Repository revision
10:2dae863c8f42

Repository 'split_file_to_collection'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection

Split file tool metadata
Miscellaneous
Split file
to dataset collection
split_file_to_collection
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
0.5.2
None
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.4.0
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.1.1
split_file_to_collection
Requirements (dependencies defined in the <requirements> tag set)
name version type
python 3.5 package
Additional information about this tool
mkdir ./out &&
        python '$__tool_directory__/split_file_to_collection.py'
            --out ./out
            --in '$split_parms.input'
            --ftype '$split_parms.select_ftype'
            #if $split_parms.select_ftype == "tabular":
                --top '$split_parms.top'
                --by '$split_parms.split_by.select_split_by'
                #if $split_parms.split_by.select_split_by == "col":
                    --id_column '$split_parms.split_by.id_col'
                    --match '$split_parms.split_by.match_regex'
                    --sub '$split_parms.split_by.sub_regex'
                #else
                    #if $split_parms.split_by.select_mode.mode == "numnew":
                        --numnew '$split_parms.split_by.select_mode.numnew'
                    #else
                        --chunksize $split_parms.split_by.select_mode.chunksize
                    #end if
                    #if $split_parms.split_by.select_allocate.allocate == "random":
                        --rand
                        --seed '$split_parms.split_by.rand.seed'
                    #end if
                    #if $split_parms.split_by.select_allocate.allocate == "batch":
                        --batch
                    #end if
                #end if
            #else
                #if $split_parms.select_ftype == "generic"
                    #if $split_parms.split_method.select_split_method == "regex"
                        --generic_re '$split_parms.split_method.generic_regex'
                        #if $split_parms.split_method.split_after == 'true':
                            --split_after
                        #end if
                    #else
                        --generic_num $split_parms.split_method.record_length
                    #end if
                #end if
                #if $split_parms.select_mode.mode == "numnew":
                    --numnew '$split_parms.select_mode.numnew'
                #else
                    --chunksize $split_parms.select_mode.chunksize
                #end if
                #if $split_parms.select_allocate.allocate == "random":
                    --rand
                    --seed '$split_parms.select_allocate.seed'
                #end if
                #if $split_parms.select_allocate.allocate == "batch":
                    --batch
                #end if
            #end if
        #if ($split_parms.select_ftype == "tabular" and $split_parms.split_by.select_split_by == "row"):
             --file_names '$split_parms.split_by.newfilenames'
             --file_ext '$split_parms.select_ftype'
        #end if
        #if $split_parms.select_ftype != "tabular":
            --file_names '$split_parms.newfilenames'
            #if $split_parms.select_ftype == "generic"
                --file_ext '$split_parms.input.ext'
            #else
                --file_ext '$split_parms.select_ftype'
            #end if
        #end if
None
False
Functional tests
name inputs outputs required files
Test-1 split_parms|input: test.tabular
split_parms|top: 2
split_parms|split_by|id_col: 1
split_parms|split_by|match_regex: (.*)\.mgf
split_parms|split_by|sub_regex: \1.tab
split_parms|split_by|select_split_by: col
split_parms|select_ftype: tabular
 test.tabular
Test-2 split_parms|input: test.tabular
split_parms|top: 2
split_parms|split_by|select_mode|numnew: 2
split_parms|split_by|select_mode|mode: numnew
split_parms|split_by|newfilenames: test
split_parms|split_by|select_split_by: row
split_parms|select_ftype: tabular
 test.tabular
Test-3 split_parms|input: test.tabular
split_parms|top: 2
split_parms|split_by|select_mode|numnew: 2
split_parms|split_by|select_mode|mode: numnew
split_parms|split_by|newfilenames: batch_tab
split_parms|split_by|select_allocate|allocate: batch
split_parms|split_by|select_split_by: row
split_parms|select_ftype: tabular
 test.tabular
Test-4 split_parms|input: test.tabular
split_parms|top: 2
split_parms|split_by|select_mode|chunksize: 2
split_parms|split_by|select_mode|mode: chunk
split_parms|split_by|newfilenames: batch_tab
split_parms|split_by|select_allocate|allocate: batch
split_parms|split_by|select_split_by: row
split_parms|select_ftype: tabular
 test.tabular
Test-5 split_parms|input: karyotype.txt
split_parms|select_mode|numnew: 24
split_parms|select_mode|mode: numnew
split_parms|newfilenames: chr
split_parms|select_allocate|allocate: batch
split_parms|select_ftype: txt
 karyotype.txt
Test-6 split_parms|input: psm.tabular
split_parms|top: 1
split_parms|split_by|id_col: 10
split_parms|split_by|match_regex: (.*)\.mgf
split_parms|split_by|sub_regex: \1.tab
split_parms|split_by|select_split_by: col
split_parms|select_ftype: tabular
 psm.tabular
Test-7 split_parms|input: demo758Dacentroid.mgf
split_parms|select_mode|numnew: 3
split_parms|select_mode|mode: numnew
split_parms|newfilenames: demo
split_parms|select_ftype: mgf
 demo758Dacentroid.mgf
Test-8 split_parms|input: test.fasta
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: test
split_parms|select_ftype: fasta
 test.fasta
Test-9 split_parms|input: test.fasta
split_parms|select_mode|chunksize: 3
split_parms|select_mode|mode: chunk
split_parms|newfilenames: test
split_parms|select_ftype: fasta
 test.fasta
Test-10 split_parms|input: test.fastq
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: test
split_parms|select_ftype: fastq
 test.fastq
Test-11 split_parms|input: test.fastq
split_parms|split_method|record_length: 4
split_parms|split_method|select_split_method: number
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: test
split_parms|select_ftype: generic
 test.fastq
Test-12 split_parms|input: test.fasta
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: rand
split_parms|select_allocate|seed: 1010
split_parms|select_allocate|allocate: random
split_parms|select_ftype: fasta
 test.fasta
Test-13 split_parms|input: test.fasta
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: fasta_batch
split_parms|select_allocate|allocate: batch
split_parms|select_ftype: fasta
 test.fasta
Test-14 split_parms|input: test.tabular
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: test
split_parms|select_ftype: txt
 test.tabular
Test-15 split_parms|input: test.tabular
split_parms|split_method|generic_regex: ^.*
split_parms|split_method|select_split_method: regex
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: test
split_parms|select_ftype: generic
 test.tabular
Test-16 split_parms|input: test.fasta
split_parms|split_method|generic_regex: ^>.*
split_parms|split_method|select_split_method: regex
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: rand
split_parms|select_allocate|seed: 1010
split_parms|select_allocate|allocate: random
split_parms|select_ftype: generic
 test.fasta
Test-17 split_parms|input: 3_molecules.sdf
split_parms|select_mode|numnew: 10
split_parms|select_mode|mode: numnew
split_parms|newfilenames: mol
split_parms|select_allocate|allocate: batch
split_parms|select_ftype: sdf
 3_molecules.sdf
Test-18 split_parms|input: 3_molecules.sdf
split_parms|select_mode|chunksize: 1
split_parms|select_mode|mode: chunk
split_parms|newfilenames: mol
split_parms|select_allocate|allocate: batch
split_parms|select_ftype: sdf
 3_molecules.sdf
Test-19 split_parms|input: test.fasta
split_parms|split_method|generic_regex: ^[^>].*
split_parms|split_method|split_after: true
split_parms|split_method|select_split_method: regex
split_parms|select_mode|numnew: 2
split_parms|select_mode|mode: numnew
split_parms|newfilenames: rand
split_parms|select_allocate|seed: 1010
split_parms|select_allocate|allocate: random
split_parms|select_ftype: generic
 test.fasta
Test-20 split_parms|input: test.tabular
split_parms|top: 2
split_parms|split_by|select_mode|chunksize: 1
split_parms|split_by|select_mode|mode: chunk
split_parms|split_by|select_allocate|allocate: batch
split_parms|split_by|select_split_by: row
split_parms|select_ftype: tabular
 test.tabular