<tool id="rcas" name="RCAS" version="1.5.4">
    <description>- RNA Centric Annotation System</description>
    <requirements>
        <requirement type="package" version="1.5.4">bioconductor-rcas</requirement>
    </requirements>
    <stdio>
        <regex match="Execution halted" source="both" level="fatal" description="Execution halted." />
        <exit_code range="1:" />
    </stdio>
    <command><![CDATA[
        cat '$script_file' &&
            #if $analysis_type.analysis_type_selector == 'single_set_analysis':
                Rscript '$script_file' &&
                mv *RCAS.report.html RCAS.report.html
                #if $run_annot == "TRUE":
                    &&
                    mv Figure*summarizeQueryRegions.data.tsv summarizeQueryRegions.data.tsv &&
                    mv Figure*query_gene_types.data.tsv query_gene_types.data.tsv &&
                    mv Figure*transcriptBoundaryCoverage.fiveprime.data.tsv transcriptBoundaryCoverage.fiveprime.data.tsv &&
                    mv Figure*transcriptBoundaryCoverage.threeprime.data.tsv transcriptBoundaryCoverage.threeprime.data.tsv &&
                    mv Figure*exonIntronBoundaryCoverage.fiveprime.data.tsv exonIntronBoundaryCoverage.fiveprime.data.tsv &&
                    mv Figure*exonIntronBoundaryCoverage.threeprime.data.tsv exonIntronBoundaryCoverage.threeprime.data.tsv &&
                    mv Figure*coverageprofilelist.data.tsv coverageprofilelist.data.tsv &&
                    mv Table*getTargetedGenesTable.data.tsv getTargetedGenesTable.data.tsv
                #end if
                #if $analysis_type.run_go == "TRUE":
                    &&
                    mv Table*goBP.data.tsv goBP.data.tsv &&
                    mv Table*goMF.data.tsv goMF.data.tsv &&
                    mv Table*goCC.data.tsv goCC.data.tsv
                #end if

                #if $analysis_type.gsea_set.run_gsea == "TRUE":
                    &&
                    mv Table*GSEA.data.tsv GSEA.data.tsv
                #end if
            #else:
                 Rscript '$script_file'
            #end if
    ]]></command>
    <configfiles>
        <configfile name="script_file"><![CDATA[
        #import re
        library("RCAS")
            #if $analysis_type.analysis_type_selector == 'single_set_analysis':
                runReport(queryFilePath = '${analysis_type.single_bed_file}',
                gffFilePath = '${input_gtf_file}',
                genomeVersion = '${genome_version}',
                #if $analysis_type.run_go
                    goAnalysis = TRUE,
                #end if
                #if $analysis_type.gsea_set.run_gsea
                    msigdbAnalysis = TRUE,
                    msigdbFilePath = '${$analysis_type.gsea_set.input_human_msigdb_gmt}',
                #end if
                sampleN = '${analysis_type.downsampling}',
                annotationSummary = ${run_annot},
                motifAnalysis = ${run_motif},
                outDir = getwd(),
                #if $analysis_type.output_raw_tables
                    printProcessedTables = TRUE,
                #end if
                selfContained = TRUE)
            #elif $analysis_type.analysis_type_selector == 'multi_set_analysis':
                library("mgcv")
                paths <- c('#echo "','".join(map(str, $analysis_type.multi_bed_file))#')
                #set $ids = [re.sub('[^\w\-]', '_', str($bed_file.element_identifier)) for $bed_file in $analysis_type.multi_bed_file]
                ids <- c('#echo "','".join($ids)#')
                projData <- data.frame('sampleName' = ids, 'bedFilePath' = paths, stringsAsFactors = FALSE)
                projDataFile <- file.path(getwd(), 'myProjDataFile.tsv')
                write.table(projData, projDataFile, sep = '\t', quote =FALSE, row.names = FALSE)
                gtfFilePath = '${input_gtf_file}'
                databasePath <- file.path(getwd(), 'myProject.sqlite')
                invisible(createDB(dbPath = databasePath, projDataFile = projDataFile, gtfFilePath = gtfFilePath, 
                    motifAnalysis = ${run_motif},
                    annotationSummary = ${run_annot},
                    genomeVersion = '${genome_version}'))
                sampleData <- data.frame('sampleName' = ids, 'sampleGroup' = ids, stringsAsFactors = FALSE)
                sampleDataFile <- file.path(getwd(), 'mySampleDataTable.tsv')
                write.table(sampleData, sampleDataFile, sep = '\t', quote =FALSE, row.names = FALSE)
                runReportMetaAnalysis(dbPath = databasePath, sampleTablePath = sampleDataFile, outFile = file.path(getwd(), 'RCAS.multi_sample_report.html'))
            #end if
         ]]></configfile>
    </configfiles>
    <inputs>
        <param name="genome_version" type="select" label="Genome Version">
            <option value="hg19" selected="true">hg19</option>
            <option value="hg38">hg38</option>
            <option value="mm9">mm9</option>
            <option value="mm10">mm10</option>
            <option value="dm3">dm3</option>
            <option value="ce10">ce10</option>
        </param>

        <param name="input_gtf_file" type="data" format="GTF" label="Reference annotation in ENSEMBL GTF format" />

        <conditional name="analysis_type">
            <param name="analysis_type_selector" type="select" label="Select analysis type">
                <option value="single_set_analysis" selected="true">Single sample analysis</option>
                <option value="multi_set_analysis">Multi sample analysis</option>
            </param>
            <!-- Single dataset analysis -->
            <when value="single_set_analysis">
                <param name="single_bed_file" type="data" format="bed"
                       label="Single sample analysis BED file"
                       help="Genomic BED file used for single sample analysis"/>
                <param name="run_go" label="Run GO term enrichment analysis" 
                       type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="False" 
                       help="Run GO term enrichment analysis (supported genome versions: hg19, hg38, mm9, mm10, dm3)" />
                <conditional name="gsea_set">
                    <param name="run_gsea" type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="false" label="Run gene set enrichment analysis"/>
                    <when value="FALSE" />
                    <when value="TRUE">
                        <param name="input_human_msigdb_gmt" type="data" format="tabular"
                               label="Provide human Molecular Signatures Database (MSigDB) file" 
                               help="This database file is needed for gene set enrichment analysis (supported genome versions: hg19, hg38, mm9, mm10, dm3). For non-human species, the human MSigDB will be automatically converted." />
                    </when>
                </conditional>
                <param name="downsampling" label="Downsampling (N)" type="text" value="0" 
                       help="Randomly sample down query regions to (N). To activate sampling a positive integer value smaller than the total number of query regions should be given. Default value is 0 (i.e. no downsampling applied)" />
                <param name="output_raw_tables" type="boolean" falsevalue="FALSE" truevalue="TRUE" value="False" 
                       label="Output raw data tables"
                       help="Output single sample analysis raw data tables that are used for plots/tables as text files"/>
            </when>
            <!-- Multiple datasets meta analysis -->
            <when value="multi_set_analysis">
                <param name="multi_bed_file" type="data" format="bed"
                       label="Multi sample analysis BED files" multiple="true"
                       help="Genomic BED files used for multi sample analysis. NOTE that the dataset name inside the Galaxy history is used as identifier for each set, resulting in plots with the Galaxy dataset names corresponding to their respective input BED files."/>
            </when>
        </conditional>

        <!-- Parameters common to multi and single set analysis -->
        <param name="run_annot" label="Output annotation summaries" type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="True" help="Output annotation summaries from overlap operations" />
        <param name="run_motif" label="Run motif analysis" type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="False" help="Run motif analysis for each input dataset and each transcript region" />
    </inputs>
    <outputs>
        <data name="report" format="html" from_work_dir="RCAS.report.html" label="${tool.name} on ${on_string}: single sample analysis report HTML">
            <filter>analysis_type["analysis_type_selector"] == "single_set_analysis"</filter>
        </data>
        <data name="summarizeQueryRegions" format="tsv" from_work_dir="summarizeQueryRegions.data.tsv" label="${tool.name} on ${on_string}: Query regions summary">
            <filter>run_annot is True and analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="query_gene_types" format="tsv" from_work_dir="query_gene_types.data.tsv" label="${tool.name} on ${on_string}: Query gene types">
            <filter>run_annot is True and analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="transcriptBoundaryCoverage.fiveprime" format="tsv" from_work_dir="transcriptBoundaryCoverage.fiveprime.data.tsv" label="${tool.name} on ${on_string}: Transcript boundary coverage (5')">
            <filter>run_annot is True and analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="transcriptBoundaryCoverage.threeprime" format="tsv" from_work_dir="transcriptBoundaryCoverage.threeprime.data.tsv" label="${tool.name} on ${on_string}: Transcript boundary coverage (3')">
            <filter>run_annot is True and analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="exonIntronBoundaryCoverage.fiveprime" format="tsv" from_work_dir="exonIntronBoundaryCoverage.fiveprime.data.tsv" label="${tool.name} on ${on_string}: Exon-intron boundary coverage (5')">
            <filter>run_annot is True and analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="exonIntronBoundaryCoverage.threeprime" format="tsv" from_work_dir="exonIntronBoundaryCoverage.threeprime.data.tsv" label="${tool.name} on ${on_string}: Exon-intron boundary coverage (3')">
            <filter>run_annot is True and analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="coverageprofilelist" format="tsv" from_work_dir="coverageprofilelist.data.tsv" label="${tool.name} on ${on_string}: Coverage profile list">
            <filter>run_annot is True and analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="getTargetedGenesTable" format="tsv" from_work_dir="getTargetedGenesTable.data.tsv" label="${tool.name} on ${on_string}: Targeted genes">
            <filter>run_annot is True and analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="goCC" format="tsv" from_work_dir="goCC.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (cellular compartments)">
            <filter>analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['run_go'] is True and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="goBP" format="tsv" from_work_dir="goBP.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (biological processes)">
            <filter>analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['run_go'] is True and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="goMF" format="tsv" from_work_dir="goMF.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (molecular functions)">
            <filter>analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['run_go'] is True and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="GSEA" format="tsv" from_work_dir="GSEA.data.tsv" label="${tool.name} on ${on_string}: Gene set enrichment analysis">
            <filter>analysis_type["analysis_type_selector"] == "single_set_analysis" and analysis_type['gsea_set']['run_gsea'] is True and analysis_type['output_raw_tables'] is True</filter>
        </data>
        <data name="multi_report" format="html" from_work_dir="RCAS.multi_sample_report.html" label="${tool.name} on ${on_string}: multi sample analysis report HTML">
            <filter>analysis_type["analysis_type_selector"] == "multi_set_analysis"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="analysis_type_selector" value="single_set_analysis"/>
            <param name="single_bed_file" value="input.TIA1.bed"/>
            <param name="input_gtf_file" value="input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf"/>
            <param name="input_human_msigdb_gmt" value="input.msigdb_test.gmt"/>
            <param name="run_annot" value="TRUE"/>
            <param name="run_go" value="TRUE"/>
            <param name="run_gsea" value="TRUE"/>
            <param name="run_motif" value="TRUE"/>
            <param name="output_raw_tables" value="TRUE"/>
            <param name="genome_version" value="hg19" />
            <output name="report" file="input.TIA1.bed.RCAS.report.html" ftype="html" compare="sim_size"/>
            <output name="summarizeQueryRegions" file="summarizeQueryRegions.data.tsv" ftype="tsv"/>
            <output name="query_gene_types" file="query_gene_types.data.tsv" ftype="tsv"/>
            <output name="transcriptBoundaryCoverage.fiveprime" file="transcriptBoundaryCoverage.fiveprime.data.tsv" ftype="tsv"/>
            <output name="transcriptBoundaryCoverage.threeprime" file="transcriptBoundaryCoverage.threeprime.data.tsv" ftype="tsv"/>
            <output name="exonIntronBoundaryCoverage.fiveprime" file="exonIntronBoundaryCoverage.fiveprime.data.tsv" ftype="tsv"/>
            <output name="exonIntronBoundaryCoverage.threeprime" file="exonIntronBoundaryCoverage.threeprime.data.tsv" ftype="tsv"/>
            <output name="coverageprofilelist" file="coverageprofilelist.data.tsv" ftype="tsv"/>
            <output name="getTargetedGenesTable" file="getTargetedGenesTable.data.tsv" ftype="tsv"/>
            <output name="goCC" file="goCC.data.tsv" ftype="tsv" compare="sim_size"/>
            <output name="goBP" file="goBP.data.tsv" ftype="tsv" compare="sim_size"/>
            <output name="goMF" file="goMF.data.tsv" ftype="tsv" compare="sim_size"/>
            <output name="GSEA" file="GSEA.data.tsv" ftype="tsv"/>
        </test>
        <test>
            <param name="analysis_type_selector" value="multi_set_analysis"/>
            <param name="multi_bed_file" value="EIF4A3Sauliere20121a.bed,EIF4A3Sauliere20121b.bed,FMR1_Ascano2012a_hg19.bed,FMR1_Ascano2012b_hg19.bed,FUS_Nakaya2013c_hg19.bed,FUS_Nakaya2013d_hg19.bed"/>
            <param name="input_gtf_file" value="hg19.sample.gtf"/>
            <param name="run_annot" value="TRUE"/>
            <param name="run_motif" value="TRUE"/>
            <param name="genome_version" value="hg19" />
            <output name="multi_report" file="test2_multi_set_analysis_report.html" ftype="html" compare="sim_size" delta="20000"/>
        </test>
    </tests>
    <help><![CDATA[

**Introduction**

RCAS is an R/Bioconductor package designed as a generic reporting tool for the functional analysis of transcriptome-wide regions of interest detected by high-throughput experiments. Such transcriptomic regions could be, for instance, signal peaks detected by CLIP-Seq analysis for protein-RNA interaction sites, RNA modification sites (alias the epitranscriptome), CAGE-tag locations, or any other collection of query regions at the level of the transcriptome. RCAS produces in-depth annotation summaries and coverage profiles based on the distribution of the query regions with respect to transcript features (exons, introns, 5’/3’ UTR regions, exon-intron boundaries, promoter regions). Moreover, RCAS can carry out functional enrichment analyses of annotated gene sets, GO terms, and de novo motif discovery. RCAS is available in the Bioconductor repository, packaged in multiple environments including Conda, Galaxy, and Guix, and as a webservice at http://rcas.mdc-berlin.de/.

Currently supported genome builds are hg19 and hg38 (human), mm9 and mm10 (mouse), dm3 (fly), and ce10 (worm). Modules for annotation summaries and motif analysis are supported for each of these genome builds. GO term and gene-set enrichment analyses are supported for hg19, hg38, mm9, mm10, and dm3. ce10 is currently not supportedfor GO/GSEA modules.


-----

**Inputs**

1. One (single sample analysis) or several (multi sample analysis) genomic target region files in BED format
2. A genome reference annotation file in GTF format
3. A human Molecular Signatures Database (MSigDB) (only in single sample analysis for gene set enrichment analysis)

-----

**Outputs**

The outputs consist of a dynamic HTML file (both for single and multi sample analysis) and optionally a number (depending on selected options) of tabular files (single sample analysis only).
The dynamic HTML file is composed of interactive tables and figures,
which can be downloaded and viewed with a web browser.

The tabular files contain the RCAS analysis results, corresponding to the 
respective figures in the HTML file:

1. Annotation summary for query regions

  * Query regions summary
  * Query gene types
  * Transcript boundary coverage (5')
  * Transcript boundary coverage (3')
  * Exon-intron boundary coverage (5')
  * Exon-intron boundary coverage (3')
  * Coverage profile list
  * Targeted genes

2. GO term analysis results

  * GO term enrichment (cellular compartments)
  * GO term enrichment (biological processes)
  * GO term enrichment (molecular functions)

3. Gene set enrichment analysis results

4. Motif analysis results (no table output in 1.5.4.)

    ]]></help>
    <citations>
        <citation type="doi">10.1093/nar/gkx120</citation>
    </citations>
</tool>