Skip to content

Add files for the examles in user guide #51

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
Dec 12, 2017
Merged

Add files for the examles in user guide #51

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Empty file added _includes/cwl/03-input/whale.txt
View file
Open in desktop
Empty file.
Binary file added _includes/cwl/04-output/hello.tar
View file
Open in desktop
Binary file not shown.
Binary file added _includes/cwl/06-params/hello.tar
View file
Open in desktop
Binary file not shown.
18 changes: 18 additions & 0 deletions _includes/cwl/20-software-requirements/InterProScan-apps.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
type: enum
name: apps
symbols:
- TIGRFAM
- SFLD
- SUPERFAMILY
- Gene3D
- Hamap
- Coils
- ProSiteProfiles
- SMART
- CDD
- PRINTS
- PIRSF
- ProSitePatterns
- Pfam
- ProDom
- MobiDBLite
3 changes: 3 additions & 0 deletions _includes/cwl/20-software-requirements/custom-types.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,3 @@
proteinFile:
class: File
path: test_proteins.fasta
34 changes: 34 additions & 0 deletions _includes/cwl/20-software-requirements/test_proteins.fasta
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@
>Q97R95
MKYKRIVFKVGTSSLTNEDGSLSRSKVKDITQQLAMLHEAGHELILVSSGAIAAGFGALG
FKKRPTKIADKQASAAVGQGLLLEEYTTNLLLRQIVSAQILLTQDDFVDKRRYKNAHQAL
SVLLNRGAIPIINENDSVVIDELKVGDNDTLSAQVAAMVQADLLVFLTDVDGLYTGNPNS
DPRAKRLERIETINREIIDMAGGAGSSNGTGGMLTKIKAATIATESGVPVYICSSLKSDS
MIEAAEETEDGSYFVAQEKGLRTQKQWLAFYAQSQGSIWVDKGAAEALSQYGKSLLLSGI
VEAEGVFSYGDIVTVFDKESGKSLGKGRVQFGASALEDMLRSQKAKGVLIYRDDWISITP
EIQLLFTEF
>A2VDN9
MEVKGKKKLTGKGTKMSQEKSKFHKNNDSGSSKTFPKKVVKEGGPKITSKNFEKTATKPGKKGVKQFKNKQQGDRIPKNK
FQQANKFNQKRKFQPDSKSDESAAKKPKWDEFKKKKKELKQSRQLSDKTNYDIVIRAKQIWEILRRKDCDKEKRVKLMSD
LQKLIQGKIKTIAFAHDSTRVIQCYIQFGNEEQRKQAFEELRGDLVELSKAKYSRNIVKKFLMYGSKAQIAEIIRSFKGH
VRKLLRHAEASAIVEYAYNDKAILEQRNMLTEELYGNTFQLYKSADHPTLDKVLEVQPEKLELIMDEMKQILTPMAQKEA
VIKHSLVHKVFLDFFTYAPPKLRSEMIEAIREAVVYLAHTHDGARVAMYCLWHGTPKDRKVIVKTMKTYIEKVANGQYSH
LVLLAAFDCIDDTKLVKQIIISEIINSLPNIVNDKYGRKVLLYLLSPRDPAHTVREIIEVLQKGDGNAHSKKDTEIRRRE
LLESISPALLSYLQGHAQEVVLDKSACVLVADILGTATGDVQPAMDAVASLAAAELHPGGKDGELHIAEHPAGHLVLKWL
IEQDKKMKERGREGCFAKTLIERVGVKNLKSWASVNRGAIILSSLLQSSDQEVANKVKAGLKSLIPALEKSKNTSKGIEM
LLEKLTA
>A2YIW7
MAAEEGVVIACHNKDEFDAQMTKAKEAGKVVIIDFTASWCGPCRFIAPVFAEYAKKFPGAVFLKVDVDELKEVAEKYNVE
AMPTFLFIKDGAEADKVVGARKDDLQNTIVKHVGATAASASA
>P22298
GRGLLPFVLLALGIXAPWAVEGAENALKGGACPPRKIVQCLRYEKPKCTSDWQCPDKKKC
CRDTCAIKCLNPVAITNPVKVKPGKCPVVYGQCMMLNPPNHCKTDSQCLGDLKCCKSMCG
KVCLTPVKA
>A0B6J9
MSKIGKSIRLERIIDRKTRKTVIVPMDHGLTVGPIPGLIDLAAAVDKVAEGGANAVLGHM
GLPLYGHRGYGKDVGLIIHLSASTSLGPDANHKVLVTRVEDAIRVGADGVSIHVNVGAED
EAEMLRDLGMVARRCDLWGMPLLAMMYPRGAKVRSEHSVEYVKHAARVGAELGVDIVKTN
YTGSPETFREVVRGCPAPVVIAGGPKMDTEADLLQMVYDAMQAGAAGISIGRNIFQAENP
TLLTRKLSKIVHEGYTPEEAARLKL
>P02939
MNRTKLVLGAVILGSTLLAGCSSNAKIDQLSTDVQTLNAKVDQLSNDVTAIRSDVQAAKD
DAARANQRLDNQAHSYRK
21 changes: 21 additions & 0 deletions _includes/cwl/21-1st-workflow/arguments.cwl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
label: Example trivial wrapper for Java 7 compiler
hints:
DockerRequirement:
dockerPull: java:7-jdk
baseCommand: javac
arguments: ["-d", $(runtime.outdir)]
inputs:
src:
type: File
inputBinding:
position: 1
outputs:
classfile:
type: File
outputBinding:
glob: "*.class"

Binary file added _includes/cwl/21-1st-workflow/hello.tar
View file
Open in desktop
Binary file not shown.
19 changes: 19 additions & 0 deletions _includes/cwl/21-1st-workflow/tar-param.cwl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [tar, xf]
inputs:
tarfile:
type: File
inputBinding:
position: 1
extractfile:
type: string
inputBinding:
position: 2
outputs:
example_out:
type: File
outputBinding:
glob: $(inputs.extractfile)
26 changes: 26 additions & 0 deletions _includes/cwl/22-nested-workflows/1st-workflow.cwl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: Workflow
inputs:
inp: File
ex: string

outputs:
classout:
type: File
outputSource: compile/classfile

steps:
untar:
run: tar-param.cwl
in:
tarfile: inp
extractfile: ex
out: [example_out]

compile:
run: arguments.cwl
in:
src: untar/example_out
out: [classfile]
21 changes: 21 additions & 0 deletions _includes/cwl/22-nested-workflows/arguments.cwl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
label: Example trivial wrapper for Java 7 compiler
hints:
DockerRequirement:
dockerPull: java:7-jdk
baseCommand: javac
arguments: ["-d", $(runtime.outdir)]
inputs:
src:
type: File
inputBinding:
position: 1
outputs:
classfile:
type: File
outputBinding:
glob: "*.class"

19 changes: 19 additions & 0 deletions _includes/cwl/22-nested-workflows/tar-param.cwl
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,19 @@
#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [tar, xf]
inputs:
tarfile:
type: File
inputBinding:
position: 1
extractfile:
type: string
inputBinding:
position: 2
outputs:
example_out:
type: File
outputBinding:
glob: $(inputs.extractfile)