Galaxy | Australia | Published Workflow | COVID-19: variation analysis reporting

COVID-19: variation analysis reporting

Step	Annotation
Step 1: Input parameter Number of Clusters Not available.
Step 2: Input dataset gene products translations select at runtime
Step 3: Input dataset collection Variation data to report select at runtime
Step 4: Input parameter AF Filter Not available.
Step 5: Input parameter DP Filter Not available.
Step 6: Input parameter DP_ALT Filter Not available.
Step 7: Compose text parameter value components components 1 Choose the type of parameter for this field Text Parameter Enter text that should be part of the computed value (AF < components 2 Choose the type of parameter for this field Float Parameter Enter float that should be part of the computed value Not available. components 3 Choose the type of parameter for this field Text Parameter Enter text that should be part of the computed value ) \| (DP < components 4 Choose the type of parameter for this field Integer Parameter Enter integer that should be part of the computed value Not available. components 5 Choose the type of parameter for this field Text Parameter Enter text that should be part of the computed value ) \| (DP4[2] + DP4[3] < components 6 Choose the type of parameter for this field Integer Parameter Enter integer that should be part of the computed value Not available. components 7 Choose the type of parameter for this field Text Parameter Enter text that should be part of the computed value )
Step 8: Compose text parameter value components components 1 Choose the type of parameter for this field Text Parameter Enter text that should be part of the computed value min_af_ components 2 Choose the type of parameter for this field Float Parameter Enter float that should be part of the computed value Not available. components 3 Choose the type of parameter for this field Text Parameter Enter text that should be part of the computed value \|min_dp_ components 4 Choose the type of parameter for this field Integer Parameter Enter integer that should be part of the computed value Not available. components 5 Choose the type of parameter for this field Text Parameter Enter text that should be part of the computed value \|min_dp_alt_ components 6 Choose the type of parameter for this field Integer Parameter Enter integer that should be part of the computed value Not available.
Step 9: SnpSift Filter Input variant list in VCF format Output dataset 'output' from step 3 Type of filter expression Simple expression Filter criteria Not available. Invert filter False Filter mode Add a value to the FILTER field of selected variants Value to add to FILTER field of selected variants Not available.
Step 10: SnpSift Extract Fields Variant input file in VCF format Output dataset 'output' from step 9 Fields to extract CHROM POS FILTER REF ALT DP AF DP4 SB EFF[].IMPACT EFF[].FUNCLASS EFF[].EFFECT EFF[].GENE EFF[].CODON EFF[].AA EFF[*].TRID One effect per line True multiple field separator Empty. empty field text .
Step 11: Replace column File in which you want to replace some values Output dataset 'output' from step 10 Replace information file Output dataset 'output' from step 2 Which column should be replaced? 16 Skip this many starting lines 1 Delimited by Tab When an unknown value is encountered Skip / Do not print Do not perform replacement on lines starting with #
Step 12: Datamash Input tabular dataset Output dataset 'outfile_replace' from step 11 Group by fields 1,2,3,4,5,6,7,8,9 Input file has a header line True Print header line True Sort input False Print all fields from input file False Ignore case when grouping False Operation to perform on each groups Operation to perform on each group 1 Type Combine all values On column 10 Operation to perform on each group 2 Type Combine all values On column 11 Operation to perform on each group 3 Type Combine all values On column 12 Operation to perform on each group 4 Type Combine all values On column 13 Operation to perform on each group 5 Type Combine all values On column 14 Operation to perform on each group 6 Type Combine all values On column 15 Operation to perform on each group 7 Type Combine all values On column 16
Step 13: Replace File to process Output dataset 'out_file' from step 12 Find pattern \t([^\t,]+),[^\t]+\t([^\t,]+),[^\t]+\t([^\t,]+),[^\t]+\t([^\t,]+),[^\t]+\t([^\t,]+),[^\t]+\t([^\t,]+),[^\t]+\t([^\t,]+),[^\s]+ Replace with \t$1\t$2\t$3\t$4\t$5\t$6\t$7 Find-Pattern is a regular expression True Replace all occurences of the pattern True Case-Insensitive search False Find whole-words False Ignore first line True Find and Replace text in entire line
Step 14: Replace File to process Output dataset 'outfile' from step 13 Find pattern (GroupBy\|collapse)$([^)]+)$ Replace with $2 Find-Pattern is a regular expression True Replace all occurences of the pattern True Case-Insensitive search False Find whole-words False Ignore first line False Find and Replace text in entire line
Step 15: Collapse Collection Collection of files to collapse into single dataset Output dataset 'outfile' from step 14 Keep one header line True Prepend File name True Where to add dataset name Same line and each line in dataset
Step 16: Compute Add expression str(c5) + '>' + str(c6) as a new column to Output dataset 'output' from step 15 Round result? NO Skip a header line yes The new column name change Avoid scientific notation no
Step 17: Compute Add expression str(int(c3)) + ':' + str(c18) as a new column to Output dataset 'out_file1' from step 16 Round result? NO Skip a header line yes The new column name change_with_pos Avoid scientific notation no
Step 18: Replace File to process Output dataset 'out_file1' from step 17 Find pattern EFF[*]. Replace with Empty. Find-Pattern is a regular expression False Replace all occurences of the pattern True Case-Insensitive search False Find whole-words False Ignore first line False Find and Replace text in entire line
Step 19: Datamash Input tabular dataset Output dataset 'outfile' from step 18 Group by fields 3 Input file has a header line True Print header line True Sort input True Print all fields from input file False Ignore case when grouping False Operation to perform on each groups Operation to perform on each group 1 Type Count Unique values On column 1 Operation to perform on each group 2 Type minimum On column 8 Operation to perform on each group 3 Type maximum On column 8 Operation to perform on each group 4 Type Count Unique values On column 18 Operation to perform on each group 5 Type Count Unique values On column 12
Step 20: Filter Filter Output dataset 'outfile' from step 18 With following condition c4=='PASS' or c4=='.' Number of header lines to skip 1
Step 21: Datamash Input tabular dataset Output dataset 'outfile' from step 18 Group by fields 19 Input file has a header line True Print header line True Sort input True Print all fields from input file False Ignore case when grouping False Operation to perform on each groups Operation to perform on each group 1 Type Count Unique values On column 1 Operation to perform on each group 2 Type minimum On column 8 Operation to perform on each group 3 Type maximum On column 8 Operation to perform on each group 4 Type Combine all values On column 1 Operation to perform on each group 5 Type Combine all values On column 8
Step 22: Datamash Input tabular dataset Output dataset 'out_file1' from step 20 Group by fields 3 Input file has a header line True Print header line True Sort input True Print all fields from input file False Ignore case when grouping False Operation to perform on each groups Operation to perform on each group 1 Type Count Unique values On column 1
Step 23: Datamash Input tabular dataset Output dataset 'out_file1' from step 20 Group by fields 19 Input file has a header line True Print header line True Sort input True Print all fields from input file False Ignore case when grouping False Operation to perform on each groups Operation to perform on each group 1 Type Count Unique values On column 1
Step 24: Join 1st file Output dataset 'out_file1' from step 20 Column to use from 1st file 19 2nd File Output dataset 'out_file' from step 21 Column to use from 2nd file 1 Output lines appearing in Both 1st & 2nd file. First line is a header line True Ignore case False Value to put in unpaired (empty) fields 0
Step 25: Join 1st file Output dataset 'outfile' from step 18 Column to use from 1st file 3 2nd File Output dataset 'out_file' from step 22 Column to use from 2nd file 1 Output lines appearing in Both 1st & 2nd file. First line is a header line True Ignore case False Value to put in unpaired (empty) fields 0
Step 26: Join 1st file Output dataset 'out_file1' from step 17 Column to use from 1st file 19 2nd File Output dataset 'out_file' from step 23 Column to use from 2nd file 1 Output lines appearing in Both 1st & 2nd file. First line is a header line True Ignore case False Value to put in unpaired (empty) fields 0
Step 27: Datamash Input tabular dataset Output dataset 'output' from step 24 Group by fields 1 Input file has a header line True Print header line True Sort input True Print all fields from input file True Ignore case when grouping False Operation to perform on each groups Operation to perform on each group 1 Type Combine all unique values On column 2
Step 28: Join 1st file Output dataset 'output' from step 25 Column to use from 1st file 1 2nd File Output dataset 'out_file' from step 19 Column to use from 2nd file 1 Output lines appearing in Both 1st & 2nd file. First line is a header line True Ignore case False Value to put in unpaired (empty) fields 0
Step 29: Cut Cut columns c2,c3,c4,c5,c6,c7,c8,c9,c10,c11,c12,c13,c14,c15,c16,c17,c18 Delimited by Tab From Output dataset 'output' from step 26
Step 30: Cut Cut columns c4,c6,c7,c12,c13,c14,c15,c16,c17,c18,c20,c21,c22,c25,c23,c24,c19 Delimited by Tab From Output dataset 'out_file' from step 27
Step 31: Cut Cut columns c2,c1,c4,c5,c6,c7,c8,c10,c9,c11,c12,c13,c14,c15,c16,c17,c22,c23,c24,c25,c18 Delimited by Tab From Output dataset 'output' from step 28
Step 32: Select last Text file Output dataset 'out_file1' from step 29 Operation Keep everything from this line on Number of lines 2
Step 33: Select first File to select Output dataset 'out_file1' from step 29 Operation Keep first lines Number of lines 1
Step 34: Replace File to process Output dataset 'out_file1' from step 30 Find pattern unique$Sample$\tcollapse$Sample$\tcollapse$AF$ Replace with SAMPLES(above-thresholds)\tSAMPLES(all)\tAFs(all) Find-Pattern is a regular expression True Replace all occurences of the pattern True Case-Insensitive search False Find whole-words False Ignore first line False Find and Replace text in entire line
Step 35: Sort Sort Query Output dataset 'out_file1' from step 31 Number of header lines 1 Column selections Column selections 1 on column 1 in Ascending order Flavor Alphabetical sort Column selections 2 on column 2 in Ascending order Flavor Fast numeric sort (-n) Output unique values False Ignore case False
Step 36: Unknown Tool with id 'toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column/0.2'
Step 37: Sort Sort Query Output dataset 'outfile' from step 34 Number of header lines 1 Column selections Column selections 1 on column 1 in Ascending order Flavor General numeric sort ( scientific notation -g) Output unique values False Ignore case False
Step 38: Concatenate datasets Concatenate Dataset Output dataset 'outfile' from step 33 Datasets Dataset 1 Select Output dataset 'split_output' from step 36
Step 39: Variant Frequency Plot Variant lists data Output dataset 'out_file1' from step 38 Variant Frequency Threshold 0.0 Image Properties: Plot output format SVG Cell Ratio 0.67 Color palette used for the gene annotations Set3 Perform Clustering? Yes Number of clusters Not available. Clustering method ward.D2

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COVID-19: variation analysis reporting

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