Mercurial > repos > vijay > pancancer_alternative_genes_pathwaymapper
diff alternative_genes_pathwaymapper.xml @ 0:c594c4333b76 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 23:31:32 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alternative_genes_pathwaymapper.xml Wed Dec 16 23:31:32 2020 +0000 @@ -0,0 +1,81 @@ +<tool id="pancancer_alternative_genes_pathwaymapper" name="PAPAA: PanCancer alternative genes pathwaymapper" version="@VERSION@"> + <description>alternative genes pathwaymapper</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="stdio"/> + <version_command><![CDATA['papaa_alternative_genes_pathwaymapper.py' --version]]></version_command> + <command><![CDATA[ + mkdir 'classifier' && + ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' && + papaa_alternative_genes_pathwaymapper.py + --classifier_decisions 'classifier' + #if $genes and str($genes): + --genes '$genes' + #end if + #if $path_genes and str($path_genes): + --path_genes '$path_genes' + #end if + #if $filename_mut and $filename_mut is not None: + --filename_mut '$filename_mut' + #end if + #if $filename_sample and $filename_sample is not None: + --filename_sample '$filename_sample' + #end if + @INPUTS_COPY_NUMBER_FILE_CONDITIONAL@ + > '${log}' + ]]> + </command> + <inputs> + <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/> + <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/> + <param argument="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/> + <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv"/> + <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/> + <expand macro="inputs_copy_number_file_conditional" /> + </inputs> + <outputs> + <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/> + <data format="txt" name="pathway_metrics_pathwaymapper" label="${tool.name} on ${on_string} (pathway_metrics_pathwaymapper.txt)" from_work_dir="classifier/tables/pathway_metrics_pathwaymapper.txt"/> + <data format="tabular" name="all_gene_metric_ranks" label="${tool.name} on ${on_string} (all_gene_metric_ranks.tsv)" from_work_dir="classifier/tables/all_gene_metric_ranks.tsv"/> + </outputs> + <tests> + <test> + <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/> + <param name="genes" value="ERBB2,PIK3CA,KRAS,AKT1"/> + <param name="path_genes" value="path_genes.txt" ftype="txt"/> + <param name="filename_mut" value="pancan_mutation_freeze_t1p.tsv.gz" ftype="tabular"/> + <param name="filename_sample" value="sample_freeze.tsv" ftype="tabular"/> + <param name="copy_number" value="yes"/> + <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular"/> + <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular"/> + <param name="filename_raw_mut" value="mc3.v0.2.8.PUBLIC_t1p.maf.gz" ftype="tabular"/> + <output name="log" file="alternative_genes_pathwaymapper_Log.txt"/> + <output name="pathway_metrics_pathwaymapper" file="pathway_metrics_pathwaymapper.txt" /> + <output name="all_gene_metric_ranks" file="all_gene_metric_ranks.tsv" /> + </test> + </tests> + <help><![CDATA[ + + **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_alternative_genes_pathwaymapper.py:** + + **Inputs:** + --gene Comma separated string of HUGO symbols for target genes or targenes_list.csv file + --path_genes Comma separated string of HUGO symbols for all genes in the target pathway or path_genes.txt file + --classifier_decisions String of the location of classifier decisions with predictions or scores + --filename_mut Filename of sample/gene mutations to use in model + --filename_mut_burden Filename of sample mutation burden to use in model + --filename_sample Filename of patient/samples to use in model + --filename_copy_loss Filename of copy number loss + --filename_copy_gain Filename of copy number gain + + **Outputs:** + Calculate and display metrics for targene classification + + Calculate and display pathway metrics ("pathway_metrics_pathwaymapper.txt") + + Visualize Distribution of AUROC and AUPRC for all genes and Get Metrics for All Genes ("all_gene_metric_ranks.tsv) ]]> + </help> + <expand macro="citations" /> +</tool>