--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rcas.xml	Thu Apr 13 12:36:05 2017 -0400
@@ -0,0 +1,228 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<tool id="rcas" name="RNA Centric Annotation System" version="1.1.1">
+    <requirements>
+        <requirement type="package" version="1.1.1">bioconductor-rcas</requirement>
+    </requirements>
+    <stdio>
+        <regex match="Execution halted" source="both" level="fatal" description="Execution halted." />
+        <exit_code range="1:" />
+    </stdio>
+    <command><![CDATA[Rscript '$script_file'
+
+            &&
+            mv *RCAS.report.html RCAS.report.html
+
+
+            #if $run_anot == "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 $run_GOrich == "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 $choice.run_PATHrich == "TRUE":
+                &&
+                mv Table*GSEA.data.tsv GSEA.data.tsv
+            #end if
+
+
+            #if $run_motif == "TRUE":
+                &&
+                mv Table*motif_analysis_table.data.tsv motif_analysis_table.data.tsv
+            #end if]]></command>
+    <configfiles>
+        <configfile name="script_file">library("RCAS")
+
+           runReport(queryFilePath = '${input_BED}',
+
+           gffFilePath = '${input_GTF}',
+
+           #if $choice.run_PATHrich == "TRUE":
+                msigdbFilePath = '${choice.input_human_msigdb_gmt}',
+           #end if
+
+           annotationSummary = ${run_anot},
+
+           goAnalysis = ${run_GOrich},
+
+           msigdbAnalysis = ${choice.run_PATHrich},
+
+           motifAnalysis = ${run_motif},
+
+           genomeVersion = '${genomeVersion}',
+
+           outDir = getwd(),
+
+           printProcessedTables = TRUE,
+
+           sampleN = '${downsampling}',
+
+           selfContained = TRUE)</configfile>
+    </configfiles>
+    <inputs>
+        <param name="genomeVersion" type="select" label="Genome Version">
+            <option value="hg19" selected="true">hg19</option>
+            <option value="dm3">dm3</option>
+            <option value="ce10">ce10</option>
+            <option value="mm9">mm9</option>
+        </param>
+        <param name="input_BED" type="data" format="BED" label="Target regions in BED format" help="The coordinates should be in accord with Genome Version." />
+        <param name="input_GTF" type="data" format="GTF" label="Reference annotation in ENSEMBL GTF format" />
+        <param name="run_anot" label="Run annotation." type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="True" help="Use this option if you want to run annotation." />
+        <param name="run_GOrich" label="Run GO term enrichment" type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="False" help="Use this option if you want to run GO term enrichment (supported genome versions: hg19, mm9, dm3)." />
+        <conditional name="choice">
+            <param name="run_PATHrich" type="select" label="Run gene set enrichment" help="Use this option if you want to run gene set enrichment.">
+                <option value="FALSE" selected="True">No</option>
+                <option value="TRUE">Yes</option>
+            </param>
+            <when value="TRUE">
+                <param name="input_human_msigdb_gmt" type="data" format="tabular" label="Human Molecular Signatures Database (MSigDB)" help="The database is usesd for gene set enrichment (supported genome versions: hg19, mm9, dm3). For non-human species, the human MSigDB will be automatically converted accordingly." />
+            </when>
+            <when value="FALSE" />
+        </conditional>
+        <param name="run_motif" label="Run motif search" type="boolean" falsevalue="FALSE" truevalue="TRUE" checked="False" help="Use this option if you want to run motif search." />
+        <param name="downsampling" label="Downsampling (N)" type="text" value="0" help="Randomly sample query regions down to (N)" />
+    </inputs>
+    <outputs>
+        <data name="report" format="html" from_work_dir="RCAS.report.html" label="${tool.name} on ${on_string}: dynamic HTML" />
+        <data name="summarizeQueryRegions" format="tsv" from_work_dir="summarizeQueryRegions.data.tsv" label="${tool.name} on ${on_string}: Query regions summary">
+            <filter>run_anot == True</filter>
+        </data>
+        <data name="query_gene_types" format="tsv" from_work_dir="query_gene_types.data.tsv" label="${tool.name} on ${on_string}: Query gene types">
+            <filter>run_anot == True</filter>
+        </data>
+        <data name="transcriptBoundaryCoverage.fiveprime" format="tsv" from_work_dir="transcriptBoundaryCoverage.fiveprime.data.tsv" label="${tool.name} on ${on_string}: Transcript boundary coverage (5')">
+            <filter>run_anot == True</filter>
+        </data>
+        <data name="transcriptBoundaryCoverage.threeprime" format="tsv" from_work_dir="transcriptBoundaryCoverage.threeprime.data.tsv" label="${tool.name} on ${on_string}: Transcript boundary coverage (3')">
+            <filter>run_anot == True</filter>
+        </data>
+        <data name="exonIntronBoundaryCoverage.fiveprime" format="tsv" from_work_dir="exonIntronBoundaryCoverage.fiveprime.data.tsv" label="${tool.name} on ${on_string}: Exon-intron boundary coverage (5')">
+            <filter>run_anot == True</filter>
+        </data>
+        <data name="exonIntronBoundaryCoverage.threeprime" format="tsv" from_work_dir="exonIntronBoundaryCoverage.threeprime.data.tsv" label="${tool.name} on ${on_string}: Exon-intron boundary coverage (3')">
+            <filter>run_anot == True</filter>
+        </data>
+        <data name="coverageprofilelist" format="tsv" from_work_dir="coverageprofilelist.data.tsv" label="${tool.name} on ${on_string}: Coverage profile list">
+            <filter>run_anot == True</filter>
+        </data>
+        <data name="getTargetedGenesTable" format="tsv" from_work_dir="getTargetedGenesTable.data.tsv" label="${tool.name} on ${on_string}: Targeted genes">
+            <filter>run_anot == True</filter>
+        </data>
+        <data name="goCC" format="tsv" from_work_dir="goCC.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (cellular compartments)">
+            <filter>run_GOrich == True</filter>
+        </data>
+        <data name="goBP" format="tsv" from_work_dir="goBP.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (biological processes)">
+            <filter>run_GOrich == True</filter>
+        </data>
+        <data name="goMF" format="tsv" from_work_dir="goMF.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (molecular functions)">
+            <filter>run_GOrich == True</filter>
+        </data>
+        <data name="GSEA" format="tsv" from_work_dir="GSEA.data.tsv" label="${tool.name} on ${on_string}: Gene set enrichment analysis">
+            <filter>choice['run_PATHrich'] == "TRUE"</filter>
+        </data>
+        <data name="motif" format="tsv" from_work_dir="motif_analysis_table.data.tsv" label="${tool.name} on ${on_string}: Motif">
+            <filter>run_motif == True</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input_BED" value="input.TIA1.bed" />
+            <param name="input_GTF" value="input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf" />
+            <param name="input_human_msigdb_gmt" value="input.msigdb_test.gmt" />
+            <param name="run_anot" value="TRUE" />
+            <param name="run_GOrich" value="TRUE" />
+            <param name="run_PATHrich" value="TRUE" />
+            <param name="run_motif" value="TRUE" />
+            <param name="genomeVersion" value="hg19" />
+            <output name="report" file="output.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" />
+            <output name="motif" file="motif_analysis_table.data.tsv" ftype="tsv" compare="sim_size" />
+        </test>
+    </tests>
+    <help><![CDATA[.. class:: infomark
+
+**Purpose**
+
+RNA Centric Annotation System (RCAS) automatically generates
+dynamic annotations for custom input files
+that contain transcriptomic target regions.
+RCAS automatically summarizes annotated features
+that overlap with targets in the BED file,
+and perform enrichment analysis of
+Gene Ontology (GO) terms, gene set and motifs.
+
+-----
+
+.. class:: infomark
+
+**Inputs**
+
+1. A target region file in BED format
+2. A reference annotation file in GTF format
+3. A Human Molecular Signatures Database (MSigDB) (only needed for gene set enrichment)
+
+-----
+
+.. class:: infomark
+
+**Outputs**
+
+The outputs consist of a dynamic HTML file and
+a dozen of tabular files.
+The dynamic HTML file is composed of the interactive tables and figures,
+which can be downloaded and viewed with a web browser.
+
+The tabular files correspond to the respective figures in the HTML file,
+which are the results
+of different RCAS analysis, as following:
+
+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]]></help>
+    <citations>
+        <citation type="doi">10.1093/nar/gkx120</citation>
+    </citations>
+</tool>