Allsorts¶
Allsorts
· 2 contributors · 1 version
- usage: ALLSorts [-h] -samples SAMPLES [-labels LABELS]
- [-destination DESTINATION] [-test] [-train] [-model_dir MODEL_DIR] [-njobs NJOBS] [-cv CV] [-verbose] [-comparison] [-force] [-parents]
ALLSorts CLI
Quickstart¶
from janis_bioinformatics.tools.oshlack.allsorts.versions import AllSorts_0_1_0 wf = WorkflowBuilder("myworkflow") wf.step( "allsorts_step", AllSorts_0_1_0( samples=None, ) ) wf.output("out_predictions", source=allsorts_step.out_predictions) wf.output("out_probabilities", source=allsorts_step.out_probabilities) wf.output("out_distributions", source=allsorts_step.out_distributions) wf.output("out_waterfalls", source=allsorts_step.out_waterfalls)
OR
- Install Janis
- Ensure Janis is configured to work with Docker or Singularity.
- Ensure all reference files are available:
Note
More information about these inputs are available below.
- Generate user input files for Allsorts:
# user inputs
janis inputs Allsorts > inputs.yaml
inputs.yaml
samples: samples.csv
- Run Allsorts with:
janis run [...run options] \
--inputs inputs.yaml \
Allsorts
Information¶
ID: | Allsorts |
---|---|
URL: | No URL to the documentation was provided |
Versions: | v0.1.0 |
Container: | breons/allsorts:0.1.0 |
Authors: | Michael Franklin, Jiaan Yu |
Citations: | None |
Created: | 2020-09-02 |
Updated: | 2020-09-11 |
Outputs¶
name | type | documentation |
---|---|---|
out_predictions | csv | |
out_probabilities | csv | |
out_distributions | File | |
out_waterfalls | File |
Additional configuration (inputs)¶
name | type | prefix | position | documentation |
---|---|---|---|---|
samples | csv | -samples | (-s) Path to samples (rows) x genes (columns) csv file representing a raw counts matrix. Note: hg19 only supported currently, use other references at own risk. | |
labels | Optional<csv> | -labels | (-l) (Optional) Path to samples true labels. CSV with samples (rows) x [sample id, label] (cols). This will enable re-labelling mode. Note: labels must reflect naming conventions used within this tool. View the ALLSorts GitHub Wiki for further details. | |
destination | Optional<String> | -destination | (-d) Path to where you want the final report to be saved. | |
verbose | Optional<Boolean> | -verbose | (-v) (flag, default=False) Verbose. Print stage progress. | |
comparison | Optional<Boolean> | -comparison | Rebuild comparisons for labelled visualisations. | |
force | Optional<Boolean> | -force | (-f) (flag, default=False) Force. Bypass warnings without user confirmation. | |
parents | Optional<Boolean> | -parents | (-p) Include parent meta-subtypes in predictions. Note: This may remove previously unclassified samples. |
Workflow Description Language¶
version development
task Allsorts {
input {
Int? runtime_cpu
Int? runtime_memory
Int? runtime_seconds
Int? runtime_disks
File samples
File? labels
String? destination
Boolean? verbose
Boolean? comparison
Boolean? force
Boolean? parents
}
command <<<
set -e
ALLSorts \
-samples '~{samples}' \
~{if defined(labels) then ("-labels '" + labels + "'") else ""} \
~{if defined(select_first([destination, "."])) then ("-destination '" + select_first([destination, "."]) + "'") else ""} \
~{if (defined(verbose) && select_first([verbose])) then "-verbose" else ""} \
~{if (defined(comparison) && select_first([comparison])) then "-comparison" else ""} \
~{if (defined(force) && select_first([force])) then "-force" else ""} \
~{if (defined(parents) && select_first([parents])) then "-parents" else ""}
>>>
runtime {
cpu: select_first([runtime_cpu, 1])
disks: "local-disk ~{select_first([runtime_disks, 20])} SSD"
docker: "breons/allsorts:0.1.0"
duration: select_first([runtime_seconds, 86400])
memory: "~{select_first([runtime_memory, 4])}G"
preemptible: 2
}
output {
File out_predictions = glob("predictions.csv")[0]
File out_probabilities = glob("probabilities.csv")[0]
File out_distributions = glob("distributions.png")[0]
File out_waterfalls = glob("waterfalls.png")[0]
}
}
Common Workflow Language¶
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.2
label: Allsorts
doc: |
usage: ALLSorts [-h] -samples SAMPLES [-labels LABELS]
[-destination DESTINATION] [-test] [-train]
[-model_dir MODEL_DIR] [-njobs NJOBS] [-cv CV] [-verbose]
[-comparison] [-force] [-parents]
ALLSorts CLI
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
- class: DockerRequirement
dockerPull: breons/allsorts:0.1.0
inputs:
- id: samples
label: samples
doc: |-
(-s) Path to samples (rows) x genes (columns) csv file representing a raw counts matrix. Note: hg19 only supported currently, use other references at own risk.
type: File
inputBinding:
prefix: -samples
separate: true
- id: labels
label: labels
doc: |-
(-l) (Optional) Path to samples true labels. CSV with samples (rows) x [sample id, label] (cols). This will enable re-labelling mode. Note: labels must reflect naming conventions used within this tool. View the ALLSorts GitHub Wiki for further details.
type:
- File
- 'null'
inputBinding:
prefix: -labels
separate: true
- id: destination
label: destination
doc: (-d) Path to where you want the final report to be saved.
type: string
default: .
inputBinding:
prefix: -destination
separate: true
- id: verbose
label: verbose
doc: (-v) (flag, default=False) Verbose. Print stage progress.
type:
- boolean
- 'null'
inputBinding:
prefix: -verbose
separate: true
- id: comparison
label: comparison
doc: Rebuild comparisons for labelled visualisations.
type:
- boolean
- 'null'
inputBinding:
prefix: -comparison
separate: true
- id: force
label: force
doc: (-f) (flag, default=False) Force. Bypass warnings without user confirmation.
type:
- boolean
- 'null'
inputBinding:
prefix: -force
separate: true
- id: parents
label: parents
doc: |-
(-p) Include parent meta-subtypes in predictions. Note: This may remove previously unclassified samples.
type:
- boolean
- 'null'
inputBinding:
prefix: -parents
separate: true
outputs:
- id: out_predictions
label: out_predictions
type: File
outputBinding:
glob: predictions.csv
loadContents: false
- id: out_probabilities
label: out_probabilities
type: File
outputBinding:
glob: probabilities.csv
loadContents: false
- id: out_distributions
label: out_distributions
type: File
outputBinding:
glob: distributions.png
loadContents: false
- id: out_waterfalls
label: out_waterfalls
type: File
outputBinding:
glob: waterfalls.png
loadContents: false
stdout: _stdout
stderr: _stderr
baseCommand:
- ALLSorts
arguments: []
hints:
- class: ToolTimeLimit
timelimit: |-
$([inputs.runtime_seconds, 86400].filter(function (inner) { return inner != null })[0])
id: Allsorts