<?xml version="1.0"?>
<tool name="BloomTree Manager - Create" id="btman_create" version="1.0.0">
    <description>a Sequence Bloom Tree</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code">
<![CDATA[
    python '$__tool_directory__/create.py'
    
    --explist '${explist}'

    --qualitycontrol ${conditional_quality.quality_control}
    #if $conditional_quality.quality_control == '0':
        --qualitythreshold 0.0
    #elif $conditional_quality.quality_control == '1':
        --qualitythreshold ${conditional_quality.quality_threshold}
    #end if

    --klen ${kmer_len}
    --minabundance ${min_abundance}

    --outfile '${outfile}'
]]>
    </command>
    <inputs>
        <param format="tabular" name="explist" type="data" label="Select a file with the list of experiments" help="This should be a tabular file with two columns. Take a look at the tool documentation for a detailed explanation about the its content." />

        <conditional name="conditional_quality">
            <param name="quality_control" type="boolean" checked="false" truevalue="1" falsevalue="0" label="Apply a quality control procedure" />
            <when value="1">
                <param name="quality_threshold" size="1" type="float" value="0.8" min="0.0" max="1.0" label="Quality threshold" help="If the number of sequences flagged as poor quality on the total number of sequences in a file is less than this threshold, the sequence file will be excluded." />
            </when>
        </conditional>

        <param name="kmer_len" type="integer" value="21" min="0" label="K-mer length" />
        <param name="min_abundance" type="integer" value="2" min="0" label="Bloom filter minimum abundance" help="This value is the minimum abundance cutoff for the creation of the Bloom filters. It is worth noting that the same minimum abundance is used for each Bloom filter." />
    </inputs>
    <outputs>
        <data format="txt" name="outfile" label="${tool.name} SBT: Result" from_work_dir="btman.create.txt" />
    </outputs>

    <help><![CDATA[
This tool is part of the BloomTree Manager Framework that allow to create a Sequence Bloom Tree starting 
with a set of FASTA or FASTQ files. It allows also to control the quality of the input dataset and 
exclude the files that do not reach a specified quality level.

-----

**Input file**

The input file for this tool must contain two columns with their values delimited by a tab.
The first column contains a list of SRA accessions, and the second column contains a unique identifier
for each set of SRA accessions.

The input file is structured like the example below::
    
    SRR805782  blood
    SRR837459  blood
    SRR837458  blood
    SRR837453  blood
    SRR837456  blood
    ...
    SRR791048  breast
    SRR553483  breast
    SRR553482  breast
    SRR791045  breast
    ...
    SRR950876  brain
    SRR786621  brain

It is worth noting that for each cluster of accessions, every accession should be unique.
It is indeed possible to repeat an accession in multiple clusters.

The tool will create a Sequence Bloom Tree for each cluster of accessions.

-----

**Output**

The tool returns a single text file only. It contains the a tree identifier, one for
each cluster of accessions specified in the input file, that can be used with the
Query tool of the BloomTree Manager Suite to search for the presence of a set of
specific transcripts.

Take a look at the Query tool documentation for a detailed description about how
to query a Sequence Bloom Tree.

-----

.. class:: infomark

**Notes**

This Galaxy tool has been developed by Fabio Cumbo.

Please visit this GithHub_repository_ for more information about the BloomTree Manager

.. _GithHub_repository: https://github.com/fabio-cumbo/bloomtree-manager
    ]]></help>

    <expand macro="citations" />
</tool>