Mercurial > repos > proteore > proteore_heatmap_visualization
diff heatmap.xml @ 0:edbb84a94a36 draft
planemo upload commit bdd7e8a1f08c11db2a9f1b6db5535c6d32153b2b
| author | proteore |
|---|---|
| date | Tue, 18 Dec 2018 09:58:49 -0500 |
| parents | |
| children | b8a5139cf5b9 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/heatmap.xml Tue Dec 18 09:58:49 2018 -0500 @@ -0,0 +1,168 @@ +<tool id="heatmap" name="HeatMap" version="2018.12.12"> + <description></description> + <requirements> + <requirement type="package" version="4.7.1">r-plotly</requirement> + <requirement type="package" version="0.14.1">r-heatmaply</requirement> + <requirement type="package" version="2.1.1">phantomjs</requirement> + <requirement type="package" version="2.2.1">pandoc</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + Rscript $__tool_directory__/heatmap_viz.R + --input='$file' + --output="$file.name" + --type='$output_type' + --cols='$select_data_columns.cols' + --row_names=$rownames + --header='$header' + --col_text_angle='$angle_col' + --dist="$distance" + --clust="$clustering" + --dendrogram="$dendrogram" + + ]]></command> + <inputs> + <param name="file" type="data" format="txt,tabular" label="Select your file (table)" help="" /> + <param name="header" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Does your file contain a header?" /> + <conditional name="select_data_columns"> + <param name="enter_cols" type="select" label="Select columns or a range of columns containing expression values"> + <option value="cols_number">Select columns to be used one by one</option> + <option value="cols_range">Select a range of columns to be used</option> + </param> + <when value="cols_number"> + <param name="cols" type="text" label="Enter column number (separated by a comma)" help="For example : c3,c5,c7"/> + </when> + <when value="cols_range"> + <param name="cols" type="text" label="Enter a range of column number, first and last column separated by ':'" help="For example : c2:c7"/> + </when> + </conditional> + <param name="rownames" type="text" value="c1" label="Enter column number containing row labels" help="for example : c1 if labels are in column n°1"/> + <param type="integer" name="angle_col" label="Angle of column labels" value="0" min="-90" max="90" /> + <param name="clustering" type="select" label="Clustering method" value="average"> + <option value="ward.D">Ward</option> + <option value="ward.D2">Ward2</option> + <option value="single">Single linkage (nearest neighbor)</option> + <option value="complete">Complete linkage (farthest neighbor)</option> + <option value="average" selected="true">Group average linkage (UPGMA)</option> + <option value="mcquitty">Simple average method (WPGMA)</option> + <!--option value="median">Median (WPGMC)</option> + <option value="centroid">Centroid (UPGMC)</option--> + </param> + <param name="distance" type="select" label="Distance measurement method" value="euclidean"> + <option value="euclidean" selected="true">Euclidean</option> + <option value="pearson" selected="true">Pearson</option> + <option value="spearman">Spearman</option> + <option value="kendall">Kendall</option> + <option value="maximum">Maximum</option> + <option value="manhattan">Manhattan</option> + <option value="canberra">Canberra</option> + <option value="binary">Binary</option> + <option value="minkowski">Minkowski</option> + </param> + <param name="dendrogram" type="select" label="Apply clustering on :" value="both"> + <option value="row">Rows</option> + <option value="column">Columns</option> + <option value="both" selected="true">Rows and columns</option> + <option value="none">None</option> + </param> + + <param name="output_type" type="select" label="Select output format"> + <option value="html">html</option> + <option value="pdf">pdf</option> + <option value="jpeg">jpeg</option> + <option value="png">png</option> + </param> + + </inputs> + <outputs> + <data name="output" format="html"> + <discover_datasets pattern="(?P<designation>.+)\.html" ext="html" visible="true" assign_primary_output="true"/> + <filter>output_type=="html"</filter> + </data> + <data name="pdf" format="pdf"> + <discover_datasets pattern="(?P<designation>.+)\.pdf" ext="pdf" visible="true" assign_primary_output="true"/> + <filter>output_type=="pdf"</filter> + </data> + <data name="jpeg" format="jpg"> + <discover_datasets pattern="(?P<designation>.+)\.jpg" ext="jpg" visible="true" assign_primary_output="true"/> + <filter>output_type=="jpeg"</filter> + </data> + <data name="png" format="png"> + <discover_datasets pattern="(?P<designation>.+)\.png" ext="png" visible="true" assign_primary_output="true"/> + <filter>output_type=="png"</filter> + </data> + </outputs> + <tests> + <test> + <output name="output" file="heatmap.html"/> + </test> + </tests> + <help><![CDATA[ +**Description** + +This tool allows users to generate, cluster and visualize expression-based heat maps from transcriptomic, proteomic and metabolomic experiments. +It is based on heatmaply, an R package for easily creating interactive cluster heatmaps (see reference below) + +----- + +**Input** + +A file (tab-delimited) having a column with labels (e.g. a gene name, Uniprot accession number...) and colums with numerical value (intensities) for clustering. +See table below for an example input file + +.. csv-table:: example of input file + :header: "Uniprot","iBAQ_CTR1","iBAQ_CTR2","iBAQ_CTR3","iBAQ_pTCN1","iBAQ_pTCN2","iBAQ_pTCN3" + + + "Q49AN9",17.4091970440807,16.0474907255521,14.9687330755858,21.8454060245779,18.9468529040903,21.2330797498008 + "O00148",14.1001686145694,14.806777888004,15.3555560564928,17.2942797505583,18.2106568817514,16.9479095182613 + "F5H6E2",15.0235503328855,16.6142578028388,20.5969569088489,14.6615767253835,17.9752549753108,20.4023495267791 + "E9PPW7",18.0770953690935,15.312218369812,13.8048301075204,17.5522130063356,15.9664520099065,15.1597932646987 + "O00483",17.4188205774495,16.783665086968,15.1589556127476,19.7398973660168,20.8648965533665,20.1781898785682 + "O00571",12.9049717044645,16.717296441372,13.8708732177805,19.8879681981565,21.0815521014477,17.4710040202845 + +----- + +**Parameters** + +"Select columns or a range of columns containing expression values": choose the columns to use to perform clustering and to create the heatmap. +You can enter specific column number (e.g. c2,c5 will create a heatmap for column 2 and 5 corresponding to condition from the example file above ) or a range of columns to use (e.g. c2:c7 will consider all replicates of each condition in the example above)). + +"Enter column number containing row labels": enter the column number containing the rows labels (e.g. "c1" in the example above). + +"Angle of column labels": In case of long label name, you might want to incline the column labels for practical display. + +"Clustering method": methods for computing hierarchical clustering (six available) + +"Distance measurement method": function used to compute the distance (dissimilarity) between both rows and columns (nine available). The options "pearson", "spearman" and "kendall" can +be used to use correlation-based clustering. + +----- + +**Output** + +Default output is html; it allows browsing the heatmap in an interactive way (of note: for large file, display and interactivity can be altered) +pdf, jpeg or png format are propsoed for static output. + +----- + +.. class:: infomark + +**Authors** +Galili T, O'Callaghan A, Sidi J, Sievert C. heatmaply: an R package for creating interactive cluster heatmaps for online publishing. Bioinformatics. 2018. 34(9):1600-1602. doi: 10.1093/bioinformatics/btx657. PubMed PMID: 29069305 + +----- + +.. class:: infomark + +**Galaxy integration** + +David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR + +Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR + +This work has been partially funded through the French National Agency for Research (ANR) IFB project. + +Contact support@proteore.org for any questions or concerns about the Galaxy implementation of this tool. + + ]]></help> +</tool>