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ConcatPhyl tool metadata

Miscellaneous

Name: ConcatPhyl

Description: Concatenation and phylogeny

Id: concatphyl

Guid: toolshed.g2.bx.psu.edu/repos/abims-sbr/concatphyl/concatphyl/2.0.2

Version: 2.0.2

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/abims-sbr/concatphyl/concatphyl/2.0.2 (this tool)

concatphyl

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

Requirements:

name

version

type

python

2.7

package

raxml

8.2.9

package

Functional tests

name

inputs

outputs

required files

Test-1

rapid_bootstrap_random_seed: 123456789
random_seed: 1234567890
format|base_model: GTRGAMMA
input_alignments: ['input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta', 'input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta', 'input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta', 'input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta']
input_filter_assemblies: ['input_filter_assemblies/AcAcaud_trinity.fasta', 'input_filter_assemblies/AmAmphi_trinity.fasta', 'input_filter_assemblies/ApApomp_trinity.fasta', 'input_filter_assemblies/PgPgras_trinity.fasta', 'input_filter_assemblies/PhPhess_trinity.fasta', 'input_filter_assemblies/ThThelep_trinity.fasta']
raxml1: True
raxml3: True
raxml4: True
format|format_run: nucleic
number_of_runs: 100
number_of_runs_bootstop:
search_algorithm: d
out: nothing

attributes: name

input_filter_assemblies/AcAcaud_trinity.fasta
input_filter_assemblies/AmAmphi_trinity.fasta
input_filter_assemblies/ApApomp_trinity.fasta
input_filter_assemblies/PgPgras_trinity.fasta
input_filter_assemblies/PhPhess_trinity.fasta
input_filter_assemblies/ThThelep_trinity.fasta
input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta
input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta
input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta
input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta
name

Test-2

rapid_bootstrap_random_seed: 1234567890
random_seed: 1234567890
format|base_model: GTRGAMMA
input_alignments: ['input_from_CDS_Search/orthogroup_17_sp3_sp3.fasta', 'input_from_CDS_Search/orthogroup_147_sp3_sp3.fasta', 'input_from_CDS_Search/orthogroup_183_sp3_sp3.fasta', 'input_from_CDS_Search/orthogroup_334_sp3_sp3.fasta']
input_filter_assemblies: ['input_filter_assemblies/AcAcaud_trinity.fasta', 'input_filter_assemblies/AmAmphi_trinity.fasta', 'input_filter_assemblies/ApApomp_trinity.fasta', 'input_filter_assemblies/PgPgras_trinity.fasta', 'input_filter_assemblies/PhPhess_trinity.fasta', 'input_filter_assemblies/ThThelep_trinity.fasta']
raxml1: True
raxml3: True
raxml4: True
format|format_run: nucleic
number_of_runs: 100
number_of_runs_bootstop:
search_algorithm: a
out: nothing

attributes: name
attributes: name

Test-3

attributes: name
attributes: name