diff pancancer_classifier.xml @ 0:20b049f5b3f5 draft default tip

"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pancancer_classifier.xml	Wed Dec 16 23:32:43 2020 +0000
@@ -0,0 +1,207 @@
+<tool id="pancancer_classifier" name="PAPAA: PanCancer classifier" version="@VERSION@" python_template_version="3.6">
+    <description>classifier for pathway aberrant activity</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <version_command>
+        <![CDATA['papaa_pancancer_classifier.py' --version]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        papaa_pancancer_classifier.py
+        #if $folds and $folds is not None:
+        --folds '$folds'
+        #end if
+        #if $seed and $seed is not None:
+        --seed '$seed'
+        #end if
+        $drop
+        #if $filter_count and $filter_count is not None:
+        --filter_count '$filter_count'
+        #end if
+        #if $filter_prop and $filter_prop is not None:
+        --filter_prop '$filter_prop'
+        #end if
+        #if $num_features and $num_features is not None:
+        --num_features '$num_features'
+        #end if
+        @INPUTS_ALPHAS@
+        @INPUTS_L1_RATIOS@
+        #if $alt_genes and str($alt_genes) != '':
+        --alt_genes '$alt_genes'
+        #end if
+        #if $alt_diseases and str($alt_diseases) != '':
+        --alt_diseases '$alt_diseases'
+        #end if
+        #if $alt_filter_count and $alt_filter_count is not None:
+        --alt_filter_count '$alt_filter_count'
+        #end if
+        #if $alt_filter_prop and $alt_filter_prop is not None:
+        --alt_filter_prop '$alt_filter_prop'
+        #end if
+        --classifier_results 'classifier'
+        @INPUT_REMOVE_HYPER@
+        $keep_intermediate
+        @INPUTS_BASIC@
+        @INPUTS_GENES_DISEASES@
+        $drop
+        $shuffled
+        $shuffled_before_training
+        $no_mutation
+        #if str($drop_x_genes)
+        --drop_x_genes '$drop_x_genes'
+        #end if
+        $drop_expression
+        $drop_covariates
+        @INPUTS_COPY_NUMBER_CLASS_FILE_CONDITIONAL@
+        > '${log}'
+        ]]>
+    </command>
+    <inputs>
+        <expand macro="inputs_basic" />
+        <expand macro="inputs_genes_diseases" />
+        <param argument="--seed" label="option to set seed" name="seed" optional="true" type="integer" value="1234"/>
+        <param argument="--folds" label="Number of cross validation folds to perform" name="folds" optional="true" type="integer" value="5"/>
+        <param argument="--drop" checked="false" label="Decision to drop input genes from X matrix" name="drop" type="boolean" truevalue="--drop" falsevalue=""/>
+        <expand macro="inputs_copy_number_class_file_conditional" />
+        <param argument="--filter_count" label="Min number of mutations in diseases to include" name="filter_count" optional="true" type="integer" value="15"/>
+        <param argument="--filter_prop" label="Min proportion of positives to include disease" name="filter_prop" optional="true" type="float" value="0.05"/>
+        <param argument="--num_features" label="Number of MAD genes to include in classifier" name="num_features" optional="true" type="integer" value="8000"/>
+        <expand macro="input_alphas" />
+        <expand macro="input_l1_ratios" />
+        <param argument="--alt_genes" label="alternative genes to test performance" name="alt_genes" optional="true" type="text" />
+        <param argument="--alt_diseases" label="The alternative diseases to test performance" name="alt_diseases" optional="true" type="text" />
+        <param argument="--alt_filter_count" label="Min number of mutations in disease to include in alternate" name="alt_filter_count" optional="true" type="integer" value="15"/>
+        <param argument="--alt_filter_prop" label="Min proportion of positives to include disease in alternate" name="alt_filter_prop" optional="true" type="float" value="0.05"/>
+        <expand macro="input_remove_hyper" />
+        <param argument="--keep_intermediate" checked="false" label="Keep intermediate ROC values for plotting" name="keep_intermediate" type="boolean" truevalue="--keep_intermediate" falsevalue=""/>
+        <param argument="--shuffled" checked="false" label="Shuffle the input gene exprs matrix alongside" name="shuffled" type="boolean" truevalue="--shuffled" falsevalue=""/>
+        <param argument="--shuffled_before_training" checked="false" label="Shuffle the gene exprs matrix before training" name="shuffled_before_training" type="boolean" truevalue="--shuffled_before_training" falsevalue=""/>
+        <param argument="--no_mutation" checked="false" label="Remove mutation data from y matrix" name="no_mutation" type="boolean" truevalue="--no_mutation" falsevalue=""/>
+        <param argument="--drop_x_genes" label="Comma separated list of genes to be dropped from X matrix" name="drop_x_genes" optional="true" type="text" value=""/>
+        <param argument="--drop_expression" checked="false" label="Decision to drop gene expression values from X" name="drop_expression" type="boolean" truevalue="--drop_expression" falsevalue=""/>
+        <param argument="--drop_covariates" checked="false" label="Decision to drop covariate information from X" name="drop_covariates" type="boolean" truevalue="--drop_covariates" falsevalue=""/>
+    </inputs>
+    <outputs>
+        <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)" />
+        <data format="tabular" name="alt_gene_alt_disease_summary" label="${tool.name} on ${on_string} (alt_gene_alt_disease_summary.tsv)" from_work_dir="classifier/alt_gene_alt_disease_summary.tsv"/>
+        <data format="csv" name="alt_summary_counts" label="${tool.name} on ${on_string} (alt_summary_counts.csv" from_work_dir="classifier/alt_summary_counts.csv"/>
+        <data format="tabular" name="classifier_coefficients" label="${tool.name} on ${on_string} (classifier_coefficients.tsv)" from_work_dir="classifier/classifier_coefficients.tsv"/>
+        <data format="txt" name="classifier_summary" label="${tool.name} on ${on_string} (classifier_summary.txt)" from_work_dir="classifier/classifier_summary.txt"/>
+        <data format="tabular" name="pancan_roc_results" label="${tool.name} on ${on_string} (pancan_roc_results.tsv)" from_work_dir="classifier/pancan_roc_results.tsv"/>
+        <data format="csv" name="summary_counts" label="${tool.name} on ${on_string} (summary_counts.csv)" from_work_dir="classifier/summary_counts.csv"/>
+        <data format="pdf" name="cv_heatmap" label="${tool.name} on ${on_string} (cv_heatmap.pdf)" from_work_dir="classifier/cv_heatmap.pdf"/>
+        <collection name="disease_figures" type="list:list" label="Disease classifier figures">
+          <discover_datasets pattern="classifier_(?P&lt;identifier_1&gt;.+)__pred_(?P&lt;identifier_0&gt;.+)\.pdf" format="pdf" directory="classifier/disease" visible="false" />
+        </collection>
+        <data format="pdf" name="all_disease_pr" label="${tool.name} on ${on_string} (all_disease_pr.pdf)" from_work_dir="classifier/all_disease_pr.pdf"/>
+        <data format="pdf" name="all_disease_roc" label="${tool.name} on ${on_string} (all_disease_roc.pdf)" from_work_dir="classifier/all_disease_roc.pdf"/>
+        <data format="pdf" name="alt_gene_alt_disease_aupr_bar" label="${tool.name} on ${on_string} (alt_gene_alt_disease_aupr_bar.pdf)" from_work_dir="classifier/alt_gene_alt_disease_aupr_bar.pdf"/>
+        <data format="pdf" name="alt_gene_alt_disease_auroc_bar" label="${tool.name} on ${on_string} (alt_gene_alt_disease_auroc_bar.pdf)" from_work_dir="classifier/alt_gene_alt_disease_auroc_bar.pdf"/>
+        <data format="pdf" name="disease_aupr" label="${tool.name} on ${on_string} (disease_aupr.pdf)" from_work_dir="classifier/disease_aupr.pdf"/>
+        <data format="pdf" name="disease_auroc" label="${tool.name} on ${on_string} (disease_auroc.pdf)" from_work_dir="classifier/disease_auroc.pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="genes" value="ERBB2,PIK3CA,KRAS,AKT1"/>
+            <param name="diseases" value="GBM"/>
+            <param name="x_matrix" value="pancan_rnaseq_freeze_t1p.tsv.gz" ftype="tabular"/>
+            <param name="filename_mut" value="pancan_mutation_freeze_t1p.tsv.gz" ftype="tabular"/>
+            <param name="filename_mut_burden" value="mutation_burden_freeze.tsv" ftype="tabular"/>
+            <param name="filename_sample" value="sample_freeze.tsv" ftype="tabular"/>
+            <param name="seed" value="1234"/>
+            <param name="folds" value="5"/>
+            <param name="drop" value="true"/>
+            <param name="copy_number" value="true"/>
+            <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_cancer_gene_classification" value="cosmic_cancer_classification.tsv" ftype="tabular"/>
+            <param name="filter_count" value="15"/>
+            <param name="filter_prop" value="0.05"/>
+            <param name="num_features" value="8000"/>
+            <param name="alphas" value="0.1,0.13,0.15,0.18,0.2,0.3,0.4,0.6,0.7"/>
+            <param name="l1_ratios" value="0.1,0.125,0.15,0.2,0.25,0.3,0.35"/>
+            <param name="alt_genes" value="PTEN,PIK3R1,STK11"/>
+            <param name="alt_diseases" value="GBM"/>
+            <param name="alt_filter_count" value="15"/>
+            <param name="alt_filter_prop" value="0.05"/>
+            <param name="remove_hyper" value="true"/>
+            <param name="keep_intermediate" value="true"/>
+            <param name="shuffled" value="true"/>
+            <param name="shuffled_before_training" value="false"/>
+            <param name="no_mutation" value="false"/>
+            <param name="drop_expression" value="false"/>
+            <param name="drop_covariates" value="false"/>
+            <output name="log" file="Log.txt"/>
+            <output name="alt_gene_alt_disease_summary" file="alt_gene_alt_disease_summary.tsv"/>
+            <output name="alt_summary_counts" file="alt_summary_counts.csv"/>
+            <output name="classifier_coefficients" file="classifier_coefficients.tsv"/>
+            <output name="classifier_summary" file="classifier_summary.txt"/>
+            <output name="pancan_roc_results">
+              <assert_contents>
+                  <has_line line="&#009;fpr&#009;tpr&#009;threshold&#009;train_type&#009;disease" />
+                  <has_n_columns n="6" />
+                  <has_n_lines n="253" />
+              </assert_contents>
+            </output>
+            <output name="summary_counts" file="summary_counts.csv"/>
+            <output name="cv_heatmap" file="cv_heatmap.pdf" compare="sim_size" delta="50"/>
+            <output name="all_disease_pr" file="all_disease_pr.pdf" compare="sim_size" delta="50" />
+            <output name="all_disease_roc" file="all_disease_roc.pdf" compare="sim_size" delta="50"/>
+            <output name="alt_gene_alt_disease_aupr_bar" file="alt_gene_alt_disease_aupr_bar.pdf" compare="sim_size" delta="50"/>
+            <output name="alt_gene_alt_disease_auroc_bar" file="alt_gene_alt_disease_auroc_bar.pdf" compare="sim_size" delta="50"/>
+            <output name="disease_aupr" file="disease_aupr.pdf" compare="sim_size" delta="50"/>
+            <output name="disease_auroc" file="disease_auroc.pdf" compare="sim_size" delta="50"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+        
+        **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_pancancer_classifier.py:**
+
+            **Inputs:**
+                --genes     comma separated string of HUGO symbols for target genes or targenes_list.csv file
+                --diseases  comma separated string of disease types/TCGA acronyms for classifier
+                            default: Auto (will pick diseases from filter args)
+                --folds     number of cross validation folds
+                            default: 5
+                --seed  value specifies the initial value of the random number seed
+                        default: 1234
+                --drop  drop the input genes from the X matrix
+                        default: False if flag omitted
+                --copy_number   optional flag to supplement copy number to define Y
+                                default: False if flag omitted
+                --filter_count  int of low count of mutation to include disease
+                                default: 15
+                --filter_prop   float of low proportion of mutated samples per disease
+                                default: 0.05
+                --num_features  int of number of genes to include in classifier
+                                default: 8000
+                --alphas    comma separated string of alphas to test in pipeline default: '0.1,0.15,0.2,0.5,0.8,1'
+                --l1_ratios     comma separated string of l1 parameters to test
+                                default: '0,0.1,0.15,0.18,0.2,0.3'
+                --alt_genes     comma separated string of alternative genes to test
+                                default: None
+                --alt_diseases  comma separated string of alternative diseases to test
+                                default: Auto
+                --alt_filter_count  int of low count of mutations to include alt_diseases
+                                    default: 15
+                --alt_filter_prop   float of low proportion of mutated samples alt_disease
+                                    default: 0.05
+                --classifier_results    string of the location to save the classifier results/figures
+                                        default: Auto
+                --remove_hyper  store_true: remove hypermutated samples
+                                default: False if flag omitted
+                --keep_intermediate     store_true: keep intermediate roc curve items
+                                        default: False if flag omitted
+                --x_matrix  string of which feature matrix to use
+                            default: raw
+                --remove_hyper  store_true: remove hypermutated samples
+                                default: False if flag omitted
+                --keep_intermediate     store_true: keep intermediate roc curve items
+                                        default: False if flag omitted
+        
+            **Outputs:**
+            ROC curves, AUROC across diseases, and classifier coefficients  ]]>
+    </help>
+    <expand macro="citations" />
+</tool>