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Thermo tool metadata

Miscellaneous

Name: Thermo

Description: RAW file converter

Id: thermo_raw_file_converter

Guid: toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.3.4+galaxy0

Version: 1.3.4+galaxy0

Version command string: ThermoRawFileParser.sh --version

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.3.4+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.3.3+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.3.2+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.2.3+galaxy0

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.2.3

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.1.10

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.1.2

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/1.1.0

toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter/0.0.1

thermo_raw_file_converter

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

Requirements:

name

version

type

thermorawfileparser

1.3.4

package

Additional information about this tool

Command:

#import re

#set $input_name = re.sub('[^\w\-\.]', '_', $input_file.element_identifier.replace(".raw", "") + ".raw")
ln -s -f '$input_file' '$input_name' &&

ThermoRawFileParser.sh
    --input='$input_name'
    --output_file='$output'
    -f=$format_cond.output_format
    #if $output_metadata_selector != "off":
        --metadata="$output_metadata_selector"
        --metadata_output_file='$output_metadata'
    #end if
    #if $format_cond.output_format == "0"
        $format_cond.mgfPrecursor
    #end if
    #if $format_cond.output_format in ['1', '2']
        $format_cond.zlib_boolean
        $format_cond.peakpicking_boolean
    #end if
    $ignore_instrument_errors_boolean
    $allDetectors
    $includeExceptionData
    #if $msLevel != ''
        --msLevel="$msLevel"
    #end if

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

input_file: really_small.raw
format_cond|mgfPrecursor: True
format_cond|output_format: 0

name: value

really_small.raw
value

Test-2

input_file: really_small.raw
format_cond|output_format: 1
output_metadata_selector: 0

name: value
name: value

really_small.raw
value

Test-3

input_file: really_small.raw
format_cond|zlib_boolean: False
format_cond|peakpicking_boolean: False
format_cond|output_format: 1
output_metadata_selector: 0

name: value
name: value

really_small.raw
value

Test-4

input_file: really_small.raw
format_cond|output_format: 2
output_metadata_selector: 1
ignore_instrument_errors_boolean: True
allDetectors: True
includeExceptionData: True
msLevel: 1

name: value
name: value

really_small.raw
value