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Repository revision

Revision: 17:73d82de36369

Repository 'camera_annotate'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate

CAMERA.annotate tool metadata

Miscellaneous

Name: CAMERA.annotate

Description: CAMERA annotate function. Returns annotation results (isotope peaks, adducts and fragments) and a diffreport if more than one condition.

Id: abims_CAMERA_annotateDiffreport

Guid: toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.4

Version: 2.2.4

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/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.5

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.4 (this tool)

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.3

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.2

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.1

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.2.0

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.5

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.3

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.1.0

toolshed.g2.bx.psu.edu/repos/lecorguille/camera_annotate/abims_CAMERA_annotateDiffreport/2.0.1

abims_CAMERA_annotateDiffreport

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

Requirements:

name

version

type

r-snow

0.4_2

package

bioconductor-xcms

3.0.0

package

bioconductor-camera

1.34.0

package

bioconductor-multtest

2.28.0

package

r-batch

1.1_4

package

graphicsmagick

1.3.23

package

Functional tests

name

inputs

outputs

required files

Test-1

findisotopes|maxcharge: 3
image: faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData
findgeneral|mzabs: 0.015
export|numDigitsRT: 1
findisotopes|maxiso: 4
groupfwhm|sigma: 6
findgeneral|ppm: 5
diffreport|options|value: into
export|convertRTMinute: True
file_load_section|file_load_conditional|file_load_select: yes
findisotopes|minfrac: 0.5
diffreport|options|h: 480
diffreport|options|option: show
groupfwhm|perfwhm: 0.6
diffreport|options|sortpval: False
export|intval: into
diffreport|options|w: 640
diffreport|options|eicwidth: 200
export|numDigitsMZ: 4
diffreport|options|mzdec: 2
quick_block|quick: TRUE
diffreport|options|eicmax: 200
file_load_section|file_load_conditional|input: ['wt15.CDF', 'ko16.CDF', 'ko15.CDF', 'wt16.CDF']

attributes: name

faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData
wt15.CDF
ko16.CDF
ko15.CDF
wt16.CDF
name

Test-2

findisotopes|maxcharge: 3
image: faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData
findgeneral|mzabs: 0.015
export|numDigitsRT: 1
findisotopes|maxiso: 4
groupfwhm|sigma: 6
findgeneral|ppm: 5
diffreport|options|value: into
export|convertRTMinute: True
file_load_section|file_load_conditional|file_load_select: yes
findisotopes|minfrac: 0.5
diffreport|options|h: 480
diffreport|options|option: show
groupfwhm|perfwhm: 0.6
diffreport|options|sortpval: False
export|intval: into
diffreport|options|w: 640
diffreport|options|eicwidth: 200
export|numDigitsMZ: 4
diffreport|options|mzdec: 2
quick_block|quick: TRUE
diffreport|options|eicmax: 200
file_load_section|file_load_conditional|input: ['wt15.CDF', 'ko16.CDF', 'ko15.CDF', 'wt16.CDF']

attributes: name

faahKO-single.xset.merged.group.retcor.group.fillpeaks-xcms3.RData
wt15.CDF
ko16.CDF
ko15.CDF
wt16.CDF
name

Test-3

findisotopes|maxcharge: 3
image: faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData
findgeneral|mzabs: 0.015
export|numDigitsRT: 1
quick_block|findadducts|polarity: negative
findisotopes|maxiso: 4
groupfwhm|sigma: 6
quick_block|groupcorr|calcCiS: True
findgeneral|ppm: 5
diffreport|options|value: into
export|convertRTMinute: True
file_load_section|file_load_conditional|file_load_select: yes
findisotopes|minfrac: 0.5
quick_block|groupcorr|cor_eic_th: 0.75
diffreport|options|h: 480
quick_block|groupcorr|pval: 0.05
quick_block|groupcorr|graphMethod: hcs
quick_block|groupcorr|calcIso: False
diffreport|options|option: show
groupfwhm|perfwhm: 0.6
quick_block|findadducts|rules_block|rules_select: TRUE
diffreport|options|sortpval: False
export|numDigitsMZ: 4
diffreport|options|w: 640
diffreport|options|eicwidth: 200
export|intval: into
quick_block|groupcorr|calcCaS: False
diffreport|options|mzdec: 2
quick_block|quick: FALSE
diffreport|options|eicmax: 200
file_load_section|file_load_conditional|input: ['wt15.CDF', 'ko16.CDF', 'ko15.CDF', 'wt16.CDF']
quick_block|findadducts|rules_block|rules: CASMI_extended_NEG_rules.csv

attributes: name

faahKO-single.xset.merged.group.retcor.group.fillpeaks.RData
CASMI_extended_NEG_rules.csv
wt15.CDF
ko16.CDF
ko15.CDF
wt16.CDF
name