Mercurial > repos > vijay > pancancer_visualize_decisions

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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:30:56 +0000
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1 <tool id="pancancer_visualize_decisions" name="PAPAA: PanCancer visualize decisions" version="@VERSION@">
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2 <description>visualize decisions</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <version_command><![CDATA['papaa_visualize_decisions.py' --version]]></version_command>
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9 <command><![CDATA[
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10 mkdir 'classifier' &&
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11 ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' &&
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12 papaa_visualize_decisions.py
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13 --classifier_decisions 'classifier'
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14 #if str($custom):
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15 --custom '$custom'
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16 #end if
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17 > '${log}'
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18 ]]>
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19 </command>
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20 <inputs>
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21 <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>
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22 <param area="false" argument="--custom" label="comma separated list of columns to plot" name="custom" optional="true" type="text"/>
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23 </inputs>
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24 <outputs>
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25 <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
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26 <collection name="classifier_decisions_figures" type="list" label="Disease classifier decisions figures">
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27 <discover_datasets pattern="decision_plot_(?P&lt;identifier_0&gt;.+)\.pdf" format="pdf" directory="classifier/figures" visible="false" />
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28 </collection>
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29 <data format="pdf" name="total_decisions" label="${tool.name} on ${on_string} (total_decisions.pdf)" from_work_dir="classifier/figures/total_decisions.pdf"/>
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30 <data format="pdf" name="hyper_mutated" label="${tool.name} on ${on_string} (hyper_mutated.pdf)" from_work_dir="classifier/figures/hyper_mutated.pdf" />
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31 <collection name="custom_classifier_decisions_figures" type="list" label="custom classifier decisions figures">
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32 <filter>custom != ""</filter>
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33 <discover_datasets pattern="(?P&lt;identifier_0&gt;.+)_decision_plot\.pdf" format="pdf" directory="classifier" visible="false" />
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34 </collection>
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
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39 <output_collection name="classifier_decisions_figures" type="list">
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40 <element name="OV" file="OV.pdf" compare="sim_size" delta="50"/>
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41 <element name="LUAD" file="LUAD.pdf" compare="sim_size" delta="50"/>
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42 <element name="GBM" file="GBM.pdf" compare="sim_size" delta="50"/>
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43 </output_collection>
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44 <output name="log" file="visualize_decisions_Log.txt"/>
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45 <output name="total_decisions" file="total_decisions.pdf" compare="sim_size" delta="30"/>
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46 <output name="hyper_mutated" file="hyper_mutated.pdf" compare="sim_size" delta="30"/>
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47 </test>
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48 </tests>
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49 <help><![CDATA[
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50 **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_visualize_decisions.py:**
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51
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52 **Inputs:**
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53 --classifier_decisions String of the folder location of classifier_decisions.tsv
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54 --custom comma separated list of columns to plot (optional: True)
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55
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56 **Outputs:**
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57 Visualize decision function for all samples ("total_decisions.pdf")
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58
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59 Plot disease type specific decision functions ("decision_plot_{}.pdf")
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60
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61 Visualize decision function for hyper mutated tumors ("hyper_mutated.pdf") ]]>
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62 </help>
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63 <expand macro="citations" />
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64 </tool>