<tool id="stringtie" name="StringTie" version="1.0.1">
    <description>RNA-Seq assembler</description>
    <requirements>
        <requirement type="package" version="1.0.1">stringtie</requirement>
    </requirements>
    <command><![CDATA[
stringtie "$input_bam"
-o "$output_gtf"
-p "\${GALAXY_SLOTS:-1}"
#if str($guide.use_guide) == 'yes':
    -C "$coverage" -G "$guide.guide_gff" $guide.input_estimation
    #if str($guide.output_ballgown) == '-b':
        $guide.output_ballgown `pwd`
    #end if
#end if
#if str($option_set.options) == 'advanced':
    -l "$option_set.name_prefix"
    -f "$option_set.fraction"
    -m "$option_set.min_tlen"
    -a "$option_set.min_anchor_len"
    -j "$option_set.min_anchor_cov"
    -c "$option_set.min_bundle_cov"
    -s "$option_set.maxcov"
    -g "$option_set.bdist"    
    -M "$option_set.bundle_fraction" $option_set.sensitive $option_set.disable_trimming
#end if
]]>
</command>
    <inputs>
        <param format="bam" label="BAM file to assemble" name="input_bam" type="data" />
        <conditional name="guide">
            <param label="Use GFF file to guide assembly" name="use_guide" type="select">
                <option value="yes">Use GFF</option>
                <option selected="True" value="no">Do not use GFF</option>
            </param>
            <when value="no" />
            <when value="yes">
                <param format="gtf,gff3" help="(-G)" label="Reference annotation to use for guiding the assembly process" name="guide_gff" type="data" />
                <param falsevalue="" help="(-e)" label="Perform abundance estimation only of input transcripts" name="input_estimation" truevalue="-e" type="boolean" />
                <param falsevalue="" help="(-b)" label="Output additional files for use in Ballgown" name="output_ballgown" truevalue="-b" type="boolean" />
            </when>
        </conditional>
        <conditional name="option_set">
            <param label="Options" name="options" type="select">
                <option selected="True" value="default">Use defaults</option>
                <option value="advanced">Specify advanced options</option>
            </param>
            <when value="default" />
            <when value="advanced">
                <param falsevalue="" help="(-t)" label="Disable trimming of predicted transcripts based on coverage" name="disable_trimming" truevalue="-t" type="boolean" />
                <param falsevalue="" help="(-S)" label="Increase sensitivity" name="sensitive" truevalue="-S" type="boolean" />
                <param help="(-l)" label="Name prefix for output transcripts" name="name_prefix" type="text" value="STRG" />
                <param help="(-f)" label="Minimum isoform fraction" max="1.0" min="0.0" name="fraction" type="float" value="0.15" />
                <param help="(-m)" label="Minimum assembled transcript length" name="min_tlen" type="integer" value="200" />
                <param help="(-a)" label="Minimum anchor length for junctions" name="min_anchor_len" type="integer" value="10" />
                <param help="(-j)" label="Minimum junction coverage" name="min_anchor_cov" type="integer" value="1" />
                <param help="(-c)" label="Minimum bundle reads per bp coverage to consider for assembly" name="min_bundle_cov" type="integer" value="2" />
                <param help="(-s)" label="Coverage saturation threshold" name="maxcov" type="integer" value="1000000" />
                <param help="(-g)" label="Gap between read mappings triggering a new bundle" name="bdist" type="integer" value="50" />
                <param help="(-M)" label="Fraction of bundle allowed to be covered by multi-hit reads" name="bundle_fraction" type="float" value="0.95" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="gtf" label="${tool.name} on ${on_string}: Assembled transcripts" name="output_gtf" />
        <data format="gff3" label="${tool.name} on ${on_string}: Coverage" name="coverage">
            <filter>guide['use_guide'] == "yes"</filter>
        </data>
        <data format="tabular" from_work_dir="e_data.ctab" label="${tool.name} on ${on_string}: exon-level expression measurements" name="exon_expression">
            <filter>guide['output_ballgown']</filter>
        </data>
        <data format="tabular" from_work_dir="i_data.ctab" label="${tool.name} on ${on_string}: intron-level expression measurements" name="intron_expression">
            <filter>guide['output_ballgown']</filter>
        </data>
        <data format="tabular" from_work_dir="t_data.ctab" label="${tool.name} on ${on_string}: transcript-level expression measurements" name="transcript_expression">
            <filter>guide['output_ballgown']</filter>
        </data>
        <data format="tabular" from_work_dir="e2t.ctab" label="${tool.name} on ${on_string}: exon to transcript mapping" name="exon_transcript_mapping">
            <filter>guide['output_ballgown']</filter>
        </data>
        <data format="tabular" from_work_dir="i2t.ctab" label="${tool.name} on ${on_string}: intron to transcript mapping" name="intron_transcript_mapping">
            <filter>guide['output_ballgown']</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
            <param name="use_guide" value="no" />
            <param name="options" value="default" />
            <output file="stringtie_out1.gtf" ftype="gtf" name="output_gtf" />
        </test>
        <test>
            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
            <param name="use_guide" value="no" />
            <param name="options" value="advanced" />
            <param name="fraction" value="0.17" />
            <output file="stringtie_out2.gtf" ftype="gtf" name="output_gtf" />
        </test>
        <test>
            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
            <param name="use_guide" value="yes" />
            <param name="guide_gff" value="stringtie_in.gtf" />
            <param name="options" value="default" />
            <output file="stringtie_out3.gtf" ftype="gtf" name="output_gtf" />
        </test>
        <test>
            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
            <param name="use_guide" value="yes" />
            <param name="guide_gff" value="stringtie_in.gtf" />
            <param name="options" value="advanced" />
            <param name="fraction" value="0.17" />
            <output file="stringtie_out4.gtf" ftype="gtf" name="output_gtf" />
        </test>
        <test>
            <param ftype="bam" name="input_bam" value="stringtie_in1.bam" />
            <param name="use_guide" value="yes" />
            <param name="output_ballgown" value="yes" />
            <param name="guide_gff" value="stringtie_in.gtf" />
            <param name="options" value="default" />
            <output file="ballgown/e_data.ctab" ftype="tabular" name="exon_expression" />
            <output file="ballgown/i_data.ctab" ftype="tabular" name="intron_expression" />
            <output file="ballgown/t_data.ctab" ftype="tabular" name="transcript_expression" />
            <output file="ballgown/e2t.ctab" ftype="tabular" name="exon_transcript_mapping" />
            <output file="ballgown/i2t.ctab" ftype="tabular" name="intron_transcript_mapping" />
            <output file="stringtie_out5.gtf" ftype="gtf" name="output_gtf" />
            <output file="stringtie_out_coverage.gtf" ftype="gff3" name="coverage" />
        </test>
    </tests>
    <help>
<![CDATA[
StringTie v1.0.1 usage:
 stringtie <input.bam> [-G <guide_gff>] [-l <label>] [-o <out_gtf>] [-p <cpus>]
  [-v] [-a <min_anchor_len>] [-m <min_tlen>] [-j <min_anchor_cov>] [-n sens]
  [-C <coverage_file_name>] [-s <maxcov>] [-c <min_bundle_cov>] [-g <bdist>]
  {-B | -b <dir_path>} [-e]

Assemble RNA-Seq alignments into potential transcripts.
 
 Options:
 -G reference annotation to use for guiding the assembly process (GTF/GFF3)
 -l name prefix for output transcripts (default: STRG)
 -f minimum isoform fraction (default: 0.1)
 -m minimum assembled transcript length to report (default 200bp)
 -o output path/file name for the assembled transcripts GTF (default: stdout)
 -a minimum anchor length for junctions (default: 10)
 -j minimum junction coverage (default: 1)
 -t disable trimming of predicted transcripts based on coverage
    (default: coverage trimming is enabled)
 -c minimum reads per bp coverage to consider for transcript assembly (default: 2.5)
 -s coverage saturation threshold; further read alignments will be
    ignored in a region where a local coverage depth of <maxcov> 
    is reached (default: 1,000,000);
 -v verbose (log bundle processing details)
 -g gap between read mappings triggering a new bundle (default: 50)
 -C output file with reference transcripts that are covered by reads
 -M fraction of bundle allowed to be covered by multi-hit reads (default:0.95)
 -p number of threads (CPUs) to use (default: 1)
 -B enable output of Ballgown table files which will be created in the
    same directory as the output GTF (requires -G, -o recommended)
 -b enable output of Ballgown table files but these files will be 
    created under the directory path given as <dir_path>
 -e only estimates the abundance of given reference transcripts (requires -G)
 ]]>
    </help>
    <citations>
        <citation type="doi">doi:10.1038/nbt.3122</citation>
    </citations>
</tool>