Merge pull request #51 from tom-tan/add-files-for-examples

mr-c · web-flow · commit bdc352fc82b4 · 2017-12-12T09:55:03.000+02:00
Add files for the examles in user guide
diff --git a/_includes/cwl/03-input/whale.txt b/_includes/cwl/03-input/whale.txt
diff --git a/_includes/cwl/04-output/hello.tar b/_includes/cwl/04-output/hello.tar
diff --git a/_includes/cwl/06-params/hello.tar b/_includes/cwl/06-params/hello.tar
diff --git a/_includes/cwl/20-software-requirements/InterProScan-apps.yml b/_includes/cwl/20-software-requirements/InterProScan-apps.yml
@@ -0,0 +1,18 @@
+type: enum
+name: apps
+symbols:
+ - TIGRFAM
+ - SFLD
+ - SUPERFAMILY
+ - Gene3D
+ - Hamap
+ - Coils
+ - ProSiteProfiles
+ - SMART
+ - CDD
+ - PRINTS
+ - PIRSF
+ - ProSitePatterns
+ - Pfam
+ - ProDom
+ - MobiDBLite
diff --git a/_includes/cwl/20-software-requirements/custom-types.yml b/_includes/cwl/20-software-requirements/custom-types.yml
@@ -0,0 +1,3 @@
+proteinFile:
+    class: File
+    path: test_proteins.fasta
diff --git a/_includes/cwl/20-software-requirements/test_proteins.fasta b/_includes/cwl/20-software-requirements/test_proteins.fasta
@@ -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
diff --git a/_includes/cwl/21-1st-workflow/arguments.cwl b/_includes/cwl/21-1st-workflow/arguments.cwl
@@ -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"
+
diff --git a/_includes/cwl/21-1st-workflow/hello.tar b/_includes/cwl/21-1st-workflow/hello.tar
diff --git a/_includes/cwl/21-1st-workflow/tar-param.cwl b/_includes/cwl/21-1st-workflow/tar-param.cwl
@@ -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)
diff --git a/_includes/cwl/22-nested-workflows/1st-workflow.cwl b/_includes/cwl/22-nested-workflows/1st-workflow.cwl
@@ -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]
diff --git a/_includes/cwl/22-nested-workflows/arguments.cwl b/_includes/cwl/22-nested-workflows/arguments.cwl
@@ -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"
+
diff --git a/_includes/cwl/22-nested-workflows/tar-param.cwl b/_includes/cwl/22-nested-workflows/tar-param.cwl
@@ -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)

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,3 @@`
	`1`	`+proteinFile:`
	`2`	`+ class: File`
	`3`	`+ path: test_proteins.fasta`