Mercurial > repos > nick > dunovo
changeset 7:e7b88ffb8294 draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
| author | nick |
|---|---|
| date | Fri, 10 Nov 2017 09:33:29 -0500 |
| parents | 23f5d9316694 |
| children | 658eefb99fd7 |
| files | align_families.xml correct_barcodes.xml dunovo.xml make_families.xml tool_dependencies.xml |
| diffstat | 5 files changed, 15 insertions(+), 15 deletions(-) [+] |
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--- a/align_families.xml Thu Nov 02 16:24:48 2017 -0400 +++ b/align_families.xml Fri Nov 10 09:33:29 2017 -0500 @@ -1,13 +1,13 @@ <?xml version="1.0"?> -<tool id="align_families" name="Du Novo: Align families" version="2.0.8"> +<tool id="align_families" name="Du Novo: Align families" version="2.0.9"> <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="7.221">mafft</requirement> - <requirement type="package" version="2.0.8">dunovo</requirement> + <requirement type="package" version="2.0.9">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> - <version_command>align_families.py --version</version_command> - <command detect_errors="exit_code">align_families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' > '$output' + <version_command>align-families.py --version</version_command> + <command detect_errors="exit_code">align-families.py --aligner $aligner --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' > '$output' </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/>
--- a/correct_barcodes.xml Thu Nov 02 16:24:48 2017 -0400 +++ b/correct_barcodes.xml Fri Nov 10 09:33:29 2017 -0500 @@ -1,11 +1,11 @@ <?xml version="1.0"?> -<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.8"> +<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="2.0.9"> <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="2.2.5">bowtie2</requirement> <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="1.10">networkx</requirement> - <requirement type="package" version="2.0.8">dunovo</requirement> + <requirement type="package" version="2.0.9">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> <version_command>correct.py --version</version_command>
--- a/dunovo.xml Thu Nov 02 16:24:48 2017 -0400 +++ b/dunovo.xml Fri Nov 10 09:33:29 2017 -0500 @@ -1,13 +1,13 @@ <?xml version="1.0"?> -<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.8"> +<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.9"> <description>from duplex sequencing alignments</description> <requirements> - <requirement type="package" version="2.0.8">dunovo</requirement> + <requirement type="package" version="2.0.9">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> - <version_command>dunovo.py --version</version_command> + <version_command>make-consensi.py --version</version_command> <command detect_errors="exit_code"> - dunovo.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2' + make-consensi.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} --min-reads $min_reads --qual $qual_thres --qual-format $qual_format --cons-thres $cons_thres --min-cons-reads $min_cons_reads '$input' --dcs1 '$dcs1' --dcs2 '$dcs2' #if $keep_sscs: --sscs1 '$sscs1' --sscs2 '$sscs2' #end if
--- a/make_families.xml Thu Nov 02 16:24:48 2017 -0400 +++ b/make_families.xml Fri Nov 10 09:33:29 2017 -0500 @@ -1,11 +1,11 @@ <?xml version="1.0"?> -<tool id="make_families" name="Du Novo: Make families" version="2.0.8"> +<tool id="make_families" name="Du Novo: Make families" version="2.0.9"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="2.0.8">dunovo</requirement> + <requirement type="package" version="2.0.9">dunovo</requirement> </requirements> <!-- TODO: Add dependency on coreutils to get paste? --> - <version_command>dunovo.py --version</version_command> + <version_command>make-consensi.py --version</version_command> <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' > '$output' </command> <inputs>
--- a/tool_dependencies.xml Thu Nov 02 16:24:48 2017 -0400 +++ b/tool_dependencies.xml Fri Nov 10 09:33:29 2017 -0500 @@ -12,10 +12,10 @@ <package name="networkx" version="1.10"> <repository changeset_revision="e761775277c1" name="package_networkx_1_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="dunovo" version="2.0.8"> + <package name="dunovo" version="2.0.9"> <install version="1.0"> <actions> - <action sha256sum="4c105e29eff271b9e32f12c5d2862b717ba960981f4820dae26e159e2a0ed33d" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.8.tar.gz</action> + <action sha256sum="6f5295b8eae0e161ee3bd28829ca140657743c695624ffc7f467f13eab2c547c" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v2.0.9.tar.gz</action> <action type="shell_command">make</action> <action type="move_directory_files"> <source_directory>.</source_directory>