Mercurial > repos > nick > dunovo
changeset 19:e5d1d90c099b draft
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'9101e88acb2d3dc022c47e0663fec1f6b9fa58a5\n'-dirty
| author | nick |
|---|---|
| date | Fri, 10 Nov 2017 08:50:09 -0500 |
| parents | 075ef42d1ce5 |
| children | 78542cc82cb6 |
| files | align_families.xml correct_barcodes.xml dunovo.xml make_consensi.xml make_families.xml tool_dependencies.xml |
| diffstat | 6 files changed, 91 insertions(+), 91 deletions(-) [+] |
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--- a/align_families.xml Thu Nov 02 15:46:18 2017 -0400 +++ b/align_families.xml Fri Nov 10 08:50:09 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 15:46:18 2017 -0400 +++ b/correct_barcodes.xml Fri Nov 10 08:50:09 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 15:46:18 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,80 +0,0 @@ -<?xml version="1.0"?> -<tool id="dunovo" name="Du Novo: Make consensus reads" version="2.0.8"> - <description>from duplex sequencing alignments</description> - <requirements> - <requirement type="package" version="2.0.8">dunovo</requirement> - <!-- TODO: require Python 2.7 --> - </requirements> - <version_command>dunovo.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' - #if $keep_sscs: - --sscs1 '$sscs1' --sscs2 '$sscs2' - #end if - </command> - <inputs> - <param name="input" type="data" format="tabular" label="Aligned input reads" /> - <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> - <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="Consensus % threshold" help="The consensus base must be present in more than this fraction of the reads, or "N" will be used."/> - <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="If no base at the position appears in at least this many reads, "N" will be used."/> - <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> - <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> - <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> - <option value="solexa">Solexa (PHRED 0 = "@")</option> - </param> - <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" /> - <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the number of processes used, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET."/> - </inputs> - <outputs> - <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/> - <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/> - <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)"> - <filter>keep_sscs</filter> - </data> - <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)"> - <filter>keep_sscs</filter> - </data> - </outputs> - <tests> - <test> - <param name="input" value="families.msa.tsv"/> - <output name="dcs1" file="families.dcs_1.fa"/> - <output name="dcs2" file="families.dcs_2.fa"/> - </test> - </tests> - <help> - -**What it does** - -This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families. - ------ - -**Input** - -This expects the output format of the "Align families" tool. - ------ - -**Output** - -This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file. - - </help> - <citations> - <citation type="bibtex">@article{Stoler2016, - author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton}, - doi = {10.1186/s13059-016-1039-4}, - issn = {1474-760X}, - journal = {Genome biology}, - number = {1}, - pages = {180}, - pmid = {27566673}, - publisher = {Genome Biology}, - title = {{Streamlined analysis of duplex sequencing data with Du Novo.}}, - url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673}, - volume = {17}, - year = {2016} - }</citation> - </citations> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_consensi.xml Fri Nov 10 08:50:09 2017 -0500 @@ -0,0 +1,80 @@ +<?xml version="1.0"?> +<tool id="make_consensi" name="Du Novo: Make consensus reads" version="2.0.9"> + <description>from duplex sequencing alignments</description> + <requirements> + <requirement type="package" version="2.0.9">dunovo</requirement> + <!-- TODO: require Python 2.7 --> + </requirements> + <version_command>make-consensi.py --version</version_command> + <command detect_errors="exit_code"> + 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 + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Aligned input reads" /> + <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> + <param name="cons_thres" type="float" value="0.5" min="0.5" max="1.0" label="Consensus % threshold" help="The consensus base must be present in more than this fraction of the reads, or "N" will be used."/> + <param name="min_cons_reads" type="integer" value="0" min="0" label="Minimum number of reads for a consensus base." help="If no base at the position appears in at least this many reads, "N" will be used."/> + <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> + <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> + <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> + <option value="solexa">Solexa (PHRED 0 = "@")</option> + </param> + <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences as well" /> + <param name="phone" type="boolean" truevalue="--phone-home" falsevalue="" checked="False" label="Send usage data" help="Report helpful usage data to the developer, to better understand the use cases and performance of the tool. The only data which will be recorded is the name and version of the tool, the size of the input data, the number of processes used, the time and memory taken to process it, and the IP address of the machine running it. Also, if the tool fails, it will report the name of the exception thrown and the line of code it occurred in. The parameters and input/output dataset names are not sent. All the reporting and recording code is available at https://github.com/NickSto/ET."/> + </inputs> + <outputs> + <data name="dcs1" format="fasta" label="$tool.name on $on_string (mate 1)"/> + <data name="dcs2" format="fasta" label="$tool.name on $on_string (mate 2)"/> + <data name="sscs1" format="fasta" label="$tool.name on $on_string (SSCS mate 1)"> + <filter>keep_sscs</filter> + </data> + <data name="sscs2" format="fasta" label="$tool.name on $on_string (SSCS mate 2)"> + <filter>keep_sscs</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="families.msa.tsv"/> + <output name="dcs1" file="families.dcs_1.fa"/> + <output name="dcs2" file="families.dcs_2.fa"/> + </test> + </tests> + <help> + +**What it does** + +This is for processing duplex sequencing data. It creates single-strand and duplex consensus reads from aligned read families. + +----- + +**Input** + +This expects the output format of the "Align families" tool. + +----- + +**Output** + +This will output final, duplex consensus reads in two FASTA files (first and second reads in the pairs). Optionally, you can save the single-strand reads too, in a separate FASTA file. + + </help> + <citations> + <citation type="bibtex">@article{Stoler2016, + author = {Stoler, Nicholas and Arbeithuber, Barbara and Guiblet, Wilfried and Makova, Kateryna D and Nekrutenko, Anton}, + doi = {10.1186/s13059-016-1039-4}, + issn = {1474-760X}, + journal = {Genome biology}, + number = {1}, + pages = {180}, + pmid = {27566673}, + publisher = {Genome Biology}, + title = {{Streamlined analysis of duplex sequencing data with Du Novo.}}, + url = {http://www.ncbi.nlm.nih.gov/pubmed/27566673}, + volume = {17}, + year = {2016} + }</citation> + </citations> +</tool>
--- a/make_families.xml Thu Nov 02 15:46:18 2017 -0400 +++ b/make_families.xml Fri Nov 10 08:50:09 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 15:46:18 2017 -0400 +++ b/tool_dependencies.xml Fri Nov 10 08:50:09 2017 -0500 @@ -12,10 +12,10 @@ <package name="networkx" version="1.10"> <repository changeset_revision="3469a6858fd4" name="package_networkx_1_10" owner="iuc" toolshed="https://testtoolshed.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>