<tool id="seq_filter_by_mapping" name="Filter sequences by mapping" version="0.0.7">
    <description>from SAM/BAM file</description>
    <requirements>
        <requirement type="package" version="1.67">biopython</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <version_command>
python $__tool_directory__/seq_filter_by_mapping.py --version
    </version_command>
    <command detect_errors="aggressive">
python $__tool_directory__/seq_filter_by_mapping.py -i '$input_file' -f '$input_file.ext' -m $pair_mode
#if $output_choice_cond.output_choice=="both"
 -p '$output_pos' -n '$output_neg'
#elif $output_choice_cond.output_choice=="pos"
 -p '$output_pos'
#elif $output_choice_cond.output_choice=="neg"
 -n '$output_neg'
#end if
## Now loop over all the mapping files
#for i in $mapping_file#'${i}' #end for#
    </command>
    <inputs>
        <param name="input_file" type="data" format="fasta,fastq,sff" label="Sequence file to be filtered" help="FASTA, FASTQ, or SFF format." />
        <param name="mapping_file" type="data" format="sam,bam" multiple="true" label="SAM/BAM mapping of those sequences" help="SAM or BAM format." />
        <conditional name="output_choice_cond">
            <param name="output_choice" type="select" label="Output mapped reads, unmapped reads, or both?">
                <option value="both">Both mapped and unmapped reads, as two files</option>
                <option value="pos">Just mapped reads, as a single file</option>
                <option value="neg">Just unmapped reads, as a single file</option>
            </param>
            <!-- Seems need these dummy entries here, compare this to indels/indel_sam2interval.xml -->
            <when value="both" />
            <when value="pos" />
            <when value="neg" />
        </conditional>
        <param name="pair_mode" type="select" label="Paired read treatment">
            <option value="lax" selected="true">Treat as a pair, allow either read to be mapped</option>
            <option value="strict">Treat as a pair, require both reads to be mapped</option>
            <!-- The following would actually be more work as have to store qname/1 and qname/2 separately for filter...
            <option value="solo">Treat independently (will split partners when only one maps)</option>
            -->
        </param>
    </inputs>
    <outputs>
        <data name="output_pos" format_source="input_file" metadata_source="input_file" label="$input_file.name (mapped)">
            <filter>output_choice_cond["output_choice"] != "neg"</filter>
        </data>
        <data name="output_neg" format_source="input_file" metadata_source="input_file" label="$input_file.name (unmapped)">
            <filter>output_choice_cond["output_choice"] != "pos"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
            <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" />
            <param name="pair_mode" value="lax" />
            <param name="output_choice" value="pos" />
            <output name="output_pos" file="SRR639755_sample_lax.fastq" ftype="fastqsanger" />
        </test>
        <test>
            <param name="input_file" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" />
            <param name="mapping_file" value="SRR639755_sample_by_coord.sam" ftype="sam" />
            <param name="pair_mode" value="strict" />
            <param name="output_choice" value="pos" />
            <output name="output_pos" file="SRR639755_sample_strict.fastq" ftype="fastqsanger" />
        </test>
    </tests>
    <help>
**What it does**

By default it divides a FASTA, FASTQ or Standard Flowgram Format (SFF) file in
two, those sequences (or read pairs) which do or don't map in the provided
SAM/BAM file. You can opt to have a single output file of just the mapping reads,
or just the non-mapping ones.

**Example Usage**

You might wish to perform a contamination screan by mapping your reads against
known contaminant reference sequences, then use this tool to select only the
unmapped reads for further analysis (e.g. *de novo* assembly).

Similarly you might wish to map your reads against a known bacterial reference,
then take the non-mapping sequences forward for analysis if looking for novel
plasmids.


**References**

If you use this Galaxy tool in work leading to a scientific publication please
cite:

Peter J.A. Cock (2014), Galaxy tool for filtering reads by mapping
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping

This tool uses Biopython to read and write SFF files, so you may also wish to
cite the Biopython application note (and Galaxy too of course):

Cock et al (2009). Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 25(11) 1422-3.
https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878.

This tool is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_mapping
    </help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btp163</citation>
    </citations>
</tool>