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Repository revision

Revision: 3:7861f3b10c68

Repository 'fastq_manipulation'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation

Manipulate FASTQ tool metadata

Miscellaneous

Name: Manipulate FASTQ

Description: reads on various attributes

Id: fastq_manipulation

Guid: toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1

Version: 1.1.1

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.5

toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.1.1 (this tool)

toolshed.g2.bx.psu.edu/repos/devteam/fastq_manipulation/fastq_manipulation/1.0.1

fastq_manipulation

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

galaxy_sequence_utils

1.1.1

package

Functional tests

name

inputs

outputs

required files

Test-1

manipulate_blocks_0|manipulation_type|manipulation|from:
match_blocks_0|match_type|match|match_selector: regex
input_file: sanger_full_range_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: translate
manipulate_blocks_0|manipulation_type|manipulation|to:
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: identifier

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-2

manipulate_blocks_0|manipulation_type|manipulation|from:
match_blocks_0|match_type|match|match_selector: regex
input_file: sanger_full_range_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: STRINGDOESNOTEXIST
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: translate
manipulate_blocks_0|manipulation_type|manipulation|to:
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: identifier

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-3

input_file: sanger_full_range_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: remove
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: miscellaneous

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-4

input_file: sanger_full_range_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: STRINGDOESNOTEXIST
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: remove
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: miscellaneous

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-5

match_blocks_0|match_type|match_type_selector: identifier
input_file: sanger_full_range_original_sanger.fastqsanger
manipulate_blocks_0|manipulation_type|manipulation|offset_type|left_column_offset: 45
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: trim
match_blocks_0|match_type|match|match_selector: regex
manipulate_blocks_0|manipulation_type|manipulation|keep_zero_length: True
manipulate_blocks_0|manipulation_type|manipulation|offset_type|base_offset_type: offsets_absolute
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence
manipulate_blocks_0|manipulation_type|manipulation|offset_type|right_column_offset: 45

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-6

match_blocks_0|match_type|match_type_selector: identifier
input_file: sanger_full_range_original_sanger.fastqsanger
manipulate_blocks_0|manipulation_type|manipulation|offset_type|left_column_offset: 47.87
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: trim
match_blocks_0|match_type|match|match_selector: regex
manipulate_blocks_0|manipulation_type|manipulation|keep_zero_length: True
manipulate_blocks_0|manipulation_type|manipulation|offset_type|base_offset_type: offsets_percent
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence
manipulate_blocks_0|manipulation_type|manipulation|offset_type|right_column_offset: 47.87

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-7

input_file: sanger_full_range_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: rev_comp
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-8

input_file: misc_dna_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: rev_comp
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

misc_dna_original_sanger.fastqsanger
name

Test-9

input_file: misc_rna_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: rev_comp
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

misc_rna_original_sanger.fastqsanger
name

Test-10

input_file: sanger_full_range_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: FAKE0001
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: rev_comp
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-11

input_file: sanger_full_range_rev_comp_1_seq.fastqsanger
match_blocks_0|match_type|match|match_by: FAKE0001
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: rev_comp
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

sanger_full_range_rev_comp_1_seq.fastqsanger
name

Test-12

input_file: sanger_full_range_original_sanger.fastqsanger
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: dna_to_rna
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

sanger_full_range_original_sanger.fastqsanger
name

Test-13

input_file: sanger_full_range_as_rna.fastqsanger
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: rna_to_dna
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

sanger_full_range_as_rna.fastqsanger
name

Test-14

input_file: sanger_full_range_as_rna.fastqsanger.gz
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: rna_to_dna
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

sanger_full_range_as_rna.fastqsanger.gz
name

Test-15

input_file: sanger_full_range_as_rna.fastqsanger.bz2
match_blocks_0|match_type|match|match_by: .*
manipulate_blocks_0|manipulation_type|manipulation|manipulation_selector: rna_to_dna
match_blocks_0|match_type|match|match_selector: regex
match_blocks_0|match_type|match_type_selector: identifier
manipulate_blocks_0|manipulation_type|manipulation_type_selector: sequence

attributes: name

sanger_full_range_as_rna.fastqsanger.bz2
name