Mercurial > repos > vijay > pancancer_visualize_decisions
view visualize_decisions.xml @ 0:f6dd27775d28 draft default tip
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author | vijay |
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date | Wed, 16 Dec 2020 23:30:56 +0000 |
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<tool id="pancancer_visualize_decisions" name="PAPAA: PanCancer visualize decisions" version="@VERSION@"> <description>visualize decisions</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <version_command><![CDATA['papaa_visualize_decisions.py' --version]]></version_command> <command><![CDATA[ mkdir 'classifier' && ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' && papaa_visualize_decisions.py --classifier_decisions 'classifier' #if str($custom): --custom '$custom' #end if > '${log}' ]]> </command> <inputs> <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/> <param area="false" argument="--custom" label="comma separated list of columns to plot" name="custom" optional="true" type="text"/> </inputs> <outputs> <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/> <collection name="classifier_decisions_figures" type="list" label="Disease classifier decisions figures"> <discover_datasets pattern="decision_plot_(?P<identifier_0>.+)\.pdf" format="pdf" directory="classifier/figures" visible="false" /> </collection> <data format="pdf" name="total_decisions" label="${tool.name} on ${on_string} (total_decisions.pdf)" from_work_dir="classifier/figures/total_decisions.pdf"/> <data format="pdf" name="hyper_mutated" label="${tool.name} on ${on_string} (hyper_mutated.pdf)" from_work_dir="classifier/figures/hyper_mutated.pdf" /> <collection name="custom_classifier_decisions_figures" type="list" label="custom classifier decisions figures"> <filter>custom != ""</filter> <discover_datasets pattern="(?P<identifier_0>.+)_decision_plot\.pdf" format="pdf" directory="classifier" visible="false" /> </collection> </outputs> <tests> <test> <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/> <output_collection name="classifier_decisions_figures" type="list"> <element name="OV" file="OV.pdf" compare="sim_size" delta="50"/> <element name="LUAD" file="LUAD.pdf" compare="sim_size" delta="50"/> <element name="GBM" file="GBM.pdf" compare="sim_size" delta="50"/> </output_collection> <output name="log" file="visualize_decisions_Log.txt"/> <output name="total_decisions" file="total_decisions.pdf" compare="sim_size" delta="30"/> <output name="hyper_mutated" file="hyper_mutated.pdf" compare="sim_size" delta="30"/> </test> </tests> <help><![CDATA[ **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_visualize_decisions.py:** **Inputs:** --classifier_decisions String of the folder location of classifier_decisions.tsv --custom comma separated list of columns to plot (optional: True) **Outputs:** Visualize decision function for all samples ("total_decisions.pdf") Plot disease type specific decision functions ("decision_plot_{}.pdf") Visualize decision function for hyper mutated tumors ("hyper_mutated.pdf") ]]> </help> <expand macro="citations" /> </tool>