[med-svn] samtools 02/03: Add CWL tools
Anton Khodak
anton-khodak-guest at moszumanska.debian.org
Sun Jan 15 08:45:14 UTC 2017
This is an automated email from the git hooks/post-receive script.
anton-khodak-guest pushed a commit to branch debian/unstable
in repository samtools.
commit 129288348521ba3ad532d4ba24eb3a5ccb74b703
Author: Anton Khodak <anton.khodak at ukr.net>
Date: Thu Jan 12 00:33:24 2017 -0800
Add CWL tools
---
debian/changelog | 6 ++
debian/copyright | 25 ++++-
debian/samtools-Dockerfile | 84 +++++++++++++++
debian/samtools-docker.yml | 5 +
debian/samtools-faidx.cwl | 78 ++++++++++++++
debian/samtools-index.cwl | 86 +++++++++++++++
debian/samtools-metadata.yaml | 73 +++++++++++++
debian/samtools-rmdup.cwl | 75 +++++++++++++
debian/samtools-sort.cwl | 106 ++++++++++++++++++
debian/samtools-view.cwl | 242 ++++++++++++++++++++++++++++++++++++++++++
10 files changed, 776 insertions(+), 4 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index d3a434c..62a2d41 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+samtools (1.3.1-4) unstable; urgency=low
+
+ * CWL files added
+
+ -- Anton Khodak <anton.khodak at ukr.net> Fri, 13 Jan 2017 06:27:27 -0800
+
samtools (1.3.1-3) unstable; urgency=medium
* Team upload.
diff --git a/debian/copyright b/debian/copyright
index eddbb8c..05fba1c 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,4 +1,4 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Source: https://github.com/samtools/samtools/archive/1.3.1.tar.gz
Files: *
@@ -7,7 +7,7 @@ Copyright: © 2008–2016, Genome Research Ltd. (GRL)
© 2009–2012 Broad Institute
© 2010 Illumina, Inc.
© 2012–2013 Peter Cock, The James Hutton Institute.
-License: MIT
+License: Expat
Files: win32/xcurses.h win32/libcurses.a
Copyright: Public Domain
@@ -37,7 +37,25 @@ License: zlib
Jean-loup Gailly Mark Adler
jloup at gzip.org madler at alumni.caltech.edu
-License: MIT
+Files: debian/*.cwl
+Copyright: the CWL project
+License: Apache-2.0
+ Licensed under the Apache License, Version 2.0 (the "License");
+ you may not use this file except in compliance with the License.
+ You may obtain a copy of the License at
+ .
+ http://www.apache.org/licenses/LICENSE-2.0
+ .
+ Unless required by applicable law or agreed to in writing, software
+ distributed under the License is distributed on an "AS IS" BASIS,
+ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ See the License for the specific language governing permissions and
+ limitations under the License.
+ .
+ On Debian systems, the complete text of the Apache 2.0 License
+ can be found in /usr/share/common-licenses/Apache-2.0 file.
+
+License: Expat
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
@@ -55,4 +73,3 @@ License: MIT
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
THE SOFTWARE.
-
diff --git a/debian/samtools-Dockerfile b/debian/samtools-Dockerfile
new file mode 100644
index 0000000..6f6b755
--- /dev/null
+++ b/debian/samtools-Dockerfile
@@ -0,0 +1,84 @@
+#################################################################
+# Dockerfile
+#
+# Software: samtools
+# Software Version: 1.2-242-4d56437
+# Description: samtools image for SciDAP
+# Website: https://samtools.github.io, http://scidap.com/
+# Provides: samtools/htslib/tabix/bgzip
+# Base Image: scidap/scidap:v0.0.1
+# Build Cmd: docker build --rm -t scidap/samtools:v1.2-242-4d56437 .
+# Pull Cmd: docker pull scidap/samtools:v1.2-242-4d56437
+# Run Cmd: docker run --rm scidap/samtools:v1.2-242-4d56437 samtools
+#################################################################
+
+### Base Image
+FROM scidap/scidap:v0.0.1
+MAINTAINER Andrey V Kartashov "porter at porter.st"
+ENV DEBIAN_FRONTEND noninteractive
+
+################## BEGIN INSTALLATION ######################
+
+WORKDIR /tmp
+
+### Install required packages (samtools)
+
+RUN apt-get clean all &&\
+ apt-get update &&\
+ apt-get install -y \
+ libncurses5-dev && \
+ apt-get clean && \
+ apt-get purge && \
+ rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* /usr/share/doc/*
+
+### Installing samtools/htslib/tabix/bgzip
+
+ENV VERSIONH 1.2.1-254-6462e34
+ENV NAMEH htslib
+ENV URLH "https://github.com/samtools/htslib/archive/${VERSIONH}.tar.gz"
+ENV SHA1H "6462e349d16e83db8647272e4b98d2a92992071f"
+
+ENV VERSION 1.2-242-4d56437
+ENV NAME "samtools"
+ENV URL "https://github.com/samtools/samtools/archive/${VERSION}.tar.gz"
+ENV SHA1 "4d56437320ad370eb0b48c204ccec7c73f653393"
+
+RUN git clone https://github.com/samtools/htslib.git && \
+cd ${NAMEH} && \
+git reset --hard ${SHA1H} && \
+make -j 4 && \
+cd .. && \
+cp ./${NAMEH}/tabix /usr/local/bin/ && \
+cp ./${NAMEH}/bgzip /usr/local/bin/ && \
+cp ./${NAMEH}/htsfile /usr/local/bin/ && \
+#RUN wget -q -O - $URLH | tar -zxv && \
+#cd ${NAMEH}-${VERSIONH} && \
+#make -j 4 && \
+#cd .. && \
+#cp ./${NAMEH}-${VERSIONH}/tabix /usr/local/bin/ && \
+#cp ./${NAMEH}-${VERSIONH}/bgzip /usr/local/bin/ && \
+#cp ./${NAMEH}-${VERSIONH}/htsfile /usr/local/bin/ && \
+strip /usr/local/bin/tabix; true && \
+strip /usr/local/bin/bgzip; true && \
+strip /usr/local/bin/htsfile; true && \
+#ln -s ./${NAMEH}-${VERSIONH}/ ./${NAMEH} && \
+
+git clone https://github.com/samtools/samtools.git && \
+cd ${NAME} && \
+git reset --hard ${SHA1} && \
+make -j 4 && \
+cp ./${NAME} /usr/local/bin/ && \
+cd .. && \
+strip /usr/local/bin/${NAME}; true && \
+rm -rf ./${NAMEH}/ && \
+rm -rf ./${NAME}/ && \
+rm -rf ./${NAMEH}
+
+#wget -q -O - $URL | tar -zxv && \
+#cd ${NAME}-${VERSION} && \
+#make -j 4 && \
+#cd .. && \
+#cp ./${NAME}-${VERSION}/${NAME} /usr/local/bin/ && \
+#strip /usr/local/bin/${NAME}; true && \
+#rm -rf ./${NAMEH}-${VERSIONH}/ && \
+#rm -rf ./${NAME}-${VERSION}/
diff --git a/debian/samtools-docker.yml b/debian/samtools-docker.yml
new file mode 100644
index 0000000..4f4348e
--- /dev/null
+++ b/debian/samtools-docker.yml
@@ -0,0 +1,5 @@
+class: DockerRequirement
+dockerPull: scidap/samtools:v1.2-242-4d56437
+#dockerImageId: scidap/samtools:v1.2-242-4d56437 #not yet ready
+dockerFile: >
+ $import: samtools-Dockerfile
diff --git a/debian/samtools-faidx.cwl b/debian/samtools-faidx.cwl
new file mode 100755
index 0000000..203c1c0
--- /dev/null
+++ b/debian/samtools-faidx.cwl
@@ -0,0 +1,78 @@
+#!/usr/bin/env cwl-runner
+#
+# To use it as stand alone tool. The working directory should not have input .fa file
+# example: "./samtools-faidx.cwl --input=./test-files/mm10.fa"
+# As part of a workflow should be no problem at all
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+- $import: envvar-global.yml
+- $import: samtools-docker.yml
+- class: InlineJavascriptRequirement
+- class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.input)
+ entryname: $(inputs.input.path.split('/').slice(-1)[0])
+inputs:
+ input:
+ type: File
+ doc: <file.fa|file.fa.gz>
+ region:
+ type: string?
+ inputBinding:
+ position: 2
+
+outputs:
+ index:
+ type: File
+ outputBinding:
+ glob: $(inputs.input.path.split('/').slice(-1)[0]) #+'.fai')
+ secondaryFiles:
+ - .fai
+ - .gzi
+
+baseCommand:
+- samtools
+- faidx
+
+arguments:
+- valueFrom: $(inputs.input.path.split('/').slice(-1)[0])
+ position: 1
+
+$namespaces:
+ s: http://schema.org/
+
+$schemas:
+- http://schema.org/docs/schema_org_rdfa.html
+
+s:mainEntity:
+ $import: samtools-metadata.yaml
+
+s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-faidx.cwl
+s:codeRepository: https://github.com/common-workflow-language/workflows
+s:license: http://www.apache.org/licenses/LICENSE-2.0
+
+s:isPartOf:
+ class: s:CreativeWork
+ s:name: Common Workflow Language
+ s:url: http://commonwl.org/
+
+s:author:
+ class: s:Person
+ s:name: Andrey Kartashov
+ s:email: mailto:Andrey.Kartashov at cchmc.org
+ s:sameAs:
+ - id: http://orcid.org/0000-0001-9102-5681
+ s:worksFor:
+ - class: s:Organization
+ s:name: Cincinnati Children's Hospital Medical Center
+ s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026
+ s:department:
+ - class: s:Organization
+ s:name: Barski Lab
+doc: |
+ samtools-faidx.cwl is developed for CWL consortium
+ Usage: samtools faidx <file.fa|file.fa.gz> [<reg> [...]]
+
diff --git a/debian/samtools-index.cwl b/debian/samtools-index.cwl
new file mode 100755
index 0000000..9bdc5b1
--- /dev/null
+++ b/debian/samtools-index.cwl
@@ -0,0 +1,86 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+- $import: envvar-global.yml
+- $import: samtools-docker.yml
+- class: InlineJavascriptRequirement
+ expressionLib:
+ - var new_ext = function() { var ext=inputs.bai?'.bai':inputs.csi?'.csi':'.bai';
+ return inputs.input.path.split('/').slice(-1)[0]+ext; };
+inputs:
+ input:
+ type: File
+ inputBinding:
+ position: 2
+
+ doc: |
+ Input bam file.
+ interval:
+ type: int?
+ inputBinding:
+ position: 1
+ prefix: -m
+ doc: |
+ Set minimum interval size for CSI indices to 2^INT [14]
+ csi:
+ type: boolean
+ default: false
+ doc: |
+ Generate CSI-format index for BAM files
+ bai:
+ type: boolean
+ default: false
+ doc: |
+ Generate BAI-format index for BAM files [default]
+outputs:
+ index:
+ type: File
+ outputBinding:
+ glob: $(new_ext())
+
+ doc: The index file
+baseCommand: [samtools, index]
+arguments:
+- valueFrom: $(inputs.bai?'-b':inputs.csi?'-c':[])
+ position: 1
+- valueFrom: $(new_ext())
+ position: 3
+
+$namespaces:
+ s: http://schema.org/
+
+$schemas:
+- http://schema.org/docs/schema_org_rdfa.html
+
+s:mainEntity:
+ $import: samtools-metadata.yaml
+
+s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-index.cwl
+s:codeRepository: https://github.com/common-workflow-language/workflows
+s:license: http://www.apache.org/licenses/LICENSE-2.0
+
+s:isPartOf:
+ class: s:CreativeWork
+ s:name: Common Workflow Language
+ s:url: http://commonwl.org/
+
+s:author:
+ class: s:Person
+ s:name: Andrey Kartashov
+ s:email: mailto:Andrey.Kartashov at cchmc.org
+ s:sameAs:
+ - id: http://orcid.org/0000-0001-9102-5681
+ s:worksFor:
+ - class: s:Organization
+ s:name: Cincinnati Children's Hospital Medical Center
+ s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026
+ s:department:
+ - class: s:Organization
+ s:name: Barski Lab
+doc: |
+ samtools-index.cwl is developed for CWL consortium
+
+
diff --git a/debian/samtools-metadata.yaml b/debian/samtools-metadata.yaml
new file mode 100644
index 0000000..64b6852
--- /dev/null
+++ b/debian/samtools-metadata.yaml
@@ -0,0 +1,73 @@
+class: s:SoftwareSourceCode
+s:name: "samtools"
+s:about: >
+ A suite of programs for interacting with high-throughput sequencing data.
+ It consists of three separate repositories: Samtools (Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format),
+ BCFtools (Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants)
+ and HTSlib (A C library for reading/writing high-throughput sequencing data).
+
+s:url: http://www.htslib.org/
+s:codeRepository: https://github.com/samtools/samtools.git
+
+s:license:
+- https://opensource.org/licenses/MIT
+- https://opensource.org/licenses/BSD-3-Clause
+
+s:targetProduct:
+ class: s:SoftwareApplication
+ s:softwareVersion: "1.2-242-4d56437"
+ s:applicationCategory: "commandline tool"
+
+s:programmingLanguage: "C, Perl"
+
+s:publication:
+- class: s:ScholarlyArticle
+ id: http://dx.doi.org/10.1093/bioinformatics/btr509
+ s:name: "(Li, 2011) A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics."
+ s:url: http://www.ncbi.nlm.nih.gov/pubmed/21903627
+- class: s:ScholarlyArticle
+ id: http://dx.doi.org/10.1093/bioinformatics/btr076
+ s:name: "(Li, 2011) Improving SNP discovery by base alignment quality. Bioinformatics."
+ s:url: http://www.ncbi.nlm.nih.gov/pubmed/21320865
+- class: s:ScholarlyArticle
+ id: http://dx.doi.org/10.1093/bioinformatics/btp352
+ s:name: "(Li et al., 2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics."
+ s:url: http://www.ncbi.nlm.nih.gov/pubmed/19505943
+
+s:discussionUrl:
+- https://lists.sourceforge.net/lists/listinfo/samtools-help
+- https://lists.sourceforge.net/lists/listinfo/samtools-devel
+
+s:creator:
+- class: s:Organization
+ s:name: "Sanger Institute"
+ s:member:
+ - class: s:Person
+ s:name: "Heng Li"
+ s:description: "wrote most of the initial source codes of SAMtools and various converters."
+- class: s:Organization
+ s:name: "Broad Institute"
+ s:member:
+ - class: s:Person
+ s:name: "Bob Handsaker"
+ s:description: |
+ A major contributor to the
+ SAM/BAM specification. He designed and implemented the BGZF format, the
+ underlying indexable compression format for the BAM format. BGZF does
+ not support arithmetic between file offsets.
+- class: s:Organization
+ s:name: "Beijing Genome Institute"
+ s:member:
+ - class: s:Person
+ s:name: "Jue Ruan"
+ s:description: |
+ Designed and implemented the
+ RAZF format, an alternative indexable compression format. RAZF is no longer
+ used by or provided with SAMtools. Source code remains available in older
+ SAMtools 0.1.x releases and from the standalone branch in the repository.
+- class: s:Person
+ s:name: "Colin Hercus"
+ s:description: "updated novo2sam.pl to support gapped alignment by novoalign."
+- class: s:Person
+ s:name: "Petr Danecek"
+ s:description: "contributed the header parsing library sam_header.c and sam2vcf.pl script."
\ No newline at end of file
diff --git a/debian/samtools-rmdup.cwl b/debian/samtools-rmdup.cwl
new file mode 100755
index 0000000..196a8e9
--- /dev/null
+++ b/debian/samtools-rmdup.cwl
@@ -0,0 +1,75 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+- $import: envvar-global.yml
+- $import: samtools-docker.yml
+- class: InlineJavascriptRequirement
+
+inputs:
+ single_end:
+ type: boolean
+ default: false
+ doc: |
+ rmdup for SE reads
+ input:
+ type: File
+ inputBinding:
+ position: 2
+
+ doc: |
+ Input bam file.
+ output_name:
+ type: string
+ inputBinding:
+ position: 3
+
+ pairend_as_se:
+ type: boolean
+ default: false
+ doc: |
+ treat PE reads as SE in rmdup (force -s)
+outputs:
+ rmdup:
+ type: File
+ outputBinding:
+ glob: $(inputs.output_name)
+
+ doc: File with removed duplicates
+baseCommand: [samtools, rmdup]
+$namespaces:
+ s: http://schema.org/
+
+$schemas:
+- http://schema.org/docs/schema_org_rdfa.html
+
+s:mainEntity:
+ $import: samtools-metadata.yaml
+
+s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-rmdup.cwl
+s:codeRepository: https://github.com/common-workflow-language/workflows
+s:license: http://www.apache.org/licenses/LICENSE-2.0
+
+s:isPartOf:
+ class: s:CreativeWork
+ s:name: Common Workflow Language
+ s:url: http://commonwl.org/
+
+s:author:
+ class: s:Person
+ s:name: Andrey Kartashov
+ s:email: mailto:Andrey.Kartashov at cchmc.org
+ s:sameAs:
+ - id: http://orcid.org/0000-0001-9102-5681
+ s:worksFor:
+ - class: s:Organization
+ s:name: Cincinnati Children's Hospital Medical Center
+ s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026
+ s:department:
+ - class: s:Organization
+ s:name: Barski Lab
+doc: |
+ samtools-rmdup.cwl is developed for CWL consortium
+
diff --git a/debian/samtools-sort.cwl b/debian/samtools-sort.cwl
new file mode 100755
index 0000000..77b5a85
--- /dev/null
+++ b/debian/samtools-sort.cwl
@@ -0,0 +1,106 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+- $import: envvar-global.yml
+- $import: samtools-docker.yml
+- class: InlineJavascriptRequirement
+
+inputs:
+ compression_level:
+ type: int?
+ inputBinding:
+ prefix: -l
+ doc: |
+ Set compression level, from 0 (uncompressed) to 9 (best)
+ threads:
+ type: int?
+ inputBinding:
+ prefix: -@
+
+ doc: Set number of sorting and compression threads [1]
+ memory:
+ type: string?
+ inputBinding:
+ prefix: -m
+ doc: |
+ Set maximum memory per thread; suffix K/M/G recognized [768M]
+ input:
+ type: File
+ inputBinding:
+ position: 1
+
+ doc: Input bam file.
+ output_name:
+ type: string
+ inputBinding:
+ position: 2
+
+ doc: Desired output filename.
+ sort_by_name:
+ type: boolean?
+ inputBinding:
+ prefix: -n
+
+ doc: Sort by read names (i.e., the QNAME field) rather than by chromosomal coordinates.
+outputs:
+ sorted:
+ type: File
+ outputBinding:
+ glob: $(inputs.output_name)
+
+baseCommand: [samtools, sort]
+arguments:
+- -f
+$namespaces:
+ s: http://schema.org/
+
+$schemas:
+- http://schema.org/docs/schema_org_rdfa.html
+
+s:mainEntity:
+ $import: samtools-metadata.yaml
+
+s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-sort.cwl
+s:codeRepository: https://github.com/common-workflow-language/workflows
+s:license: http://www.apache.org/licenses/LICENSE-2.0
+
+s:isPartOf:
+ class: s:CreativeWork
+ s:name: Common Workflow Language
+ s:url: http://commonwl.org/
+
+s:author:
+ class: s:Person
+ s:name: Andrey Kartashov
+ s:email: mailto:Andrey.Kartashov at cchmc.org
+ s:sameAs:
+ - id: http://orcid.org/0000-0001-9102-5681
+ s:worksFor:
+ - class: s:Organization
+ s:name: Cincinnati Children's Hospital Medical Center
+ s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026
+ s:department:
+ - class: s:Organization
+ s:name: Barski Lab
+doc: |
+ samtools-sort.cwl is developed for CWL consortium
+ Usage: samtools sort [options...] [in.bam]
+ Options:
+ -l INT Set compression level, from 0 (uncompressed) to 9 (best)
+ -m INT Set maximum memory per thread; suffix K/M/G recognized [768M]
+ -n Sort by read name
+ -o FILE Write final output to FILE rather than standard output
+ -O FORMAT Write output as FORMAT ('sam'/'bam'/'cram') (either -O or
+ -T PREFIX Write temporary files to PREFIX.nnnn.bam -T is required)
+ -@ INT Set number of sorting and compression threads [1]
+
+ Legacy usage: samtools sort [options...] <in.bam> <out.prefix>
+ Options:
+ -f Use <out.prefix> as full final filename rather than prefix
+ -o Write final output to stdout rather than <out.prefix>.bam
+ -l,m,n,@ Similar to corresponding options above
+
+
diff --git a/debian/samtools-view.cwl b/debian/samtools-view.cwl
new file mode 100755
index 0000000..f1b1d94
--- /dev/null
+++ b/debian/samtools-view.cwl
@@ -0,0 +1,242 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+
+requirements:
+- $import: envvar-global.yml
+- $import: samtools-docker.yml
+- class: InlineJavascriptRequirement
+
+inputs:
+ isbam:
+ type: boolean
+ default: false
+ inputBinding:
+ position: 2
+ prefix: -b
+ doc: |
+ output in BAM format
+ readswithoutbits:
+ type: int?
+ inputBinding:
+ position: 1
+ prefix: -F
+ doc: |
+ only include reads with none of the bits set in INT set in FLAG [0]
+ collapsecigar:
+ type: boolean
+ default: false
+ inputBinding:
+ position: 1
+ prefix: -B
+ doc: |
+ collapse the backward CIGAR operation
+ readsingroup:
+ type: string?
+ inputBinding:
+ position: 1
+ prefix: -r
+ doc: |
+ only include reads in read group STR [null]
+ bedoverlap:
+ type: File?
+ inputBinding:
+ position: 1
+ prefix: -L
+ doc: |
+ only include reads overlapping this BED FILE [null]
+ uncompressed:
+ type: boolean
+ default: false
+ inputBinding:
+ position: 1
+ prefix: -u
+ doc: |
+ uncompressed BAM output (implies -b)
+ readtagtostrip:
+ type: string[]?
+ inputBinding:
+ position: 1
+
+ doc: |
+ read tag to strip (repeatable) [null]
+ input:
+ type: File
+ inputBinding:
+ position: 4
+
+ doc: |
+ Input bam file.
+ readsquality:
+ type: int?
+ inputBinding:
+ position: 1
+ prefix: -q
+ doc: |
+ only include reads with mapping quality >= INT [0]
+ readswithbits:
+ type: int?
+ inputBinding:
+ position: 1
+ prefix: -f
+ doc: |
+ only include reads with all bits set in INT set in FLAG [0]
+ cigar:
+ type: int?
+ inputBinding:
+ position: 1
+ prefix: -m
+ doc: |
+ only include reads with number of CIGAR operations
+ consuming query sequence >= INT [0]
+ iscram:
+ type: boolean
+ default: false
+ inputBinding:
+ position: 2
+ prefix: -C
+ doc: |
+ output in CRAM format
+ threads:
+ type: int?
+ inputBinding:
+ position: 1
+ prefix: -@
+ doc: |
+ number of BAM compression threads [0]
+ fastcompression:
+ type: boolean
+ default: false
+ inputBinding:
+ position: 1
+ prefix: '-1'
+ doc: |
+ use fast BAM compression (implies -b)
+ samheader:
+ type: boolean
+ default: false
+ inputBinding:
+ position: 1
+ prefix: -h
+ doc: |
+ include header in SAM output
+ count:
+ type: boolean
+ default: false
+ inputBinding:
+ position: 1
+ prefix: -c
+ doc: |
+ print only the count of matching records
+ randomseed:
+ type: float?
+ inputBinding:
+ position: 1
+ prefix: -s
+ doc: |
+ integer part sets seed of random number generator [0];
+ rest sets fraction of templates to subsample [no subsampling]
+ referencefasta:
+ type: File?
+ inputBinding:
+ position: 1
+ prefix: -T
+ doc: |
+ reference sequence FASTA FILE [null]
+ region:
+ type: string?
+ inputBinding:
+ position: 5
+
+ doc: |
+ [region ...]
+ readsingroupfile:
+ type: File?
+ inputBinding:
+ position: 1
+ prefix: -R
+ doc: |
+ only include reads with read group listed in FILE [null]
+ readsinlibrary:
+ type: string?
+ inputBinding:
+ position: 1
+ prefix: -l
+ doc: |
+ only include reads in library STR [null]
+ output_name:
+ type: string
+ inputBinding:
+ position: 2
+ prefix: -o
+outputs:
+ output:
+ type: File
+ outputBinding:
+ glob: $(inputs.output_name)
+
+baseCommand: [samtools, view]
+$namespaces:
+ s: http://schema.org/
+
+$schemas:
+- http://schema.org/docs/schema_org_rdfa.html
+
+s:mainEntity:
+ $import: samtools-metadata.yaml
+
+s:downloadUrl: https://github.com/common-workflow-language/workflows/blob/master/tools/samtools-view.cwl
+s:codeRepository: https://github.com/common-workflow-language/workflows
+s:license: http://www.apache.org/licenses/LICENSE-2.0
+
+s:isPartOf:
+ class: s:CreativeWork
+ s:name: Common Workflow Language
+ s:url: http://commonwl.org/
+
+s:author:
+ class: s:Person
+ s:name: Andrey Kartashov
+ s:email: mailto:Andrey.Kartashov at cchmc.org
+ s:sameAs:
+ - id: http://orcid.org/0000-0001-9102-5681
+ s:worksFor:
+ - class: s:Organization
+ s:name: Cincinnati Children's Hospital Medical Center
+ s:location: 3333 Burnet Ave, Cincinnati, OH 45229-3026
+ s:department:
+ - class: s:Organization
+ s:name: Barski Lab
+doc: |
+ samtools-view.cwl is developed for CWL consortium
+ Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]
+
+ Options: -b output BAM
+ -C output CRAM (requires -T)
+ -1 use fast BAM compression (implies -b)
+ -u uncompressed BAM output (implies -b)
+ -h include header in SAM output
+ -H print SAM header only (no alignments)
+ -c print only the count of matching records
+ -o FILE output file name [stdout]
+ -U FILE output reads not selected by filters to FILE [null]
+ -t FILE FILE listing reference names and lengths (see long help) [null]
+ -T FILE reference sequence FASTA FILE [null]
+ -L FILE only include reads overlapping this BED FILE [null]
+ -r STR only include reads in read group STR [null]
+ -R FILE only include reads with read group listed in FILE [null]
+ -q INT only include reads with mapping quality >= INT [0]
+ -l STR only include reads in library STR [null]
+ -m INT only include reads with number of CIGAR operations
+ consuming query sequence >= INT [0]
+ -f INT only include reads with all bits set in INT set in FLAG [0]
+ -F INT only include reads with none of the bits set in INT
+ set in FLAG [0]
+ -x STR read tag to strip (repeatable) [null]
+ -B collapse the backward CIGAR operation
+ -s FLOAT integer part sets seed of random number generator [0];
+ rest sets fraction of templates to subsample [no subsampling]
+ -@ INT number of BAM compression threads [0]
+
+
--
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