Mercurial > repos > vijay > pancancer_targene_cell_line_predictions
annotate targene_cell_line_predictions.xml @ 0:872aab514d37 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 23:30:22 +0000 |
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872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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1 <tool id="pancancer_targene_cell_line_predictions" name="PAPAA: PanCancer targene cell line predictions" version="@VERSION@"> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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2 <description>targene status in ccle cell lines </description> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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3 <macros> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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4 <import>macros.xml</import> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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5 </macros> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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6 <expand macro="requirements"/> |
872aab514d37
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7 <expand macro="stdio"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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8 <version_command><![CDATA['papaa_targene_cell_line_predictions.py' --version]]></version_command> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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9 <command><![CDATA[ |
872aab514d37
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10 mkdir 'classifier' && |
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11 mkdir -p 'classifier/figures' && |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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12 mkdir -p 'classifier/figures/cell_line' && |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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13 mkdir -p 'classifier/tables' && |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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14 mkdir -p 'classifier/results' && |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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15 ln -s '${classifier_summary}' 'classifier/classifier_summary.txt' && |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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16 ln -s '${pancan_classifier_coefficients}' 'classifier/classifier_coefficients.tsv' && |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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17 ln -s '${nucleotide_mutation_scores}' 'classifier/tables/nucleotide_mutation_scores.tsv' && |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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18 ln -s '${amino_acid_mutation_scores}' 'classifier/tables/amino_acid_mutation_scores.tsv' && |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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19 papaa_targene_cell_line_predictions.py |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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20 --classifier_summary 'classifier' |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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21 #if $targenes and str($targenes): |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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22 --targenes '$targenes' |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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23 #end if |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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24 #if $path_genes and str($path_genes): |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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25 --path_genes '$path_genes' |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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26 #end if |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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27 #if $ccle_rnaseq and $ccle_rnaseq is not None: |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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28 --ccle_rnaseq '$ccle_rnaseq' |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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29 #end if |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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30 #if $ccle_mut and $ccle_mut is not None: |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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31 --ccle_mut '$ccle_mut' |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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32 #end if |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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33 #if $ccle_maf and $ccle_maf is not None: |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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34 --ccle_maf '$ccle_maf' |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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35 #end if |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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36 #if $gdsc_rnaseq and $gdsc_rnaseq is not None: |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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37 --gdsc_rnaseq '$gdsc_rnaseq' |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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38 #end if |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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39 #if $gdsc_mut and $gdsc_mut is not None: |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
vijay
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40 --gdsc_mut '$gdsc_mut' |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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41 #end if |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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42 #if $gdsc1_phar and $gdsc1_phar is not None: |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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43 --gdsc1_phar '$gdsc1_phar' |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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44 #end if |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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45 #if $gdsc2_phar and $gdsc2_phar is not None: |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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46 --gdsc2_phar '$gdsc2_phar' |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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47 #end if |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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48 > '${log}' |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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49 ]]> |
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50 </command> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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51 <inputs> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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52 <param argument="--classifier_summary" label="Classifier data" name="classifier_summary" optional="false" type="data" format="txt" help="classifer_summary.txt"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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53 <param label="pancancer classifier coefficients" name="pancan_classifier_coefficients" optional="false" type="data" format="tabular" help="classifier_coefficients.tsv"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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54 <param label="nucleotide mutation scores" name="nucleotide_mutation_scores" optional="false" type="data" format="tabular" help="nucleotide_mutation_scores.tsv"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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55 <param label="amino acid mutation scores" name="amino_acid_mutation_scores" optional="false" type="data" format="tabular" help="amino_acid_mutation_scores.tsv"/> |
872aab514d37
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56 <param argument="--targenes" label="Comma separated string of HUGO targene symbols" name="targenes" optional="False" type="text" value="ERBB2_MUT,PIK3CA_MUT,KRAS_MUT,AKT1_MUT"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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57 <param argument="--path_genes" label="string of the genes to extract or genelist file" name="path_genes" optional="true" type= "data" format="txt"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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58 <param argument="--ccle_rnaseq" label="Filename ccle rnaseq data" name="ccle_rnaseq" optional="false" type="data" format="tabular" help="data/ccle_rnaseq_genes_rpkm_20180929_mod.tsv"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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59 <param argument="--ccle_mut" label="Filename ccle mutational data" name="ccle_mut" optional="true" type="data" format="txt" help="data/CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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60 <param argument="--ccle_maf" label="Filename ccle variant data" name="ccle_maf" optional="true" type="data" format="txt" help="data/CCLE_DepMap_18Q1_maf_20180207.txt" /> |
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61 <param argument="--gdsc_rnaseq" label="Filename gdsc rnaseq data" name="gdsc_rnaseq" optional="false" type="data" format="tabular" help="data/GDSC_EXP_CCLE_converted_name.tsv"/> |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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62 <param argument="--gdsc_mut" label="Filename gdsc mutational data" name="gdsc_mut" optional="true" type="data" format="tabular" help="data/GDSC_CCLE_common_mut_cnv_binary.tsv"/> |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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63 <param argument="--gdsc1_phar" label="Filename for gdsc1 pharmacological data file" name="gdsc1_phar" optional="false" type="data" format="txt" help="data/gdsc1_ccle_pharm_fitted_dose_data.txt"/> |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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64 <param argument="--gdsc2_phar" label="Filename for gdsc2 pharmacological data file" name="gdsc2_phar" optional="false" type="data" format="txt" help="data/gdsc2_ccle_pharm_fitted_dose_data.txt"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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65 </inputs> |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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66 <outputs> |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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67 <data format="txt" name="log" label="${tool.name} on ${on_string} (Log)"/> |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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68 <data format="png" name="ccle_histogram" label="${tool.name} on ${on_string} (ccle_histogram.png)" from_work_dir="classifier/figures/ccle_histogram.png"/> |
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"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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69 <data format="tabular" name="ccle_targene_classifier_scores" label="${tool.name} on ${on_string} (ccle_targene_classifier_scores.tsv)" from_work_dir="classifier/tables/ccle_targene_classifier_scores.tsv"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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70 <data format="pdf" name="ccle_targene_WT_MUT_predictions" label="${tool.name} on ${on_string} (ccle_targene_WT_MUT_predictions.pdf)" from_work_dir="classifier/figures/cell_line/ccle_targene_WT_MUT_predictions.pdf"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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71 <data format="csv" name="updated_data_nucleotide_scores" label="${tool.name} on ${on_string} (updated_data_nucleotide_scores.csv)" from_work_dir="classifier/tables/updated_data_nucleotide_scores.csv"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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72 <data format="csv" name="updated_data_aminoacid_scores" label="${tool.name} on ${on_string} (updated_data_aminoacid_scores.csv)" from_work_dir="classifier/tables/updated_data_aminoacid_scores.csv"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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73 <data format="png" name="gdsc_scores_histogram" label="${tool.name} on ${on_string} (gdsc_scores_histogram.png)" from_work_dir="classifier/figures/gdsc_scores_histogram.png"/> |
872aab514d37
"planemo upload for repository http://github.com/nvk747/papaa/galaxy/ commit 954b283ef7f82f59f55476a4b3a230d655187ac1"
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74 <data format="tabular" name="gdsc_targene_classifier_scores" label="${tool.name} on ${on_string} (gdsc_targene_classifier_scores.tsv)" from_work_dir="classifier/tables/gdsc_targene_classifier_scores.tsv"/> |
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75 <data format="pdf" name="gdsc_targene_WT_MUT_predictions" label="${tool.name} on ${on_string} (gdsc_targene_WT_MUT_predictions.pdf)" from_work_dir="classifier/figures/cell_line/gdsc_targene_WT_MUT_predictions.pdf"/> |
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76 <data format="tabular" name="gdsc1_targene_pharmacology_predictions" label="${tool.name} on ${on_string} (gdsc1_targene_pharmacology_predictions.tsv)" from_work_dir="classifier/tables/gdsc1_targene_pharmacology_predictions.tsv"/> |
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77 <data format="tabular" name="gdsc2_targene_pharmacology_predictions" label="${tool.name} on ${on_string} (gdsc2_targene_pharmacology_predictions.tsv)" from_work_dir="classifier/tables/gdsc2_targene_pharmacology_predictions.tsv"/> |
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78 <data format="tabular" name="gdsc1_ccle_targene_pharmacology_predictions" label="${tool.name} on ${on_string} (gdsc1_ccle_targene_pharmacology_predictions.tsv)" from_work_dir="classifier/tables/gdsc1_ccle_targene_pharmacology_predictions.tsv"/> |
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79 <data format="tabular" name="gdsc2_ccle_targene_pharmacology_predictions" label="${tool.name} on ${on_string} (gdsc2_ccle_targene_pharmacology_predictions.tsv)" from_work_dir="classifier/tables/gdsc2_ccle_targene_pharmacology_predictions.tsv"/> |
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80 </outputs> |
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81 <tests> |
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82 <test> |
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83 <param name="classifier_summary" value="classifier_summary.txt" ftype="txt"/> |
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84 <param name="pancan_classifier_coefficients" value="classifier_coefficients.tsv" ftype="tabular"/> |
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85 <param name="nucleotide_mutation_scores" value="nucleotide_mutation_scores.tsv" ftype="tabular"/> |
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86 <param name="amino_acid_mutation_scores" value="amino_acid_mutation_scores.tsv" ftype="tabular"/> |
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87 <param name="targenes" value="ERBB2_MUT,PIK3CA_MUT,KRAS_MUT,AKT1_MUT"/> |
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88 <param name="path_genes" value="path_genes.txt" ftype="txt"/> |
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89 <param name="ccle_rnaseq" value="ccle_rnaseq_genes_rpkm_20180929_mod_t5p.tsv.gz" ftype="tabular"/> |
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90 <param name="ccle_mut" value="CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct.gz" ftype="tabular"/> |
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91 <param name="ccle_maf" value="CCLE_DepMap_18Q1_maf_20180207_t1p.txt.gz" ftype="txt"/> |
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92 <param name="gdsc_rnaseq" value="GDSC_EXP_CCLE_converted_name_t10p.tsv.gz" ftype="tabular"/> |
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93 <param name="gdsc_mut" value="GDSC_CCLE_common_mut_cnv_binary.tsv.gz" ftype="tabular"/> |
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94 <param name="gdsc1_phar" value="gdsc1_ccle_pharm_fitted_dose_data_t10p.txt.gz" ftype="txt"/> |
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95 <param name="gdsc2_phar" value="gdsc2_ccle_pharm_fitted_dose_data_t10p.txt.gz" ftype="txt"/> |
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96 <output name="log" file="targene_cell_line_predictions_Log.txt" lines_diff="2"/> |
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97 <output name="ccle_histogram" file="ccle_histogram.png" compare="sim_size" delta="50"/> |
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98 <output name="ccle_targene_classifier_scores" file="ccle_targene_classifier_scores.tsv" /> |
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99 <output name="ccle_targene_WT_MUT_predictions" file="ccle_targene_WT_MUT_predictions.pdf" compare="sim_size" delta="100"/> |
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100 <output name="updated_data_nucleotide_scores" file="updated_data_nucleotide_scores.csv" /> |
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101 <output name="updated_data_aminoacid_scores" file="updated_data_aminoacid_scores.csv" /> |
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102 <output name="gdsc_scores_histogram" file="gdsc_scores_histogram.png" /> |
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103 <output name="gdsc_targene_classifier_scores" file="gdsc_targene_classifier_scores.tsv" /> |
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104 <output name="gdsc_targene_WT_MUT_predictions" file="gdsc_targene_WT_MUT_predictions.pdf" compare="sim_size" delta="50"/> |
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105 <output name="gdsc1_targene_pharmacology_predictions"> |
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106 <assert_contents> |
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107 <has_line line="	GDSC1_cell_line	NLME_CURVE_ID	COSMIC_ID	SANGER_MODEL_ID	TCGA_DESC	DRUG_ID	Compound	PUTATIVE_TARGET	PATHWAY_NAME	MIN_CONC	MAX_CONC	LN_IC50	AUC	RMSE	Z_SCORE	tissue	ERBB2_MUT	PIK3CA_MUT	KRAS_MUT	AKT1_MUT	targene_status	weight	sample_name	predictions" /> |
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108 <has_n_columns n="25" /> |
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109 <has_n_lines n="10281" /> |
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110 </assert_contents> |
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111 </output> |
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112 <output name="gdsc2_targene_pharmacology_predictions"> |
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113 <assert_contents> |
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114 <has_line line="	GDSC1_cell_line	NLME_CURVE_ID	COSMIC_ID	SANGER_MODEL_ID	TCGA_DESC	DRUG_ID	Compound	PUTATIVE_TARGET	PATHWAY_NAME	MIN_CONC	MAX_CONC	LN_IC50	AUC	RMSE	Z_SCORE	tissue	ERBB2_MUT	PIK3CA_MUT	KRAS_MUT	AKT1_MUT	targene_status	weight	sample_name	predictions" /> |
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115 <has_n_columns n="25" /> |
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116 <has_n_lines n="10281" /> |
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117 </assert_contents> |
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118 </output> |
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119 <output name="gdsc1_ccle_targene_pharmacology_predictions" file="gdsc1_ccle_targene_pharmacology_predictions.tsv" /> |
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120 <output name="gdsc2_ccle_targene_pharmacology_predictions" file="gdsc2_ccle_targene_pharmacology_predictions.tsv" /> |
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121 </test> |
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122 </tests> |
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123 <help><![CDATA[ |
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124 |
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125 **Pancancer_Aberrant_Pathway_Activity_Analysis scripts/viz/papaa_targene_cell_line_predictions_mod.py:** |
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126 |
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127 **Inputs:** |
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128 --targenes comma separated string of HUGO symbols for target genes or targenes_list.csv file |
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129 --path_genes comma separated string of HUGO symbols for all genes in the target pathway or path_genes.txt file |
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130 --classifier_summary String of the location of classifier_summary file |
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131 --ccle_rnaseq Filename of CCLE gene expression data file |
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132 --ccle_mut Filename of CCLE cell lines/gene mutations data file |
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133 --ccle_maf Filename of CCLE mutational variant level data file |
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134 --gdsc_rnaseq Filename of GDSC gene expression data file |
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135 --gdsc_mut Filename of GDSC cell lines/gene mutations data file |
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136 --gdsc1_phar Filename of GDSC1 pharmacological response data |
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137 --gdsc2_phar Filename of GDSC2 pharmacological response data |
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138 |
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139 **Outputs:** |
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140 Generate predictions for CCLE data using targene classifier(ccle_histogram.png) |
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141 |
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142 Generate classifier scores for CCLE cell lines and combines CCLE mutational data and variant data with classifier scores (ccle_targene_classifier_scores.tsv) |
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143 |
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144 Performs t-test on classifier weights across targene mutant vs targene wildtype cell-line groups(ccle_targene_WT_MUT_predictions.pdf) |
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145 |
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146 Add CCLE nucleotide scores at variant level and update nucleotide_mutation_scores.tsv (updated_data_nucleotide_scores.csv) |
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147 |
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148 Add CCLE protein scores at variant level and update aminoacid_mutation_scores.tsv (updated_data_aminoacid_scores.csv) |
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149 |
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150 Generate predictions for GDSC data using targene classifier(gdsc_scores_histogram.png) |
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151 |
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152 Generate classifier scores for GDSC cell lines and combines CCLE mutational data and variant data with classifier scores (gdsc_targene_classifier_scores.tsv) |
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153 |
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154 Performs t-test on classifier weights across targene mutant vs targene wildtype cell-line groups(gdsc_targene_WT_MUT_predictions.pdf) |
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155 |
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156 Apply GDSC classifier scores to evaluate GDSC1 pharmacological data response(gdsc1_targene_pharmacology_predictions.tsv) |
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157 |
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158 Apply GDSC classifier scores to evaluate GDSC2 pharmacological data response(gdsc2_targene_pharmacology_predictions.tsv) |
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159 |
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160 Apply CCLE classifier scores to evaluate GDSC1 pharmacological data response(gdsc1_ccle_targene_pharmacology_predictions.tsv) |
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161 |
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162 Apply CCLE classifier scores to evaluate GDSC2 pharmacological data response(gdsc2_ccle_targene_pharmacology_predictions.tsv) ]]> |
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163 </help> |
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164 <expand macro="citations" /> |
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165 </tool> |