| Next changeset 1:b63d6673f883 (2015-11-23) |
|
Commit message:
planemo upload commit 35b743e6492923c0e2b1e5e434eaf4e56d268108 |
|
added:
align_families.xml duplex.xml make_families.xml tool_dependencies.xml |
| b |
| diff -r 000000000000 -r d2e46adc199e align_families.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align_families.xml Mon Nov 23 22:06:21 2015 -0500 |
| b |
| @@ -0,0 +1,64 @@ +<?xml version="1.0"?> +<tool id="align_families" name="Align families" version="0.1"> + <description>from duplex sequencing data</description> + <requirements> + <requirement type="package" version="7.221">mafft</requirement> + <requirement type="package" version="0.1">duplex</requirement> + <requirement type="set_environment">DUPLEX_DIR</requirement> + </requirements> + <command detect_errors="exit_code">python \$DUPLEX_DIR/align_families.py $input > $output + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Input reads" help="with barcodes, grouped by family"/> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <tests> + <test> + <param name="input" value="smoke.families.tsv"/> + <output name="output" file="smoke.families.aligned.tsv"/> + </test> + <test> + <param name="input" value="families.in.tsv"/> + <output name="output" file="families.sort.tsv"/> + </test> + </tests> + <help> + +**What it does** + +This is for processing duplex sequencing data. It does a multiple sequence alignment on each (single-stranded) family of reads. + +----- + +**Input** + +This expects the output format of the "Make families" tool. + +----- + +**Output** + +The output is a tabular file where each line corresponds to a (single) read. + +The columns are:: + + 1: barcode (both tags) + 2: tag order in barcode ("ab" or "ba") + 3: read mate ("1" or "2") + 4: read name + 5: read sequence, aligned ("-" for gaps) + 6: read quality scores, aligned (" " for gaps) + +----- + +**Alignments** + +The alignments are done using MAFFT, specifically the command +:: + + $ mafft --nuc --quiet family.fa > family.aligned.fa + + </help> +</tool> |
| b |
| diff -r 000000000000 -r d2e46adc199e duplex.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/duplex.xml Mon Nov 23 22:06:21 2015 -0500 |
| [ |
| @@ -0,0 +1,61 @@ +<?xml version="1.0"?> +<tool id="duplex" name="Make consensus reads" version="0.1"> + <description>from duplex sequencing data</description> + <requirements> + <requirement type="package" version="0.1">duplex</requirement> + <requirement type="set_environment">DUPLEX_DIR</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + python \$DUPLEX_DIR/duplex.py -r $min_reads -q $qual_thres -F $qual_format $input + #if $keep_sscs: + --sscs-file $sscs + #end if + > duplex.fa + && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=1 duplex.fa > $output1 + && awk -f \$DUPLEX_DIR/utils/outconv.awk -v target=2 duplex.fa > $output2 + ]]> + </command> + <inputs> + <param name="input" type="data" format="tabular" label="Aligned input reads" /> + <param name="min_reads" type="integer" value="3" min="1" label="Minimum reads per family" help="Single-strand families with fewer than this many reads will be skipped."/> + <param name="qual_thres" type="integer" value="25" min="1" label="Minimum base quality" help="Bases with a PHRED score less than this will not be counted in the consensus making."/> + <param name="qual_format" type="select" label="FASTQ format" help="Solexa should also work for Illumina 1.3+ and 1.5+, and Sanger should work for Illumina 1.8+"> + <option value="sanger" selected="true">Sanger (PHRED 0 = "!")</option> + <option value="solexa">Solexa (PHRED 0 = "@")</option> + </param> + <param name="keep_sscs" type="boolean" truevalue="true" falsevalue="" label="Output single-strand consensus sequences" /> + </inputs> + <outputs> + <data name="output1" format="fasta" label="$tool.name on $on_string (mate 1)"/> + <data name="output2" format="fasta" label="$tool.name on $on_string (mate 2)"/> + <data name="sscs" format="fasta" label="$tool.name on $on_string (SSCS)"> + <filter>keep_sscs</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="families.msa.tsv"/> + <output name="output1" file="families.cons_1.fa"/> + <output name="output2" file="families.cons_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> +</tool> |
| b |
| diff -r 000000000000 -r d2e46adc199e make_families.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/make_families.xml Mon Nov 23 22:06:21 2015 -0500 |
| b |
| @@ -0,0 +1,83 @@ +<?xml version="1.0"?> +<tool id="make_families" name="Make families" version="0.1"> + <description>from duplex sequencing data</description> + <requirements> + <requirement type="package" version="0.1">duplex</requirement> + <requirement type="set_environment">DUPLEX_DIR</requirement> + </requirements> + <command>paste $fastq1 $fastq2 + | paste - - - - + | awk -f \$DUPLEX_DIR/make-barcodes.awk -v TAG_LEN=$taglen -v INVARIANT=$invariant + | sort + > $output + </command> + <inputs> + <param name="fastq1" type="data" format="fastq" label="Sequencing reads, mate 1"/> + <param name="fastq2" type="data" format="fastq" label="Sequencing reads, mate 2"/> + <param name="taglen" type="integer" value="12" min="0" label="Tag length" help="length of each random barcode on the ends of the fragments"/> + <param name="invariant" type="integer" value="5" min="0" label="Invariant sequence length" help="length of the sequence between the tag and actual sample sequence (the restriction site, normally)"/> + </inputs> + <outputs> + <data name="output" format="tabular"/> + </outputs> + <tests> + <test> + <param name="fastq1" value="smoke_1.fq"/> + <param name="fastq2" value="smoke_2.fq"/> + <param name="taglen" value="5"/> + <param name="invariant" value="1"/> + <output name="output" file="smoke.families.tsv"/> + </test> + <test> + <param name="fastq1" value="smoke_1.fq"/> + <param name="fastq2" value="smoke_2.fq"/> + <param name="taglen" value="5"/> + <param name="invariant" value="0"/> + <output name="output" file="smoke.families.i0.tsv"/> + </test> + </tests> + <help> + +**What it does** + +This tool is for processing raw duplex sequencing data, removing the barcodes and grouping by them into families of reads from the same fragment. + +----- + +**Output** + +The output will be a tabular file where each line corresponds to a pair of input reads. + +The columns are:: + + 1: barcode (both tags joined and ordered) + 2: tag order in barcode ("ab" or "ba") + 3: read1 name + 4: read1 sequence (minus the tag and invariant sequences) + 5: read1 quality scores (minus the same tag and invariant) + 6: read2 name + 7: read2 sequence (minus the tag and invariant sequences) + 8: read2 quality scores (minus the same tag and invariant) + +----- + +**Barcode creation** + +For each pair, the tool will remove the tag at the beginning of each read and create a barcode by concatenating the two tags. The order of the tags is determined by a string comparison so that it will make an identical barcode from pairs of either order. The original tag order will be noted in the second column. + +Since pairs from opposite strands will have the same tags, but in the reverse order, this produces the same barcode for reads from the same fragment, regardless of strand. Then a simple sort will group all reads from the same strand together, separated into strands by the different "order" values. + +Examples:: + + +---------------+-----------------+ + | input tags | output | + +-------+-------+-------+---------+ + | read1 | read2 | order | barcode | + +-------+-------+-------+---------+ + | ATG | CCT | ab | ATGCCT | + +-------+-------+-------+---------+ + | CCT | ATG | ba | ATGCCT | + +-------+-------+-------+---------+ + + </help> +</tool> |
| b |
| diff -r 000000000000 -r d2e46adc199e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Nov 23 22:06:21 2015 -0500 |
| b |
| @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mafft" version="7.221"> + <repository changeset_revision="d71e007323d4" name="mafft" owner="rnateam" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="duplex" version="0.1"> + <install version="1.0"> + <actions> + <action type="download_by_url">https://github.com/makrutenko/duplex/archive/master.tar.gz</action> + <action type="shell_command">make</action> + <action type="move_directory_files"> + <source_directory>.</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> + <action type="set_environment"> + <environment_variable action="set_to" name="DUPLEX_DIR">$INSTALL_DIR</environment_variable> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency> |