Mercurial > repos > vijay > pancancer_compare_within_models
diff compare_within_models.xml @ 0:84ac2a86bde1 draft default tip
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
| author | vijay |
|---|---|
| date | Wed, 16 Dec 2020 23:29:26 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/compare_within_models.xml Wed Dec 16 23:29:26 2020 +0000 @@ -0,0 +1,120 @@ +<tool id="pancancer_compare_within_models" name="PAPAA: PanCancer compare within models" version="@VERSION@"> + <description>compare within models</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <version_command><![CDATA['papaa_compare_within_models.R' --version 2>&1 | grep PAPAA]]></version_command> + <command><![CDATA[ + mkdir 'classifier' && + mkdir -p 'classifier/figures' && + ln -s '${pancan_classifier_summary}' 'classifier/classifier_summary.txt' && + ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' && + #for $within_summary in $pancan_within_classifier_summary: + mkdir -p 'classifier/within_disease/${within_summary.element_identifier}' && + ln -s '${within_summary}' 'classifier/within_disease/${within_summary.element_identifier}/classifier_summary.txt' && + #end for + #for $within_coefficient in $pancan_within_classifier_coefficients: + mkdir -p 'classifier/within_disease/${within_coefficient.element_identifier}' && + ln -s '${within_coefficient}' 'classifier/within_disease/${within_coefficient.element_identifier}/classifier_coefficients.tsv' && + #end for + #if $include_alt.include_alt_select == 'true': + mkdir 'alt_classifier' && + ln -s '${include_alt.alt_pancan_classifier_summary}' 'alt_classifier/classifier_summary.txt' && + ln -s '${include_alt.alt_pancan_classifier_coefficients}' 'alt_classifier/classifier_coefficients.tsv' && + #for $within_summary in $include_alt.alt_pancan_within_classifier_summary: + mkdir -p 'alt_classifier/within_disease/${within_summary.element_identifier}' && + ln -s '${within_summary}' 'alt_classifier/within_disease/${within_summary.element_identifier}/classifier_summary.txt' && + #end for + #for $within_coefficient in $include_alt.alt_pancan_within_classifier_coefficients: + mkdir -p 'alt_classifier/within_disease/${within_coefficient.element_identifier}' && + ln -s '${within_coefficient}' 'alt_classifier/within_disease/${within_coefficient.element_identifier}/classifier_coefficients.tsv' && + #end for + #end if + ls -lahR && + papaa_compare_within_models.R + --pancan_model 'classifier' + #if $include_alt.include_alt_select == 'true': + --alt_model 'alt_classifier' + #end if + > '${log}' + ]]> + </command> + <inputs> + <param argument="--pancan_model" label="pancancer classifier summary" name="pancan_classifier_summary" optional="false" type="data" format="txt" help="classifer_summary.txt"/> + <param label="pancancer classifier coefficients" name="pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="classifier_coefficients.tsv"/> + <param label="pan_within classifier summary" name="pancan_within_classifier_summary" optional="false" type="data" format="txt" multiple="true" help="multiple classifer_summary.txt"/> + <param label="pan_within classifier coefficients" name="pancan_within_classifier_coefficients" optional="false" type="data" format="tabular" multiple="true" help="multiple classifier_coefficients.tsv"/> + <conditional name="include_alt"> + <param name="include_alt_select" type="select" label="Would you want to compare given model with alt gene model?" help="output of pancancer classifier and pancancer within disease for alt gene"> + <option value="false" selected="true">do not do alt gene</option> + <option value="true">do alt gene</option> + </param> + <when value="true"> + <param argument="--alt_model" label="pancancer classifier summary" name="alt_pancan_classifier_summary" optional="false" type="data" format="txt" help="alt classifer_summary.txt"/> + <param label="pancancer classifier coefficients" name="alt_pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="alt classifier_coefficients.tsv"/> + <param argument="pan_within classifier summary" label="alt_pancan_within_classifier_summary" name="alt_pancan_within_classifier_summary" optional="true" type="data" format="txt" multiple="true" help="multiple alt classifer_summary.txt"/> + <param label="alt_pancan_within classifier coefficients" name="alt_pancan_within_classifier_coefficients" optional="true" type="data" format="tabular" multiple="true" help="multiple alt classifier_coefficients.tsv"/> + </when> + <when value="false"> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)" /> + <data format="pdf" name="aupr_comparison" label="${tool.name} on ${on_string} (aupr_comparison.pdf)" from_work_dir="classifier/figures/aupr_comparison.pdf"/> + <data format="pdf" name="auroc_comparison" label="${tool.name} on ${on_string} (auroc_comparison.pdf)" from_work_dir="classifier/figures/auroc_comparison.pdf"/> + <data format="pdf" name="alt_gene_aupr_comparison" label="${tool.name} on ${on_string} (alt_gene_aupr_comparison.pdf)" from_work_dir="classifier/figures/alt_gene_aupr_comparison.pdf" > + <filter>include_alt['include_alt_select'] == 'true' </filter> + </data> + <data format="pdf" name="alt_gene_auroc_comparison" label="${tool.name} on ${on_string} (alt_gene_auroc_comparison.pdf)" from_work_dir="classifier/figures/alt_gene_auroc_comparison.pdf" > + <filter>include_alt['include_alt_select'] == 'true' </filter> + </data> + </outputs> + <tests> + <test> + <param name="pancan_classifier_summary" value="classifier_summary.txt" ftype="txt"/> + <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/> + <param name="pancan_within_classifier_summary" value="classifier_summary/GBM" > <!-- + <collection type="list"> + <element name="GBM" value="GBM_100.txt" ftype="txt"/> + </collection> --> + </param> + <param name="pancan_within_classifier_coefficients" value="classifier_coefficients/GBM"> <!-- + <collection type="list"> + <element name="GBM" value="GBM_99.tabular" ftype="tabular"/> + </collection> --> + </param> + <param name="include_alt_select" value="false"/> + <!-- + <conditional name="include_alt"> + <param name="include_alt_select" value="false"/> + <param name="alt_pancan_summary" value="alt_pancan_summary.txt" ftype="txt"/> + <param name="alt_pancan_classifier_coefficients" value="alt_pancan_classifier_coefficients.tsv" ftype="tabular"/> + <param name="alt_pan_within_classifier_summary" value="alt_pan_within_classifier_summary.txt" ftype="txt"/> + <param name="alt_pan_within_classifier_coefficients" value="alt_pan_within_classifier_coefficients.tsv" ftype="tabular"/> + </conditional> + --> + <output name="log" file="compare_within_models_Log.txt"/> + <output name="aupr_comparison" file="aupr_comparison.pdf" compare="sim_size" delta="50"/> + <output name="auroc_comparison" file="auroc_comparison.pdf" compare="sim_size" delta="50"/> + + </test> + </tests> + <help><![CDATA[ + + **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_compare_within_models.R:** + + **Inputs:** + --pancan_model String of the Directory: location of Pan classifier summary file + --alt_model String of the Directory: location of Alt gene classifier summary file + + **Outputs:** + Comparison plots for Pan and Pan_within models ("auroc_comparison.pdf" and "aupr_comparison.pdf") + + Comparison plots for altgene, alt_within, Pan_alt models ("alt_gene_auroc_comparison.pdf" and "alt_gene_aupr_comparison.pdf") ]]> + + </help> + <expand macro="citations" /> +</tool>