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<tool id="fastq_screen" name="fastq_screen" version="0.4.2">
    <description>Screen for contamination</description>
    <requirements>
        <requirement type="package" version="2.1.0">bowtie2</requirement>
        <requirement type="package" version="0.4.2">fastq_screen</requirement>
    </requirements>
    <command> 
    fastq_screen --aligner="bowtie2" --outdir="." --conf="$fastqrunconf"
    #if $sampN &gt; 0:
    --subset "$sampN"
    #end if
    "$input1"
    #if $singlePaired.sPaired == "paired":
    "$input2" 
    #end if
    ; mv *_screen.png ${outpng} ; mv *_screen.txt ${outtext}
    </command>

    <stdio>
        <regex match=".*" source="both" level="warning" description="fastqc_screen perl script output"/>
    </stdio>

    <inputs>
        <param name="jobName" type="text" size="120" value="fastq_screen" label="Job narrative (included in output names as a reminder)" 
          help="Only letters, numbers and underscores _ will be retained in this field">
           <sanitizer invalid_char="">
              <valid initial="string.letters,string.digits"><add value="_" /> </valid>
           </sanitizer>
        </param>
        <param name="sampN" type="integer" size="20" value="500000" label="Sample this number of reads. Set to 0 or less to use all"
        help="Time/precision trade off - fewer reads takes a little less time trading off precision of the estimates."/>
        <conditional name="singlePaired">
            <param name="sPaired" type="select" label="Single ended or mate-pair ended reads in this library?">
              <option value="single" selected="true">Single-end</option>
              <option value="paired">Paired-end</option>
            </param>
            <when value="single">
                <param format="fastqsanger,fastq" name="input1" type="data" label="RNA-Seq FASTQ file" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33"/>
            </when>
            <when value="paired">
                <param format="fastqsanger,fastq" name="input1" type="data" label="RNA-Seq FASTQ file, forward reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
                <param format="fastqsanger,fastq" name="input2" type="data" label="RNA-Seq FASTQ file, reverse reads" help="Nucleotide-space: Must have Sanger-scaled quality values with ASCII offset 33" />
            </when>
        </conditional>

        <!-- Genome source. -->
        <repeat name="refGenomes" title="Installed organism reference sequences to check for alignment to your fastq" min="1"
        help="For checking cell culture sequence for contamination, Mycoplasma Genitalium might be a good choice eg">
            <param name="ref" type="select" label="Bowtie2 reference genome">
                <options from_data_table="bowtie2_indexes">
                <filter type="sort_by" column="3"/>
                <validator type="no_options" message="No indexes are available for bowtie2"/>
                </options>
            </param>
        </repeat>
    </inputs>

    <outputs>
       <data format="tabular" name="outtext" label="${jobName}.xls"/>
       <data format="png" name="outpng" label="${jobName}.png"/>
    </outputs>
    <configfiles>
         <configfile name="fastqrunconf">
###### autogenerated by fastq_screen.xml for fastq_screen run
BOWTIE2 bowtie2
#for $refs in $refGenomes:
DATABASE    $refs.ref.fields.value $refs.ref.fields.path    BOWTIE2
#end for
         </configfile>
    </configfiles>
    
<help>

**What it does**
This is a Galaxy wrapper exposing software from Babraham -fastq_screen_
Designed to search sequence data in fastq files for matches to contaminants or to check the likely
species.
In QC checking, you can use it to look for (eg) sequence from contaminating mycoplasmae in cell cultures - it may be non-differential but it will be pro-inflammatory and, well, less than ideal.

Here's the help from the perl script used by this wrapper:

Fastq Screen - Screen sequences against a panel of databases

Synopsis

  fastq_screen [OPTION]... [FastQ FILE]...

Function

  Fastq Screen is intended to be used as part of a QC pipeline.
  It allows you to take a sequence dataset and search it
  against a set of bowtie databases.  It will then generate
  both a text and a graphical summary of the results to see if
  the sequence dataset contains the kind of sequences you expect
  or not.

Options

  --help -h      Print program help and exit

  --subset       Don't use the whole sequence file to search, but
                 create a temporary dataset of this size. The
                 dataset created will be of approximately (within
                 a factor of 2) of this size. If the real dataset
                 is smaller than twice the specified size then the
                 whole dataset will be used. Subsets will be taken
                 evenly from throughout the whole original dataset

  --paired       Files are paired end. Files must be specified in
                 the correct order with pairs of files coming
                 immediately after one another. Results files will
                 be named after the first file in the pair if the
                 names differ between the two files.

  --outdir       Specify a directory in which to save output files.
                 If no directory is specified then output files
                 are saved into the same directory as the input
                 file.

  --illumina1_3  Assume that the quality values are in encoded in
                 Illumina v1.3 format. Defaults to Sanger format
                 if this flag is not specified

  --quiet        Supress all progress reports on stderr and only
                 report errors

  --version      Print the program version and exit

  --threads      Specify across how many threads bowtie will be
                 allowed to run. Overrides the default value set
                 in the conf file

  --conf         Manually specify a location for the configuration
                 file to be used for this run. If not specified 
                 then the file will be taken from the same directory 
                 as the fastq_screen program

  --color        FastQ files are in colorspace. This requires that 
                 the libraries configures in the config file are 
                 colorspace indices.

  --bowtie       Specify extra parameters to be passed to bowtie. 
                 These parameters should be quoted to clearly 
                 delimit bowtie parameters from fastq_screen 
                 parameters. You should not try to use this option 
                 to override the normal search or reporting options 
                 for bowtie which are set automatically but it might 
                 be useful to allow reads to be trimmed before
                 alignment etc.

  --bowtie2      Specify extra parameters to be passed to bowtie 2. 
                 These parameters should be quoted to clearly 
                 delimit bowtie2 parameters from fastq_screen 
                 parameters. You should not try to use this option 
                 to override the normal search or reporting options 
                 for bowtie which are set automatically but it might 
                 be useful to allow reads to be trimmed before
                 alignment etc.

  --nohits       Writes to a file the sequences that did not map to 
                 any of the specified genome libraries. If the 
                 subset option is also specified, only reads from 
                 the temporary dataset that failed to align to the
                 reference genomes will be written to the output file.

  --aligner     Specify the aligner to use for the mapping. Valid 
                arguments are 'bowtie' or 'bowtie2'.
  
    
**Attributions**

Note that each component has its own license.
Good luck with figuring out your obligations.

fastq_screen - see the web site at Fastq_screen_

Galaxy_ (that's what you are using right now!) for gluing everything together 


Code and documentation comprising this tool was written by Ross Lazarus and that part is Licensed_ the same way as other rgenetics artefacts

.. _Fastq_screen: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen

.. _Galaxy: http://getgalaxy.org

.. _Licensed: https://www.gnu.org/licenses/lgpl.html

</help>
</tool>