<tool id="featurecounts" name="featureCounts" version="1.4.6.p5">
    <description>Measure gene expression in RNA-Seq experiments from SAM or BAM files.</description>
    <requirements>
        <requirement type="package" version="1.4.6.p5">featurecounts</requirement>
    </requirements>
    <version_command>featureCounts -v 2&gt;&amp;1 | grep .</version_command>
    <command><![CDATA[

        ## Check 01: do the alignments have a dbkey and is the option set to using it?
        #if $reference_gene_sets_source.source_select == "attribute" and len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) != 1
            echo "Invalid number of dbkeys are found: ${ len({ alignment.metadata.dbkey:True for alignment in $alignments }.keys()) }, while only one should be used. Make sure that the alignments are done on the same reference genome and that 'tool-data/gene_sets.loc' is configured properly!" >&2
        #else
            ## Check 02: are all alignments from the same type (bam || sam)
            #if len({ alignment.extension:True for alignment in $alignments }.keys()) != 1
                echo "Either all files must be SAM or all files must be BAM, no mixture is allowed." >&2
            #else
                featureCounts
                    -a
                    #if $reference_gene_sets_source.source_select == "indexed_filtered"
                        "$reference_gene_sets_source.reference_gene_sets"
                    #else if $reference_gene_sets_source.source_select == "indexed_all"
                        "$reference_gene_sets_source.reference_gene_sets"
                    #else if $reference_gene_sets_source.source_select == "history"
                        "$reference_gene_sets_source.reference_gene_sets"
                    #else
                        #*
                            This is a workaround to obtain the "genome.fa" file that
                            corresponds to the dbkey of the alignments.
                            Because this file is "calculated" during run-time, it can
                            be used in a workflow.
                        *#
                        "${ filter( lambda x: str( x[0] ) == str( { alignment.metadata.dbkey:True for alignment in $alignments }.keys()[0] ), $__app__.tool_data_tables[ 'gene_sets' ].get_fields() )[0][2] }"
                    #end if

                    -o "${output}"
                    -T \${GALAXY_SLOTS:-2}

                    #if $extended_parameters.parameters == "extended"
                        -t $extended_parameters.gff_feature_type
                        -g $extended_parameters.gff_feature_attribute
                        $extended_parameters.summarization_level
                        $extended_parameters.contribute_to_multiple_features
                        $extended_parameters.protocol
                        $extended_parameters.multimapping_counts
                        -Q $extended_parameters.mapping_quality
                        $extended_parameters.fragment_counting
                        $extended_parameters.check_distance
                        -d $extended_parameters.minimum_fragment_length
                        -D $extended_parameters.maximum_fragment_length
                        $extended_parameters.only_both_ends
                        $extended_parameters.exclude_chimerics
                    #end if

                    #for $alignment in $alignments
                         ${alignment}
                    #end for

                    2>&1

                #set $columns = [str(i+7) for i, alignment in enumerate($alignments)]
                #set $columns=",".join($columns)
                
                #if $format == "tabdel_default" or $format.value == "tabdel_default"
                    && cp $output tmp.txt
                    && egrep -v "^#" tmp.txt > tmp2.txt
                    && cut -f 1,$columns tmp2.txt > tmp_left.txt
                    && cut -f 6 tmp2.txt > tmp_right.txt
                    && paste tmp_left.txt tmp_right.txt > $output
                #elif $format == "tabdel_short" or $format.value == "tabdel_short"
                    && cp $output tmp.txt
                    && egrep -v "^#" tmp.txt | cut -f 1,$columns > $output
                #end if

                ## For every alignment, replace its filename for: "hid: sample name"
                #for $alignment in $alignments
                    #set $alignment_escaped = str($alignment).replace('/', '\/').replace('.', '\.')
                    #set $alignment_name_escaped = str(alignment.hid)+": "+str($alignment.name).replace('\t',' ').replace('\\','\\\\').replace("'","\\'").replace('/','\/')

                    #if $format.value == "tabdel_default" or $format.value == "tabdel_short"
                        && sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
                    #elif $format.value == "bed":
                        && $__tool_directory__/featurecounts2bed.sh -f "$output" > tmp.txt
                    #else
                        && sed -e '1,2 s/$alignment_escaped/${alignment_name_escaped}/g' $output > tmp.txt
                    #end if

                    && mv tmp.txt "${output}"

                    && sed -e '1 s/$alignment_escaped/${alignment_name_escaped}/g' $output".summary" > tmp.txt
                    && mv tmp.txt ${output}".summary"
                #end for
                && mv ${output}".summary" "${output_summary}"
            #end if
        #end if
    ]]></command>
    <inputs>
        <param name="alignments" type="data" format="bam,sam" label="Alignment file" help="The input alignment file(s) where the gene expression has to be counted. The file can have a SAM or BAM format; but ALL files in the series must be in THE SAME format." multiple="true" />

        <!-- Find out how to access the the GTF/GFF file(s) -->
        <conditional name="reference_gene_sets_source">
            <param name="source_select" type="select" label="GFF/GTF Source">
                <option value="indexed_filtered">Use a built-in index (which fits your reference)</option>
                <option value="history">Use reference from the history</option>
                <option value="indexed_all">Use a built-in index (entire list) - avoid this option if possible; only useful if you design a workflow</option>
                <option value="attribute">Use a built-in index based on the 'metadata.dbkey' attribute; ideal in workflows</option>
            </param>
            <when value="indexed_filtered">
                <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
                    <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
                        <column name="name"  index="0"/>
                        <column name="dbkey" index="1"/>
                        <column name="value" index="2"/>
                        <filter type="data_meta" ref="alignments" multiple="false" key="dbkey" column="1" />
                        <validator type="no_options" message="No indexes are available for the selected input dataset" />
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference_gene_sets" format="gff" type="data" label="Gene annotation file" help="The program assumes that the provided annotation file is in GTF format. Make sure that the gene annotation file corresponds to the same reference genome as used for the alignment." />
            </when>
            <when value="indexed_all">
                <param name="reference_gene_sets" type="select" label="Reference Gene Sets used during alignment (GFF/GTF)" >
                    <options from_data_table="gene_sets"><!-- replaces 'from_file="gene_sets"' - more strict -->
                        <column name="name"  index="0"/>
                        <column name="dbkey" index="1"/>
                        <column name="value" index="2"/>
                        <validator type="no_options" message="No indexes are available for the selected input dataset" />
                    </options>
                </param>
            </when>
            <when value="attribute">
                <!-- Do nothing, determine GTF/GFF file at runtime -->
            </when>
        </conditional>
        <param name="format" type="select" label="Output format">
            <option value="tabdel_default">Gene-name "\t" gene-count "\t" gene-length</option>
            <option value="tabdel_short" selected="true">Gene-name "\t" gene-count</option>
            <option value="bed">BED format (line per exon): chr "\t" start "\t" stop "\t" description "\t" readcount</option>
            <option value="complex">featureCounts 1.4.0+ default (extensive; complex)</option>
        </param>
        <conditional name="extended_parameters">
            <param name="parameters" type="select" label="featureCounts parameters" help="For more advanced featureCounts settings.">
                <option value="default">Default settings</option>
                <option value="extended">Extended settings</option>
            </param>
            <when value="default">
            </when>
            <when value="extended">
                <param name="gff_feature_type" type="text" value="exon"
                    label="GFF feature type filter"
                    help="Specify the feature type. Only rows which have the matched matched feature type in the provided GTF annotation file will be included for read counting. `exon' by default." />

                <param name="gff_feature_attribute" type="text" value="gene_id"
                    label="GFF gene identifier"
                    help="Specify the attribute type used to group features (eg. exons) into meta-features (eg. genes), when GTF annotation is provided. `gene_id' by default. This attribute type is usually the gene identifier. This argument is useful for the meta-feature level summarization." />

                <param name ="contribute_to_multiple_features" type="boolean" truevalue=" -O" falsevalue=""
                    label="Allow read to contribute to multiple features"
                    help="If specified, reads (or fragments if -p is specified) will be allowed to be assigned to more than one matched meta- feature (or matched feature if -f is specified)" />

                <param name="protocol" type="select" label="Strand specific protocol"
                    help="Indicate if strand-specific read counting should be performed.">
                    <option value=" -s 0" selected="true">Unstranded</option>
                    <option value=" -s 1">Stranded (forwards)</option>
                    <option value=" -s 2">Stranded (reverse)</option>
                </param>

                <param name="multimapping_counts" type="boolean" truevalue=" -M" falsevalue=""
                    label="Count multi-mapping reads/fragments"
                    help="If specified, multi-mapping reads/fragments will be counted (ie. a multi-mapping read will be counted up to N times if it has N reported mapping locations). The program uses the `NH' tag to find multi-mapping reads." />

                <param name="mapping_quality" type="integer" value="12" label="Minimum read quality"
                    help="The minimum mapping quality score a read must satisfy in order to be counted. For paired-end reads, at least one end should satisfy this criteria. 12 by default." />

                <param name="fragment_counting" type="boolean" truevalue=" -p" falsevalue="" checked="true"
                    label="PE: Count fragments instead of reads"
                    help="Paired-end specific: If specified, fragments (or templates) will be counted instead of reads." />

                <param name="check_distance" type="boolean" truevalue=" -P" falsevalue=""
                    label="PE: Check paired-end distance"
                    help="Paired-end specific: If specified, paired-end distance will be checked when assigning fragments to meta-features or features. This option is only applicable when -p (Count fragments instead of reads) is specified. The distance thresholds should be specified using -d and -D (minimum and maximum fragment/template length) options." />

                <param name="minimum_fragment_length" type="integer" value="50" label="PE: Minimum fragment/template length." />
                <param name="maximum_fragment_length" type="integer" value="600" label="PE: Maximum fragment/template length." />

                <param name="only_both_ends" type="boolean" truevalue=" -B" falsevalue=""
                    label="PE: only allow fragments with both reads aligned"
                    help="Paired-end specific: If specified, only fragments that have both ends successfully aligned will be considered for summarization. This option is only applicable for paired-end reads." />

                <param name="exclude_chimerics" type="boolean" truevalue=" -C" falsevalue="" checked="true"
                    label="PE: Exclude chimeric fragments"
                    help="Paired-end specific: If specified, the chimeric fragments (those fragments that have their two ends aligned to different chromosomes) will NOT be included for summarization. This option is only applicable for paired-end read data." />

                <param name ="summarization_level" type="boolean" truevalue=" -f" falsevalue=""
                    label="On feature level"
                    help="If specified, read summarization will be performed at the feature level. By default (-f is not specified), the read summarization is performed at the meta-feature level." />

            </when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
        <data format="tabular" name="output_summary" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])} summary" />
    </outputs>
    <tests>
        <test>
            <param name="alignments" value="featureCounts_input1.bam,featureCounts_input2.bam" ftype="bam" />
            <param name="source_select" value="history" />
            <param name="format" value="tabdel_default" />
            <param name="reference_gene_sets" value="featureCounts_guide.gff" ftype="gff" />
            <output name="output" file="output.tab"/>
            <output name="output_summary" file="output_summary.tab"/>
        </test>
    </tests>
    
    <help><![CDATA[
featureCounts
#############

Overview
--------
FeatureCounts is a light-weight read counting program written entirely in the C programming language. It can be used to count both gDNA-seq and RNA-seq reads for genomic features in in SAM/BAM files.
It has a variety of advanced parameters but its major strength is its outstanding performance: analysis of a 10GB SE BAM file takes about 7 minutes on a single average CPU (Homo Sapiens genome) [1].

Input formats
-------------
Alignments should be provided in either:

- SAM format, http://samtools.sourceforge.net/samtools.shtml#5
- BAM format

Gene regions should be provided in the GFF/GTF format:

- http://genome.ucsc.edu/FAQ/FAQformat.html#format3
- http://www.ensembl.org/info/website/upload/gff.html

Installation
------------

1. Make sure you have proper GFF/GTF files (corresponding to your reference genome used for the aligment) uploaded to your history.

2. Make sure that your gene_sets.loc is configured properly as data table. This is generally done by copying the right information into: tool_data_table_conf.xml. More info at:  https://wiki.galaxyproject.org/Admin/Tools/Data%20Tables

License
-------

**featureCounts / subread package**:

- GNU General Public License version 3.0 (GPLv3)

Contact
-------

The tool wrapper has been written by Youri Hoogstrate from the Erasmus
Medical Center (Rotterdam, Netherlands) on behalf of the Translational
Research IT (TraIT) project:

http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch

More tools by the Translational Research IT (TraIT) project can be found
in the following toolsheds:

http://toolshed.g2.bx.psu.edu/

http://testtoolshed.g2.bx.psu.edu/

References
----------
**featureCounts: an efficient general purpose program for assigning sequence reads to genomic features.**

*Liao Y1, Smyth GK, Shi W.* - Bioinformatics. 2014 Apr 1;30(7):923-30.

- http://www.ncbi.nlm.nih.gov/pubmed/24227677
- http://dx.doi.org/10.1093/bioinformatics/btt656


Acknowledgements
----------------

I would like to thank Marius van den Beek for his contribution to this galaxy wrapper.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt656</citation>
    </citations>
</tool>