Mercurial > repos > vijay > pancancer_targene_pharmacology
diff targene_pharmacology.xml @ 0:aa5e0e353148 draft default tip
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
| author | vijay |
|---|---|
| date | Wed, 16 Dec 2020 23:32:07 +0000 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/targene_pharmacology.xml Wed Dec 16 23:32:07 2020 +0000 @@ -0,0 +1,71 @@ +<tool id="pancancer_targene_pharmacology" name="PAPAA: PanCancer targene pharmacology" version="@VERSION@"> + <description>ccle pharmocology predictions </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <version_command><![CDATA['papaa_targene_pharmacology.R' --version 2>&1 | grep PAPAA]]></version_command> + <command><![CDATA[ + mkdir 'classifier' && + mkdir -p 'classifier/figures' && + mkdir -p 'classifier/figures/cell_line' && + mkdir -p 'classifier/tables' && + ln -s '${gdsc1_targene_pharmacology_predictions}' 'classifier/tables/gdsc1_targene_pharmacology_predictions.tsv' && + ln -s '${gdsc2_targene_pharmacology_predictions}' 'classifier/tables/gdsc2_targene_pharmacology_predictions.tsv' && + ln -s '${gdsc1_ccle_targene_pharmacology_predictions}' 'classifier/tables/gdsc1_ccle_targene_pharmacology_predictions.tsv' && + ln -s '${gdsc2_ccle_targene_pharmacology_predictions}' 'classifier/tables/gdsc2_ccle_targene_pharmacology_predictions.tsv' && + papaa_targene_pharmacology.R + --classifier_results 'classifier' + #if $compound and str($compound): + --compound '$compound' + #end if + > '${log}' + ]]> + </command> + <inputs> + <param label="gdsc1 targene pharmacology predictions" name="gdsc1_targene_pharmacology_predictions" optional="false" type="data" format="tabular" help="gdsc1_targene_pharmacology_predictions.tsv"/> + <param label="gdsc2 targene pharmacology predictions" name="gdsc2_targene_pharmacology_predictions" optional="false" type="data" format="tabular" help="gdsc2_targene_pharmacology_predictions.tsv"/> + <param label="gdsc1 ccle targene pharmacology predictions" name="gdsc1_ccle_targene_pharmacology_predictions" optional="false" type="data" format="tabular" help="gdsc1_ccle_targene_pharmacology_predictions.tsv"/> + <param label="gdsc2 ccle targene pharmacology predictions" name="gdsc2_ccle_targene_pharmacology_predictions" optional="false" type="data" format="tabular" help="gdsc2_ccle_targene_pharmacology_predictions.tsv"/> + <param argument="--compound" label="Filename list of compounds" name="compound" optional="false" type="data" format="txt" help="data/compounds_of_interest.txt"/> + </inputs> + <outputs> + <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/> + <data format="pdf" name="GDSC1_targene_all_drug_response" label="${tool.name} on ${on_string} (GDSC1_targene_all_drug_response.pdf)" from_work_dir="classifier/figures/cell_line/GDSC1_targene_all_drug_response.pdf"/> + <data format="pdf" name="GDSC2_targene_all_drug_response" label="${tool.name} on ${on_string} (GDSC2_targene_all_drug_response.pdf)" from_work_dir="classifier/figures/cell_line/GDSC2_targene_all_drug_response.pdf"/> + <data format="pdf" name="GDSC1_ccle_targene_all_drug_response" label="${tool.name} on ${on_string} (GDSC1_ccle_targene_all_drug_response.pdf)" from_work_dir="classifier/figures/cell_line/GDSC1_ccle_targene_all_drug_response.pdf"/> + <data format="pdf" name="GDSC2_ccle_targene_all_drug_response" label="${tool.name} on ${on_string} (GDSC2_ccle_targene_all_drug_response.pdf)" from_work_dir="classifier/figures/cell_line/GDSC2_ccle_targene_all_drug_response.pdf"/> + </outputs> + <tests> + <test> + <param name="compound" value="compounds_of_interest.txt" ftype="txt"/> + <param name="gdsc1_targene_pharmacology_predictions" value="gdsc1_targene_pharmacology_predictions.tsv" ftype="tabular"/> + <param name="gdsc2_targene_pharmacology_predictions" value="gdsc2_targene_pharmacology_predictions.tsv" ftype="tabular"/> + <param name="gdsc1_ccle_targene_pharmacology_predictions" value="gdsc1_ccle_targene_pharmacology_predictions.tsv" ftype="tabular"/> + <param name="gdsc2_ccle_targene_pharmacology_predictions" value="gdsc2_ccle_targene_pharmacology_predictions.tsv" ftype="tabular"/> + <output name="log" file="targene_pharmacology_Log.txt"/> + <output name="GDSC1_targene_all_drug_response" file="GDSC1_targene_all_drug_response.pdf" compare="sim_size" delta="50"/> + <output name="GDSC2_targene_all_drug_response" file="GDSC2_targene_all_drug_response.pdf" compare="sim_size" delta="50"/> + <output name="GDSC1_ccle_targene_all_drug_response" file="GDSC1_ccle_targene_all_drug_response.pdf" compare="sim_size" delta="50"/> + <output name="GDSC2_ccle_targene_all_drug_response" file="GDSC2_ccle_targene_all_drug_response.pdf" compare="sim_size" delta="50"/> + </test> + </tests> + <help><![CDATA[ + **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/viz/papaa_targene_pharmacology.R:** + + **Inputs:** + --classifier_results String of the location of classifier results folder + --compound Filename of list of GDSC pharmacological compounds for evaluation + + **Outputs:** + Scatter plots with visualizing drug response compared to GDSC targene classifier scores for GDSC1 pharmacological dataset (GDSC1_targene_all_drug_response.pdf) + + Scatter plots with visualizing drug response compared to CCLE targene classifier scores for GDSC1 pharmacological dataset (GDSC1_ccle_targene_all_drug_response.pdf) + + Scatter plots with visualizing drug response compared to GDSC targene classifier scores for GDSC2 pharmacological dataset (GDSC2_targene_all_drug_response.pdf) + + Scatter plots with visualizing drug response compared to CCLE targene classifier scores for GDSC2 pharmacological dataset (GDSC2_ccle_targene_all_drug_response.pdf) ]]> + </help> + <expand macro="citations" /> +</tool>