41361b
| author | galaxyp |
|---|---|
| date | Fri, 07 Dec 2018 13:43:06 -0500 |
| parents | 28180bbb8fe4 |
| children |
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--- a/metaquantome_viz.xml Thu Dec 06 08:50:19 2018 -0500 +++ b/metaquantome_viz.xml Fri Dec 07 13:43:06 2018 -0500 @@ -1,10 +1,10 @@ -<tool id="metaquantome_viz" name="MetaQuantome Visualization Plots" version="@VERSION@.0"> - <description>of taxonomic analysis, functional analysis, and function-taxonomy</description> +<tool id="metaquantome_viz" name="metaQuantome: visualize" version="@VERSION@.0"> + <description>taxonomic analysis, functional analysis, and function-taxonomy analysis results</description> <macros> <import>macros.xml</import> <xml name="img_size"> - <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/> - <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/> + <param argument="--width" type="float" value="" optional="true" label="Image width in inches"/> + <param argument="--height" type="float" value="" optional="true" label="Image height in inches"/> </xml> <xml name="common_bar_params"> <param argument="--target_rank" type="text" value="species" label="Taxonomic rank to restrict to in the plot" @@ -25,9 +25,9 @@ <param argument="--barcol" type="integer" value="1" min="1" max="6" label="Color for the bar fill"> <help> The color vector in R is - c("dodgerblue", "darkorange", "yellow2", "red2", "darkviolet", "black"), - so providing a 1 will give the "dodgerblue" color. - These same colors are also used in the heatmap and PCA plot, + c("dodgerblue", "darkorange", "yellow2", "red2", "darkviolet", "black"), + so providing a 1 will give the "dodgerblue" color. + These same colors are also used in the heatmap and PCA plot, so the colors can be tweaked to match. </help> </param> @@ -52,7 +52,6 @@ #end if --barcol=$plot.barcol #elif $plot.plottype == 'volcano': - --meancol='$plot.meancol' --fc_name='$plot.fc_name' #if $plot.textannot: --textannot='$plot.textannot' @@ -91,7 +90,30 @@ #if $plot.height: --height=$plot.height #end if - --img='outfile.png' + --img='outfile.png' && + mkdir '${ wrapped_outfile.files_path }' && + cp outfile.png '${ wrapped_outfile.files_path }' && + ## stylesheet + echo "img { + display: block; + margin-left: auto; + margin-right: auto; + max-width: 75%; + height: auto; + }" > style.css && + cp style.css '${ wrapped_outfile.files_path }' && + echo "<!DOCTYPE html> + <html> + <head> + <link rel=\"stylesheet\" type=\"text/css\" href=\"style.css\"/> + </head> + <body> + <img src=\"outfile.png\"> + <br> + <p>To download the image, right-click and choose \"Save image as...\"</p> + </body> + </html>" > wrapped_outfile.html && + cat wrapped_outfile.html ]]></command> <inputs> <expand macro="common_params"/> @@ -110,29 +132,25 @@ <expand macro="img_size"/> </when> <when value="volcano"> - <param argument="--meancol" type="text" label="Mean intensity column name" - help="Mean intensity column name for desired experimental condition"> - <validator type="empty_field"/> - </param> <param argument="--fc_name" type="text" label="Name of the fold change column in the stat dataframe"> <validator type="empty_field"/> </param> - <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" + <param argument="--textannot" type="text" optional="true" label="Name of the annotation column" help="Provides text annoatation for the plot. Optional, if missing, no text will be plotted."/> - <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false" + <param argument="--flip_fc" type="boolean" truevalue="--flip_fc" falsevalue="" checked="false" label="Flip the fold change (i.e., multiply log fold change by -1)"/> - <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" - label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction"/> + <param argument="--gosplit" type="boolean" truevalue="--gosplit" falsevalue="" checked="false" + label="Make one plot for each of BiologicalProcess, CellularComponent, and MolecularFunction GO term categories."/> <expand macro="img_size"/> </when> <when value="heatmap"> - <param argument="--filter_to_sig" type="boolean" truevalue="--filter_to_sig" falsevalue="" checked="false" + <param argument="--filter_to_sig" type="boolean" truevalue="--filter_to_sig" falsevalue="" checked="false" label="Only plot significant term" help="Necessitates use of results from `test`"/> <param argument="--alpha" type="float" value="0.05" min="0.0" max="1.0" label="If filter_to_sig, the q-value significance level"/> <expand macro="img_size"/> </when> <when value="pca"> - <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" + <param argument="--calculate_sep" type="boolean" truevalue="--calculate_sep" falsevalue="" checked="false" label="Calculate separation between groups and include in title"/> <expand macro="img_size"/> </when> @@ -157,11 +175,12 @@ <when value="name"> <param argument="--name" type="text" label="Taxonomic or functional term name"> <help> + Case-sensitive. Should be either a common taxonomic name ("Streptococcus") or functional term ("carbohydrate metabolic process"). </help> </param> </when> </conditional> - <param argument="--target_onto" type="select" optional="true" label="Restrict to GO category"> + <param argument="--target_onto" type="select" optional="false" label="GO category to restrict to"> <option value="bp">Biological Process</option> <option value="mf">Molecular Function</option> <option value="cc">Cellular Component</option> @@ -172,6 +191,7 @@ </inputs> <outputs> <data format="png" name="outfile" label="${tool.name} on ${on_string} ${plot.plottype}" from_work_dir="outfile.png"/> + <data format="html" name="wrapped_outfile" label="${tool.name} on ${on_string} ${plot.plottype}" from_work_dir="wrapped_outfile.html"/> </outputs> <tests> <test> @@ -190,7 +210,23 @@ </test> </tests> <help><![CDATA[ - TODO: Fill in help. +metaQuantome viz +=================== + +The *viz* module is the final step in the metaQuantome analysis workflow. +The available visualizations are: + +- bar plot +- volcano plot +- heatmap +- PCA plot + +Please consult the manuscript for full details on each of these plots. + +Questions, Comments, Problems, Kudos +-------------------------------------- + +Please file any issues at https://github.com/galaxyproteomics/tools-galaxyp/issues. ]]></help> <expand macro="citations" /> </tool>