Mercurial > repos > vijay > pancancer_map_mutation_class

changeset 0:54c85c40dce1 draft default tip

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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
author vijay
date Wed, 16 Dec 2020 23:31:49 +0000
parents
children
files macros.xml map_mutation_class.xml
diffstat 2 files changed, 288 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Wed Dec 16 23:31:49 2020 +0000
@@ -0,0 +1,229 @@
+<macros>
+    <token name="@VERSION@">0.1.9</token>
+
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">papaa</requirement>
+        </requirements>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+             <exit_code level="fatal" range="1:"/>
+        </stdio>
+    </xml>
+
+    <xml name="inputs_basic">
+        <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"/>
+        <yield/>
+        <param argument="--filename_mut" label="Filename mutations" name="filename_mut" optional="true" type="data" format="tabular" help="data/pancan_mutation_freeze.tsv.gz"/>
+        <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"/>
+        <param argument="--filename_sample" label="Filename of sample" name="filename_sample" optional="true" type="data" format="tabular" help="data/sample_freeze.tsv"/>
+    </xml>
+
+    <token name="@INPUTS_BASIC@"><![CDATA[
+        #if $x_matrix and $x_matrix is not None:
+        --x_matrix '$x_matrix'
+        #end if
+        #if $filename_mut and $filename_mut is not None:
+        --filename_mut '$filename_mut'
+        #end if
+        #if $filename_mut_burden and $filename_mut_burden is not None:
+        --filename_mut_burden '$filename_mut_burden'
+        #end if
+        #if $filename_sample and $filename_sample is not None:
+        --filename_sample '$filename_sample'
+        #end if
+        ]]>
+    </token>
+
+    <xml name="inputs_genes_diseases">
+        <param argument="--genes" label="Comma separated string of HUGO gene symbols" name="genes" optional="False" type="text" value="ERBB2,PIK3CA,KRAS,AKT1"/>
+        <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"/>
+    </xml>
+
+    <token name="@INPUTS_GENES_DISEASES@"><![CDATA[
+        #if $genes and $genes is not None:
+        --genes '$genes'
+        #end if
+        #if $diseases and str($diseases) != '':
+        --diseases '$diseases'
+        #end if
+        ]]>
+    </token>
+
+
+    <xml name="input_filename_raw_mut">
+        <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"/>
+    </xml>
+
+    <token name="@INPUT_FILENAME_RAW_MUT@"><![CDATA[
+        #if $filename_raw_mut and $filename_raw_mut is not None:
+        --filename_raw_mut '$filename_raw_mut'
+        #end if
+        ]]>
+    </token>
+
+
+    <xml name="input_filename_burden">
+        <param argument="--filename_burden" label="Burden file" name="filename_burden" optional="true" type="data" format="tabular" help="data/seg_based_scores.tsv"/>
+    </xml>
+
+    <token name="@INPUT_FILENAME_BURDEN@"><![CDATA[
+        #if $filename_burden and $filename_burden is not None:
+        --filename_burden '$filename_burden'
+        #end if
+        ]]>        
+    </token>
+
+    <xml name="input_filename_snaptron_samples">
+        <param argument="--sample_file" label="SNAPTRON samples" name="sample_file" optional="true" type="data" format="tabular" help="scripts/snaptron/samples.tsv.gz"/>
+    </xml>
+
+    <token name="@INPUT_FILENAME_SNAPTRON_SAMPLES@"><![CDATA[
+        #if $sample_file and $sample_file is not None:
+        --sample_file '$sample_file'
+        #end if
+        ]]>       
+    </token>
+
+
+    <xml name="input_filename_snaptron_junctions">
+        <param argument="--junction_file" label="SNAPTRON junctions" name="junction_file" optional="true" type="data" format="tabular" help="scripts/snaptron/tp53_junctions.txt.gz"/>
+    </xml>
+
+    <token name="@INPUT_FILENAME_SNAPTRON_JUNCTIONS@"><![CDATA[
+        #if $junction_file and $junction_file is not None:
+        --junction_file '$junction_file'
+        #end if
+        ]]>    
+    </token>
+
+    <xml name="inputs_copy_number_file">
+        <param argument="--filename_copy_loss" label="File with Copy number loss" name="filename_copy_loss" optional="true" type="data" format="tabular" help="data/copy_number_loss_status.tsv.gz"/>
+        <param argument="--filename_copy_gain" label="File with Copy number gain" name="filename_copy_gain" optional="true" type="data" format="tabular" help="data/copy_number_gain_status.tsv.gz"/>
+    </xml>
+
+    <xml name="inputs_copy_number_class_file">
+        <expand macro="inputs_copy_number_file" />
+        <param argument="--filename_cancer_gene_classification" label="File with cancer gene classification table" name="filename_cancer_gene_classification" optional="true" type="data" format="tabular" help="data/cosmic_cancer_classification.tsv"/>
+    </xml>
+
+    <xml name="inputs_copy_number_file_conditional">
+        <conditional name="copy_number_conditional">
+          <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
+          <when value="--copy_number">
+            <expand macro="inputs_copy_number_file" />
+          </when>
+          <when value=""/>
+        </conditional>
+    </xml>
+
+    <xml name="inputs_copy_number_class_file_conditional">
+        <conditional name="copy_number_conditional">
+          <param argument="--copy_number" checked="false" label="Supplement Y matrix with copy number events" name="copy_number" type="boolean" truevalue="--copy_number" falsevalue=""/>
+          <when value="--copy_number">
+            <expand macro="inputs_copy_number_class_file" />
+          </when>
+          <when value=""/>
+        </conditional>
+    </xml>
+
+    <token name="@INPUTS_COPY_NUMBER_FILE_PREFIX@"><![CDATA[
+        #set $copy_number_conditional = type('',(object,),{'filename_copy_loss':$filename_copy_loss,'filename_copy_gain':$filename_copy_gain})()
+                ]]>
+    </token>
+
+    <token name="@INPUTS_COPY_NUMBER_FILE@"><![CDATA[
+        #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
+        --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
+        #end if
+        #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
+        --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
+        #end if
+        ]]>
+    </token>
+    
+    <token name="@INPUTS_COPY_NUMBER_FILE_CONDITIONAL@"><![CDATA[
+        #if $copy_number_conditional.copy_number
+        $copy_number_conditional.copy_number
+        #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
+        --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
+        #end if
+        #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
+        --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
+        #end if
+        ##@INPUTS_COPY_NUMBER_FILE@
+        #end if
+        ]]>
+    </token>
+
+    <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_PREFIX@"><![CDATA[
+        #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})()
+        ]]>
+    </token>
+
+    <token name="@INPUTS_COPY_NUMBER_CLASS_FILE@"><![CDATA[
+        #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
+        --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
+        #end if
+        #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
+        --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
+        #end if
+        #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
+        --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
+        #end if
+        ]]>
+    </token>
+    
+    <token name="@INPUTS_COPY_NUMBER_CLASS_FILE_CONDITIONAL@"><![CDATA[
+        #if $copy_number_conditional.copy_number
+        $copy_number_conditional.copy_number
+        ##
+        #if $copy_number_conditional.filename_copy_loss and $copy_number_conditional.filename_copy_loss is not None:
+        --filename_copy_loss '$copy_number_conditional.filename_copy_loss'
+        #end if
+        #if $copy_number_conditional.filename_copy_gain and $copy_number_conditional.filename_copy_gain is not None:
+        --filename_copy_gain '$copy_number_conditional.filename_copy_gain'
+        #end if
+        #if $copy_number_conditional.filename_cancer_gene_classification and $copy_number_conditional.filename_cancer_gene_classification is not None:
+        --filename_cancer_gene_classification '$copy_number_conditional.filename_cancer_gene_classification'
+        #end if
+        ##@INPUTS_COPY_NUMBER_CLASS_FILE@
+        #end if
+        ]]> 
+    </token>
+
+    <xml name="input_remove_hyper">
+        <param argument="--remove_hyper" checked="false" label="Remove hypermutated samples" name="remove_hyper" type="boolean" truevalue="--remove_hyper" falsevalue=""/>
+    </xml>
+    <token name="@INPUT_REMOVE_HYPER@"><![CDATA[$remove_hyper]]></token>
+       
+    <xml name="input_alphas">
+        <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"/>
+    </xml>
+
+    <token name="@INPUTS_ALPHAS@"><![CDATA[
+        #if $alphas and $alphas is not None:
+        --alphas '$alphas'
+        #end if
+        ]]>
+    </token>
+
+    <xml name="input_l1_ratios">
+        <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"/>
+    </xml>
+
+    <token name="@INPUTS_L1_RATIOS@"><![CDATA[
+        #if $l1_ratios and $l1_ratios is not None:
+        --l1_ratios '$l1_ratios'
+        #end if
+        ]]>
+    </token>
+    <xml name="citations">
+        <citations>
+            <yield />
+        </citations>
+    </xml>
+</macros>
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/map_mutation_class.xml	Wed Dec 16 23:31:49 2020 +0000
@@ -0,0 +1,59 @@
+<tool id="pancancer_map_mutation_class" name="PAPAA: PanCancer map mutation class" version="@VERSION@">
+  <description>map mutation class</description>
+  <macros>
+    <import>macros.xml</import>
+  </macros>
+  <expand macro="requirements"/>
+  <expand macro="stdio"/>
+  <version_command><![CDATA['papaa_map_mutation_class.py' --version]]></version_command>
+  <command><![CDATA[
+      mkdir 'classifier' &&
+      ln -s '${classifier_decisions}' 'classifier/classifier_decisions.tsv' && 
+      papaa_map_mutation_class.py
+      --classifier_decisions 'classifier'
+      #if $path_genes and str($path_genes):
+      --path_genes '$path_genes'
+      #end if
+      @INPUTS_COPY_NUMBER_FILE_CONDITIONAL@
+      @INPUT_FILENAME_RAW_MUT@
+      > '${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="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/>
+    <expand macro="inputs_copy_number_file_conditional" />
+    <expand macro="input_filename_raw_mut" />
+  </inputs>
+  <outputs>
+    <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/>
+    <data format="tabular" name="mutation_classification_scores" label="${tool.name} on ${on_string} (mutation_classification_scores.tsv)" from_work_dir="classifier/tables/mutation_classification_scores.tsv"/>
+  </outputs>
+  <tests>
+        <test>
+          <param name="classifier_decisions" value="classifier_decisions.tsv" ftype="tabular"/>
+          <param name="path_genes" value="path_genes.txt" ftype="txt"/>
+          <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="map_mutation_class_Log.txt"/>
+          <output name="mutation_classification_scores" file="mutation_classification_scores.tsv" />
+        </test>
+  </tests>
+  <help><![CDATA[
+
+    **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/papaa_map_mutation_class.py:**
+      
+      **Inputs:**
+        --classifer_decisions   String of the location of folder containing classifier_decisions.tsv
+        --path_genes  comma separated string of HUGO symbols for all genes in the pathway or Pathway genes list file
+        --filename_copy_loss  Filename of copy number loss
+        --filename_copy_gain  Filename of copy number gain
+        --filename_raw_mut  Filename of raw mut MAF
+        
+      **Outputs:**
+      Merge per sample classifier scores with mutation types present in each sample and generate "mutation_classification_scores.tsv" file  ]]>
+    </help>
+    <expand macro="citations" />
+</tool>