<?xml version="1.0"?>
<tool_dependency>
    <package name="flexbar" version="2.5">
        <install version="1.0">
            <actions_group>
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url" target_filename="flexbar_v2.5_linux64.tgz">https://github.com/seqan/flexbar/releases/download/v2.5.0/flexbar_v2.5_linux64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
                    <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
flexbar - flexible barcode and adapter removal
==============================================

SYNOPSIS
    flexbar -r reads [-t target] [-b barcodes] [-a adapters] [options]

DESCRIPTION
    -h, --help
          Displays this help message.
    -H, --advanced
          Print help with advanced options.
    -i, --cite
          Show program reference for citation.

  Basic options:
    -n, --threads NUM
          Number of threads to employ. Default: 1.
    -t, --target STR
          Prefix for output file names or paths. Default: flexbar.
    -r, --reads FILE
          Fasta/q file or stdin (-) with reads that may contain barcodes.
    -p, --reads2 FILE
          Second input file of paired reads, gz and bz2 files supported.
    -f, --format STR
          Quality format: sanger, solexa, i1.3, i1.5, i1.8 (illumina 1.8+).
    -c, --color-space
          Input in color-space format csfasta or csfastq in sanger scaling.

  Barcode detection:
    -b, --barcodes FILE
          Fasta file with barcodes for demultiplexing, may contain N.
    -br, --barcode-reads FILE
          Fasta/q file containing separate barcode reads for detection.
    -be, --barcode-trim-end STR
          Type of detection, see section trim-end modes. Default: ANY.
    -bo, --barcode-min-overlap NUM
          Minimum overlap of barcode and read. Default: barcode length.
    -bt, --barcode-threshold NUM
          Allowed mismatches and gaps per overlap of 10. Default: 1.0.
    -bu, --barcode-unassigned
          Include unassigned reads in output generation.

  Adapter removal:
    -a, --adapters FILE
          Fasta file with adapters for removal that may contain N.
    -as, --adapter-seq STR
          Single adapter sequence as alternative to adapters option.
    -ae, --adapter-trim-end STR
          Type of removal, see section trim-end modes. Default: RIGHT.
    -ao, --adapter-min-overlap NUM
          Minimum overlap of adapter and read for removal. Default: 3.
    -at, --adapter-threshold NUM
          Allowed mismatches and gaps per overlap of 10. Default: 3.0.

  Filtering and trimming:
    -u, --max-uncalled NUM
          Allowed uncalled bases (N or .) for each read. Default: 0.
    -x, --pre-trim-left NUM
          Trim given number of bases on 5' read end before detection.
    -y, --pre-trim-right NUM
          Trim specified number of bases on 3' end prior to detection.
    -q, --pre-trim-phred NUM
          Trim 3' end until specified or higher quality reached.
    -k, --post-trim-length NUM
          Trim to specified read length from 3' end after removal.
    -m, --min-read-length NUM
          Minimum read length to remain after removal. Default: 18.

  Output selection:
    -o, --fasta-output
          Prefer non-quality format fasta or csfasta for output.
    -z, --zip-output STR
          Direct compression of output files. One of GZ and BZ2.
    -s, --single-reads
          Write single paired reads for too short counterparts.

  Logging and tagging:
    -l, --log-level STR
          Print chosen read alignments. One of ALL, MOD, and TAB.
    -g, --removal-tags
          Tag reads that are subject to adapter or barcode removal.

  Trim-end modes:
    ANY: longer side of read remains after removal of overlap
    LEFT: right side remains after removal, align &lt;= read end
    RIGHT: left part remains after removal, align &gt;= read start
    LEFT_TAIL: consider first n bases of reads in alignment
    RIGHT_TAIL: use only last n bases, see tail-length options

EXAMPLES
    flexbar -r reads.fq -f i1.8 -t target -b brc.fa -a adap.fa
    flexbar -r reads.csfastq.gz -a adap.fa -ao 5 -ae LEFT -c

VERSION
    flexbar version: 2.5
    Last update June 30, 2014

Advanced options: flexbar -H
        </readme>
    </package>
</tool_dependency>