| Previous changeset 2:a9cb6fb9ea94 (2017-08-24) Next changeset 4:5fbeaa41b223 (2017-10-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/dunovo commit b'a3ad9fbb3f010253808fc0c7329897a741ec9feb\n' |
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modified:
align_families.xml correct_barcodes.xml dunovo.xml make_families.xml tool_dependencies.xml |
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| diff -r a9cb6fb9ea94 -r 00dde366870a align_families.xml --- a/align_families.xml Thu Aug 24 02:13:33 2017 -0400 +++ b/align_families.xml Mon Sep 11 16:59:44 2017 -0400 |
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| @@ -1,12 +1,12 @@ <?xml version="1.0"?> -<tool id="align_families" name="Du Novo: Align families" version="0.7.6"> +<tool id="align_families" name="Du Novo: Align families" version="0.8.1"> <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="7.221">mafft</requirement> - <requirement type="package" version="0.7.6">dunovo</requirement> + <requirement type="package" version="0.8.1">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> - <command detect_errors="exit_code">align_families.py --galaxy $phone -p \${GALAXY_SLOTS:-1} '$input' > '$output' + <command detect_errors="exit_code">align_families.py --galaxy $phone --processes \${GALAXY_SLOTS:-1} '$input' > '$output' </command> <inputs> <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> |
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| diff -r a9cb6fb9ea94 -r 00dde366870a correct_barcodes.xml --- a/correct_barcodes.xml Thu Aug 24 02:13:33 2017 -0400 +++ b/correct_barcodes.xml Mon Sep 11 16:59:44 2017 -0400 |
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| @@ -1,17 +1,17 @@ <?xml version="1.0"?> -<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.7.6"> +<tool id="correct_barcodes" name="Du Novo: Correct barcodes" version="0.8.1"> <description>of duplex sequencing reads</description> <requirements> <requirement type="package" version="2.2.5">bowtie2</requirement> <requirement type="package" version="0.1.18">samtools</requirement> <requirement type="package" version="1.9">networkx</requirement> - <requirement type="package" version="0.7.6">dunovo</requirement> + <requirement type="package" version="0.8.1">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> <command detect_errors="exit_code"><![CDATA[ baralign.sh '$input' refdir barcodes.bam && samtools view -f 256 barcodes.bam - | correct.py --galaxy $phone -d $dist -m $mapq -p $pos '$input' refdir/barcodes.fa + | correct.py --galaxy $phone --dist $dist --mapq $mapq --pos $pos '$input' refdir/barcodes.fa | sort > '$output' ]]> |
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| diff -r a9cb6fb9ea94 -r 00dde366870a dunovo.xml --- a/dunovo.xml Thu Aug 24 02:13:33 2017 -0400 +++ b/dunovo.xml Mon Sep 11 16:59:44 2017 -0400 |
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| @@ -1,25 +1,21 @@ <?xml version="1.0"?> -<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.7.6"> +<tool id="dunovo" name="Du Novo: Make consensus reads" version="0.8.1"> <description>from duplex sequencing alignments</description> <requirements> - <requirement type="package" version="0.7.6">dunovo</requirement> + <requirement type="package" version="0.8.1">dunovo</requirement> <!-- TODO: require Python 2.7 --> </requirements> - <command detect_errors="exit_code"><![CDATA[ - dunovo.py --galaxy $phone -r $min_reads -q $qual_thres -F $qual_format '$input' + <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 $keep_sscs: - --sscs-file sscs.fa + --sscs1 '$sscs1' --sscs2 '$sscs2' #end if - > duplex.fa - && outconv.py duplex.fa -1 '$dcs1' -2 '$dcs2' - #if $keep_sscs: - && outconv.py sscs.fa -1 '$sscs1' -2 '$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="The threshold to use when making consensus sequences. 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="The minimum number of reads a base must appear in to be used as the consensus base. 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> @@ -41,8 +37,8 @@ <tests> <test> <param name="input" value="families.msa.tsv"/> - <output name="dcs1" file="families.cons_1.fa"/> - <output name="dcs2" file="families.cons_2.fa"/> + <output name="dcs1" file="families.dcs_1.fa"/> + <output name="dcs2" file="families.dcs_2.fa"/> </test> </tests> <citations> |
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| diff -r a9cb6fb9ea94 -r 00dde366870a make_families.xml --- a/make_families.xml Thu Aug 24 02:13:33 2017 -0400 +++ b/make_families.xml Mon Sep 11 16:59:44 2017 -0400 |
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| @@ -1,8 +1,8 @@ <?xml version="1.0"?> -<tool id="make_families" name="Du Novo: Make families" version="0.7.6"> +<tool id="make_families" name="Du Novo: Make families" version="0.8.1"> <description>of duplex sequencing reads</description> <requirements> - <requirement type="package" version="0.7.6">dunovo</requirement> + <requirement type="package" version="0.8.1">dunovo</requirement> </requirements> <!-- TODO: Add dependency on coreutils to get paste? --> <command detect_errors="exit_code">make-families.sh -t $taglen -i $invariant '$fastq1' '$fastq2' > '$output' |
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| diff -r a9cb6fb9ea94 -r 00dde366870a tool_dependencies.xml --- a/tool_dependencies.xml Thu Aug 24 02:13:33 2017 -0400 +++ b/tool_dependencies.xml Mon Sep 11 16:59:44 2017 -0400 |
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| @@ -12,10 +12,10 @@ <package name="networkx" version="1.9"> <repository changeset_revision="83df321ad85e" name="package_networkx_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> - <package name="dunovo" version="0.7.6"> + <package name="dunovo" version="0.8.1"> <install version="1.0"> <actions> - <action sha256sum="d184d192f7b7577826c240ee8f0488046b0b38e032325dcf9aa3f6c730f8ea0d" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.7.6.tar.gz</action> + <action sha256sum="f85fd35ef67c8f76af0d556a4babe9acf7b8abdd8a77232d4f4763cc7de60eed" type="download_by_url">https://github.com/galaxyproject/dunovo/archive/v0.8.1.tar.gz</action> <action type="shell_command">make</action> <action type="move_directory_files"> <source_directory>.</source_directory> |