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Commit message:
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1" |
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added:
macros.xml targene_pathway_count_heatmaps.xml |
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| diff -r 000000000000 -r dc1d71493ebf macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed Dec 16 23:29:47 2020 +0000 |
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| b'@@ -0,0 +1,229 @@\n+<macros>\n+ <token name="@VERSION@">0.1.9</token>\n+\n+ <xml name="requirements">\n+ <requirements>\n+ <requirement type="package" version="@VERSION@">papaa</requirement>\n+ </requirements>\n+ </xml>\n+\n+ <xml name="stdio">\n+ <stdio>\n+ <exit_code level="fatal" range="1:"/>\n+ </stdio>\n+ </xml>\n+\n+ <xml name="inputs_basic">\n+ <param argument="--x_matrix" label="Filename of features to use in model" name="x_matrix" optional="true" type="data" format="tabular" help="data/pancan_rnaseq_freeze.tsv.gz"/>\n+ <yield/>\n+ <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv.gz"/>\n+ <param argument="--filename_mut_burden" label="Filename of mutation burden" name="filename_mut_burden" optional="true" type="data" format="tabular" help="data/mutation_burden_freeze.tsv"/>\n+ <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>\n+ </xml>\n+\n+ <token name="@INPUTS_BASIC@"><![CDATA[\n+ #if $x_matrix and $x_matrix is not None:\n+ --x_matrix \'$x_matrix\'\n+ #end if\n+ #if $filename_mut and $filename_mut is not None:\n+ --filename_mut \'$filename_mut\'\n+ #end if\n+ #if $filename_mut_burden and $filename_mut_burden is not None:\n+ --filename_mut_burden \'$filename_mut_burden\'\n+ #end if\n+ #if $filename_sample and $filename_sample is not None:\n+ --filename_sample \'$filename_sample\'\n+ #end if\n+ ]]>\n+ </token>\n+\n+ <xml name="inputs_genes_diseases">\n+ <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>\n+ <param argument="--diseases" label="Comma sep string of TCGA disease acronyms. If no arguments are passed, filtering will default to options given in --filter_count and --filter_prop." name="diseases" optional="true" type="text" value="BLCA,BRCA,CESC,COAD,ESCA,LUAD,LUSC,OV,PRAD,READ,STAD,UCEC,UCS"/>\n+ </xml>\n+\n+ <token name="@INPUTS_GENES_DISEASES@"><![CDATA[\n+ #if $genes and $genes is not None:\n+ --genes \'$genes\'\n+ #end if\n+ #if $diseases and str($diseases) != \'\':\n+ --diseases \'$diseases\'\n+ #end if\n+ ]]>\n+ </token>\n+\n+\n+ <xml name="input_filename_raw_mut">\n+ <param argument="--filename_raw_mut" label="Filename of raw mut MAF" name="filename_raw_mut" optional="true" type="data" format="tabular" help="data/raw/mc3.v0.2.8.PUBLIC.maf"/>\n+ </xml>\n+\n+ <token name="@INPUT_FILENAME_RAW_MUT@"><![CDATA[\n+ #if $filename_raw_mut and $filename_raw_mut is not None:\n+ --filename_raw_mut \'$filename_raw_mut\'\n+ #end if\n+ ]]>\n+ </token>\n+\n+\n+ <xml name="input_filename_burden">\n+ <param argument="--filename_burden" label="Burden file" name="filename_burden" optional="true" type="data" format="tabular" help="data/seg_based_scores.tsv"/>\n+ </xml>\n+\n+ <token name="@INPUT_FILENAME_BURDEN@"><![CDATA[\n+ #if $filename_burden and $filename_burden is not None:\n+ --filename_burden \'$filename_burden\'\n+ #end if\n+ ]]> \n+ </token>\n+\n+ <xml name="input_filename_snaptron_samples">\n+ <param argument="--sample_file" label="SNAPTRON samples" name="sample_file" optional="true" type="data" format="tabular" help="scripts/snaptron/samples.tsv.gz"/>\n+ </xml>\n+\n+ <token name="@INPUT_FILENAME_SNAPTRON_SAMPLES@"><![CDATA[\n+ #if $sample_file and $sample_file is not None:\n+ --sample_file \'$sample_file\'\n+ #end if\n+ ]]> \n+ </token>\n+\n+\n+ <xml name="input_filename_snaptron_junctions">\n+ <param argument="--junction_file" label="SNAPTRON junctions" name="junct'..b'\'\n+ #end if\n+ ]]>\n+ </token>\n+ \n+ <token name="@INPUTS_COPY_NUMBER_FILE_CONDITIONAL@"><![CDATA[\n+ #if $copy_number_conditional.copy_number\n+ $copy_number_conditional.copy_number\n+ #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:\n+ --filename_copy_loss \'$copy_number_conditional.filename_copy_loss\'\n+ #end if\n+ #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:\n+ --filename_copy_gain \'$copy_number_conditional.filename_copy_gain\'\n+ #end if\n+ ##@INPUTS_COPY_NUMBER_FILE@\n+ #end if\n+ ]]>\n+ </token>\n+\n+ <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_PREFIX@"><![CDATA[\n+ #set $copy_number_conditional = type(\'\',(object,),{\'filename_copy_loss\':$filename_copy_loss,\'filename_copy_gain\':$filename_copy_gain,\'filename_cancer_gene_classification\':$filename_cancer_gene_classification})()\n+ ]]>\n+ </token>\n+\n+ <token name="@INPUTS_COPY_NUMBER_CLASS_FILE@"><![CDATA[\n+ #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:\n+ --filename_copy_loss \'$copy_number_conditional.filename_copy_loss\'\n+ #end if\n+ #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:\n+ --filename_copy_gain \'$copy_number_conditional.filename_copy_gain\'\n+ #end if\n+ #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:\n+ --filename_cancer_gene_classification \'$copy_number_conditional.filename_cancer_gene_classification\'\n+ #end if\n+ ]]>\n+ </token>\n+ \n+ <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_CONDITIONAL@"><![CDATA[\n+ #if $copy_number_conditional.copy_number\n+ $copy_number_conditional.copy_number\n+ ##\n+ #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:\n+ --filename_copy_loss \'$copy_number_conditional.filename_copy_loss\'\n+ #end if\n+ #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:\n+ --filename_copy_gain \'$copy_number_conditional.filename_copy_gain\'\n+ #end if\n+ #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:\n+ --filename_cancer_gene_classification \'$copy_number_conditional.filename_cancer_gene_classification\'\n+ #end if\n+ ##@INPUTS_COPY_NUMBER_CLASS_FILE@\n+ #end if\n+ ]]> \n+ </token>\n+\n+ <xml name="input_remove_hyper">\n+ <param argument="--remove_hyper" checked="false" label="Remove hypermutated samples" name="remove_hyper" type="boolean" truevalue="--remove_hyper" falsevalue=""/>\n+ </xml>\n+ <token name="@INPUT_REMOVE_HYPER@"><![CDATA[$remove_hyper]]></token>\n+ \n+ <xml name="input_alphas">\n+ <param argument="--alphas" label="the alphas for parameter sweep" name="alphas" optional="true" type="text" value="0.1,0.13,0.15,0.18,0.2,0.3,0.4,0.6,0.7"/>\n+ </xml>\n+\n+ <token name="@INPUTS_ALPHAS@"><![CDATA[\n+ #if $alphas and $alphas is not None:\n+ --alphas \'$alphas\'\n+ #end if\n+ ]]>\n+ </token>\n+\n+ <xml name="input_l1_ratios">\n+ <param argument="--l1_ratios" label="the l1 ratios for parameter sweep" name="l1_ratios" optional="true" type="text" value="0.1,0.125,0.15,0.2,0.25,0.3,0.35"/>\n+ </xml>\n+\n+ <token name="@INPUTS_L1_RATIOS@"><![CDATA[\n+ #if $l1_ratios and $l1_ratios is not None:\n+ --l1_ratios \'$l1_ratios\'\n+ #end if\n+ ]]>\n+ </token>\n+ <xml name="citations">\n+ <citations>\n+ <yield />\n+ </citations>\n+ </xml>\n+</macros>\n+\n' |
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| diff -r 000000000000 -r dc1d71493ebf targene_pathway_count_heatmaps.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/targene_pathway_count_heatmaps.xml Wed Dec 16 23:29:47 2020 +0000 |
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| b'@@ -0,0 +1,107 @@\n+<tool id="pancancer_pathway_count_heatmaps" name="PAPAA: PanCancer pathway count heatmaps" version="@VERSION@">\n+ <description>pathway count heatmaps</description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="stdio"/>\n+ <version_command><![CDATA[\'papaa_targene_pathway_count_heatmaps.py\' --version]]></version_command>\n+ <command><![CDATA[\n+ mkdir \'classifier\' &&\n+ mkdir -p \'classifier/tables\' &&\n+ ln -s \'${classifier_decisions}\' \'classifier/classifier_decisions.tsv\' &&\n+ ln -s \'${pathway_metrics}\' \'classifier/tables/pathway_metrics_pathwaymapper.txt\' &&\n+ ln -s \'${all_gene_metric_ranks}\' \'classifier/tables/all_gene_metric_ranks.tsv\' &&\n+ papaa_targene_pathway_count_heatmaps.py\n+ --classifier_decisions \'classifier\'\n+ #if $genes and str($genes):\n+ --genes \'$genes\'\n+ #end if\n+ #if $path_genes and str($path_genes):\n+ --path_genes \'$path_genes\'\n+ #end if\n+ @INPUTS_BASIC@\n+ #if $filename_copy_loss and $filename_copy_loss is not None:\n+ --filename_copy_loss \'$filename_copy_loss\'\n+ #end if\n+ #if $filename_copy_gain and $filename_copy_gain is not None:\n+ --filename_copy_gain \'$filename_copy_gain\'\n+ #end if\n+ #if $filename_cancer_gene_classification and $filename_cancer_gene_classification is not None:\n+ --filename_cancer_gene_classification \'$filename_cancer_gene_classification\'\n+ #end if\n+ > \'${log}\'\n+ ]]>\n+ </command>\n+ <inputs>\n+ <param argument="--classifier_decisions" label="pancancer decisions" name="classifier_decisions" optional="false" type="data" format="tabular" help="classifier_decisions.tsv"/>\n+ <param label="pancancer metrics pathwaymapper" name="pathway_metrics" optional="false" type="data" format="txt" help="pathway_metrics_pathwaymapper.txt"/>\n+ <param label="all gene metric ranks" name="all_gene_metric_ranks" optional="false" type="data" format="tabular" help="all_gene_metric_ranks.tsv"/>\n+ <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>\n+ <param argument="--path_genes" label="String of the pathway genes to extract" name="path_genes" optional="true" type= "data" format="txt"/>\n+ <expand macro="inputs_basic"/>\n+ <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv"/>\n+ <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>\n+ <param argument="--filename_copy_loss" label="File with Copy number loss" name="filename_copy_loss" optional="false" type="data" format="tabular" help="data/copy_number_loss_status.tsv"/>\n+ <param argument="--filename_copy_gain" label="File with Copy number gain" name="filename_copy_gain" optional="false" type="data" format="tabular" help="data/copy_number_gain_status.tsv"/>\n+ <param argument="--filename_cancer_gene_classification" label="File with cancer gene classification table" name="filename_cancer_gene_classification" optional="false" type="data" format="tabular" help="data/cosmic_cancer_classification.tsv"/>\n+ </inputs>\n+ <outputs>\n+ <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>\n+ <data format="pdf" name="cancer_type_mutation_heatmap" label="${tool.name} on ${on_string} (cancer_type_mutation_heatmap.pdf)" from_work_dir="classifier/cancer_type_mutation_heatmap.pdf"/>\n+ <data format="pdf" name="cancer_type_copy_number_heatmap" label="${tool.name} on ${on_string} (cancer_type_copy_number_heatmap.pdf)" from_work_dir="classifier/cancer_type_copy_number_heatmap.pdf"/>\n+'..b'<data format="txt" name="pathway_mapper_percentages" label="${tool.name} on ${on_string} (pathway_mapper_percentages.txt)" from_work_dir="classifier/tables/pathway_mapper_percentages.txt"/>\n+ <data format="tabular" name="path_events_per_sample" label="${tool.name} on ${on_string} (path_events_per_sample.tsv)" from_work_dir="classifier/tables/path_events_per_sample.tsv"/>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>\n+ <param name="x_matrix" value="pancan_rnaseq_freeze_t1p.tsv.gz" ftype="tabular"/>\n+ <param name="genes" value="ERBB2,KRAS,PIK3CA,AKT1"/>\n+ <param name="path_genes" value="path_genes.txt" ftype="txt"/>\n+ <param name="pathway_metrics_pathwaymapper" value="pathway_metrics_pathwaymapper.txt" ftype="txt"/>\n+ <param name="all_gene_metric_ranks" value="all_gene_metric_ranks.tsv" ftype="tabular"/>\n+ <param name="filename_mut" value="pancan_mutation_freeze_t1p.tsv.gz" ftype="tabular"/>\n+ <param name="filename_sample" value="sample_freeze.tsv" ftype="tabular"/>\n+ <param name="copy_number" value="yes"/>\n+ <param name="filename_copy_loss" value="copy_number_loss_status_t10p.tsv.gz" ftype="tabular" />\n+ <param name="filename_copy_gain" value="copy_number_gain_status_t10p.tsv.gz" ftype="tabular" />\n+ <param name="filename_cancer_gene_classification" value="cosmic_cancer_classification.tsv" ftype="tabular" />\n+ <output name="log" file="pathway_count_heatmaps_Log.txt"/>\n+ <output name="cancer_type_mutation_heatmap" file="cancer_type_mutation_heatmap.pdf" compare="sim_size" delta="50"/>\n+ <output name="cancer_type_copy_number_heatmap" file="cancer_type_copy_number_heatmap.pdf" compare="sim_size" delta="50"/>\n+ <output name="cancer_type_combined_total_heatmap" file="cancer_type_combined_total_heatmap.pdf" compare="sim_size" delta="50"/>\n+ <output name="pathway_mapper_percentages" file="pathway_mapper_percentages.txt" />\n+ <output name="path_events_per_sample" file="path_events_per_sample.tsv" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+ **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_targene_pathway_count_heatmaps.py:**\n+\n+ **Inputs:**\n+ --genes comma separated string of HUGO symbols for target genes or targenes_list.csv file\n+ --path_genes comma separated string of HUGO symbols for all genes in the target pathway or path_genes.txt file\n+ --classifier_decisions String of the location of classifier scores/alt_folder\n+ --x_matrix Filename of features to use in model\n+ --filename_mut Filename of sample/gene mutations to use in model\n+ --filename_mut_burden Filename of sample mutation burden to use in model\n+ --filename_sample Filename of patient/samples to use in model\n+ --filename_copy_loss Filename of copy number loss\n+ --filename_copy_gain Filename of copy number gain\n+ --filename_cancer_gene_classification Filename of cancer gene classification table\n+\n+ **Outputs:**\n+ Mutational count heatmap for all genes in the target pathway with in each cancer type (cancer_type_mutation_heatmap.pdf)\n+\n+ Copy number count heatmap for all genes in the target pathway with in each cancer type (cancer_type_copy_number_heatmap.pdf)\n+\n+ Combined count heatmap for all genes in the target pathway with in each cancer type (cancer_type_combined_total_heatmap.pdf)\n+\n+ Calculates Mutations and copy number percentages of the genes in the pathway and generates "pathway_mapper_percentages.txt" file \n+\n+ Summarizes mutation, copy, and total counts per sample by targene pathway and generates "path_events_per_sample.tsv" file ]]>\n+ </help>\n+ <expand macro="citations" />\n+</tool>\n\\ No newline at end of file\n' |