From feab9917517a3ae865c9969ce06a70bf1afbb216 Mon Sep 17 00:00:00 2001 From: Tomoya Tanjo Date: Tue, 12 Dec 2017 13:03:57 +0900 Subject: [PATCH] Add files for the examles in user guide --- _includes/cwl/03-input/whale.txt | 0 _includes/cwl/04-output/hello.tar | Bin 0 -> 10240 bytes _includes/cwl/06-params/hello.tar | Bin 0 -> 10240 bytes .../InterProScan-apps.yml | 18 ++++++++++ .../20-software-requirements/custom-types.yml | 3 ++ .../test_proteins.fasta | 34 ++++++++++++++++++ _includes/cwl/21-1st-workflow/arguments.cwl | 21 +++++++++++ _includes/cwl/21-1st-workflow/hello.tar | Bin 0 -> 2048 bytes _includes/cwl/21-1st-workflow/tar-param.cwl | 19 ++++++++++ .../cwl/22-nested-workflows/1st-workflow.cwl | 26 ++++++++++++++ .../cwl/22-nested-workflows/arguments.cwl | 21 +++++++++++ .../cwl/22-nested-workflows/tar-param.cwl | 19 ++++++++++ 12 files changed, 161 insertions(+) create mode 100644 _includes/cwl/03-input/whale.txt create mode 100644 _includes/cwl/04-output/hello.tar create mode 100644 _includes/cwl/06-params/hello.tar create mode 100644 _includes/cwl/20-software-requirements/InterProScan-apps.yml create mode 100644 _includes/cwl/20-software-requirements/custom-types.yml create mode 100644 _includes/cwl/20-software-requirements/test_proteins.fasta create mode 100644 _includes/cwl/21-1st-workflow/arguments.cwl create mode 100644 _includes/cwl/21-1st-workflow/hello.tar create mode 100644 _includes/cwl/21-1st-workflow/tar-param.cwl create mode 100644 _includes/cwl/22-nested-workflows/1st-workflow.cwl create mode 100644 _includes/cwl/22-nested-workflows/arguments.cwl create mode 100644 _includes/cwl/22-nested-workflows/tar-param.cwl diff --git a/_includes/cwl/03-input/whale.txt b/_includes/cwl/03-input/whale.txt new file mode 100644 index 00000000..e69de29b diff --git a/_includes/cwl/04-output/hello.tar b/_includes/cwl/04-output/hello.tar new file mode 100644 index 0000000000000000000000000000000000000000..155f6e6098a002706137dd31bfb19bb998911ee1 GIT binary patch literal 10240 zcmeIuK?;O0429twr6-WY+V(tMh%U+uXcdpIu5>fZs=NPf5_k~8H;<)!yLwb<7rheW zAlI-I^gZwDj+pN?4Z$ZLM6Hiz;87An^!C=Ri#T=r-;%(C5Wcvs(|FHKx{}n2=6LTU z4?FZ)&bN9awrh28zIS<7+u7EO(OM6ccaJ@V%@{dD+`{sW@Yk0&*%3eh0R#|0009IL qKmY**5I_I{1Q0*~0R#|0009ILKmY**5I_I{1Q0*~0R#}JEbsu+?iQo~ literal 0 HcmV?d00001 diff --git a/_includes/cwl/20-software-requirements/InterProScan-apps.yml b/_includes/cwl/20-software-requirements/InterProScan-apps.yml new file mode 100644 index 00000000..e42779c3 --- /dev/null +++ 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 new file mode 100644 index 00000000..ec8fb9e6 --- /dev/null +++ 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 new file mode 100644 index 00000000..ec34ed42 --- /dev/null +++ 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 \ No newline at end of file diff --git a/_includes/cwl/21-1st-workflow/arguments.cwl b/_includes/cwl/21-1st-workflow/arguments.cwl new file mode 100644 index 00000000..603b20b9 --- /dev/null +++ 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 new file mode 100644 index 0000000000000000000000000000000000000000..d30185d7c3b284ea66217135fe88d19403b5c955 GIT binary patch literal 2048 zcmeHFu?mAg40ZM^f|D+i(^H53fOK^%9j;bIIX%%+D8+wosvX4L!D5yqFX8d>NSsNj z+)9kX*ewt-