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cuffcompare_1.3.0.yaml
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cuffcompare_1.3.0.yaml
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!mobyle/program
name: cuffcompare
version: 1.3.0
title: Cuffcompare
description: 'Cuffcompare helps you: (a) compare your assembled transcripts to a reference
annotation and (b) track Cufflinks transcripts across multiple experiments (e.g.
across a time course)'
authors: Trapnell C., Williams B.A., Pertea G., Mortazavi A.M., Kwan G., van Baren
M.J., Salzberg S.L., Wold B. & Pachter L.
inputs: !mobyle/inputparagraph
children:
- !mobyle/inputprogramparameter
prompt: Initial Command
format: '"cuffcompare"'
argpos: 0
name: cufflinks_cmd
command: true
hidden: true
type: !mobyle/stringtype {}
- !mobyle/inputprogramparagraph
prompt: Input
name: input1
argpos: 2
children:
- !mobyle/inputprogramparameter
prompt: Input file format (-G)
format: ("", " -G " + str(value)) [value is not None and value != vdef]
simple: true
name: file_format
command: false
type: !mobyle/stringtype
default: 'null'
options:
- {label: Cufflinks GTF, value: 'null'}
- {label: Generic GFF, value: -G}
- !mobyle/inputprogramparameter
prompt: Input data (GTF or GFF format)
format: '" " + str( value )'
simple: true
argpos: 10
mandatory: true
name: input_0
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
prompt: Input data 2 (GTF or GFF format)
format: (""," " + str( value ))[value is not None]
simple: true
argpos: 11
name: input_1
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
prompt: A multi-fasta file with all the genomic sequences (-s)
format: ('', ' -s ' + str(value))[value is not None]
name: seq_path
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
prompt: File containing a list of GTF files to process (-i)
format: ('', ' -i ' + str(value))[value is not None]
name: file_list
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/inputprogramparagraph
prompt: Reference mRNA options
name: reference_options
argpos: 1
children:
- !mobyle/inputprogramparameter
comment: An optional "reference" annotation GTF.
prompt: Select Reference Annotation(-r)
format: (""," -r " + str(value))[value is not None and value != "upload"]
simple: true
mandatory: true
name: refernce_annotation
command: false
type: !mobyle/stringtype
default: 'null'
options:
- {label: Choose a genome annotation, value: 'null'}
- !mobyle/inputprogramparameter
comment: A set of known mRNAs to use as a reference for assessing the
accuracy of mRNAs or gene models given in input GTF/GFF file(s).Each
sample is matched against this file, and sample isoforms are tagged
as overlapping, matching, or novel where appropriate
prompt: Reference mRNA regions (GFF format) (-r)
format: ("", " -r " + str(value)) [value is not None]
simple: true
argpos: 1
mandatory: true
name: reference_region
precond: {refernce_annotation: upload}
command: false
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/inputprogramparameter
comment: Enables the "contained" transcripts to be also written in the
<outprefix>.combined.gtffile, with the attribute "contained_in" showing
the first container transfrag found. By default, without this option,
cuffcompare does not write in that file isoforms that were found to
be fully contained/covered (with the same compatible intron structure)
by other transfrags in the same locus.
prompt: Restrict results to reference mRNA regions overlapping input Cufflinks
GTF file (-R)
format: ("", " -R")[value]
argpos: 2
name: restrict_result
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Do not generate .tmap and .refmap files for each input file (-T)
format: ("", " -T")[value]
argpos: 3
name: suppress_map
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Verbose processing mode (showing all GFF parsing warnings) (-V)
format: ("", " -V")[value]
argpos: 4
name: verbose_mode
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparagraph
prompt: Options
name: Options
argpos: 5
children:
- !mobyle/inputprogramparameter
prompt: Ignore single-exon transfrags and reference transcripts (-M)
format: ("", " -M")[value]
name: discard_1
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Ignore single-exon reference transcripts (-N)
format: ("", " -N")[value]
name: discard_2
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: 'Maximum distance (range) for grouping transcript start sites
(-d):'
format: ("", " -d" + str(value)) [value is not None and value != vdef]
name: max_distance
command: false
type: !mobyle/integertype {default: 100}
- !mobyle/inputprogramparagraph
prompt: Output
name: Output
argpos: 7
children:
- !mobyle/inputprogramparameter
comment: Enables the "contained" transcripts to be also written in the
<outprefix>.combined.gtffile, with the attribute "contained_in" showing
the first container transfrag found. By default, without this option,
cuffcompare does not write in that file isoforms that were found to
be fully contained/covered (with the same compatible intron structure)
by other transfrags in the same locus.
prompt: Include the "contained" transcripts in the .combined.gtf file
(-C)
format: ("", " -C")[value]
simple: true
name: include_contained
command: false
type: !mobyle/booleantype {default: false}
- !mobyle/inputprogramparameter
prompt: Enter output prefix name (-o)
format: (" -o " + str(vdef) , " -o " + str(value))[value is not None]
simple: true
argpos: 9
name: output_0
command: false
type: !mobyle/stringtype {default: cuff_results}
outputs: !mobyle/outputparagraph
children:
- !mobyle/outputprogramparagraph
prompt: Output
name: Output
argpos: 7
children:
- !mobyle/outputprogramparameter
prompt: GTF map
filenames: str(output_0)+"."+str(input_0)+".tmap"
name: map_outfile
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Combined GTF out
filenames: str(output_0)+".combined.gtf"
name: combined_gtf
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Loci file
filenames: str(output_0)+".loci"
name: loci_file
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2044']
- !mobyle/outputprogramparameter
prompt: Stats report
filenames: str(output_0)+".stats"
name: stats_file
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Tracking file
filenames: str(output_0)+".tracking"
name: tracking_file
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard output
filenames: '"cuffcompare.out"'
name: stdout
output_type: stdout
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
- !mobyle/outputprogramparameter
prompt: Standard error
filenames: '"cuffcompare.err"'
name: stderr
type: !mobyle/formattedtype
data_terms: ['EDAM_data:2048']
env: {}