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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/rcas/ commit 3b9aec9beb72407e01f4a0c5b31c17ac3f92a851
author rnateam
date Thu, 13 Apr 2017 12:36:05 -0400
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children 7c7a2a381dfe
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-1:000000000000 0:aa9579837a2e
1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="rcas" name="RNA Centric Annotation System" version="1.1.1">
3 <requirements>
4 <requirement type="package" version="1.1.1">bioconductor-rcas</requirement>
5 </requirements>
6 <stdio>
7 <regex match="Execution halted" source="both" level="fatal" description="Execution halted." />
8 <exit_code range="1:" />
9 </stdio>
10 <command><![CDATA[Rscript '$script_file'
11
12 &&
13 mv *RCAS.report.html RCAS.report.html
14
15
16 #if $run_anot == "TRUE":
17 &&
18 mv Figure*summarizeQueryRegions.data.tsv summarizeQueryRegions.data.tsv &&
19 mv Figure*query_gene_types.data.tsv query_gene_types.data.tsv &&
20 mv Figure*transcriptBoundaryCoverage.fiveprime.data.tsv transcriptBoundaryCoverage.fiveprime.data.tsv &&
21 mv Figure*transcriptBoundaryCoverage.threeprime.data.tsv transcriptBoundaryCoverage.threeprime.data.tsv &&
22 mv Figure*exonIntronBoundaryCoverage.fiveprime.data.tsv exonIntronBoundaryCoverage.fiveprime.data.tsv &&
23 mv Figure*exonIntronBoundaryCoverage.threeprime.data.tsv exonIntronBoundaryCoverage.threeprime.data.tsv &&
24 mv Figure*coverageprofilelist.data.tsv coverageprofilelist.data.tsv &&
25 mv Table*getTargetedGenesTable.data.tsv getTargetedGenesTable.data.tsv
26 #end if
27
28
29 #if $run_GOrich == "TRUE":
30 &&
31 mv Table*goBP.data.tsv goBP.data.tsv &&
32 mv Table*goMF.data.tsv goMF.data.tsv &&
33 mv Table*goCC.data.tsv goCC.data.tsv
34 #end if
35
36
37 #if $choice.run_PATHrich == "TRUE":
38 &&
39 mv Table*GSEA.data.tsv GSEA.data.tsv
40 #end if
41
42
43 #if $run_motif == "TRUE":
44 &&
45 mv Table*motif_analysis_table.data.tsv motif_analysis_table.data.tsv
46 #end if]]></command>
47 <configfiles>
48 <configfile name="script_file">library("RCAS")
49
50 runReport(queryFilePath = '${input_BED}',
51
52 gffFilePath = '${input_GTF}',
53
54 #if $choice.run_PATHrich == "TRUE":
55 msigdbFilePath = '${choice.input_human_msigdb_gmt}',
56 #end if
57
58 annotationSummary = ${run_anot},
59
60 goAnalysis = ${run_GOrich},
61
62 msigdbAnalysis = ${choice.run_PATHrich},
63
64 motifAnalysis = ${run_motif},
65
66 genomeVersion = '${genomeVersion}',
67
68 outDir = getwd(),
69
70 printProcessedTables = TRUE,
71
72 sampleN = '${downsampling}',
73
74 selfContained = TRUE)</configfile>
75 </configfiles>
76 <inputs>
77 <param name="genomeVersion" type="select" label="Genome Version">
78 <option value="hg19" selected="true">hg19</option>
79 <option value="dm3">dm3</option>
80 <option value="ce10">ce10</option>
81 <option value="mm9">mm9</option>
82 </param>
83 <param name="input_BED" type="data" format="BED" label="Target regions in BED format" help="The coordinates should be in accord with Genome Version." />
84 <param name="input_GTF" type="data" format="GTF" label="Reference annotation in ENSEMBL GTF format" />
85 <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." />
86 <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)." />
87 <conditional name="choice">
88 <param name="run_PATHrich" type="select" label="Run gene set enrichment" help="Use this option if you want to run gene set enrichment.">
89 <option value="FALSE" selected="True">No</option>
90 <option value="TRUE">Yes</option>
91 </param>
92 <when value="TRUE">
93 <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." />
94 </when>
95 <when value="FALSE" />
96 </conditional>
97 <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." />
98 <param name="downsampling" label="Downsampling (N)" type="text" value="0" help="Randomly sample query regions down to (N)" />
99 </inputs>
100 <outputs>
101 <data name="report" format="html" from_work_dir="RCAS.report.html" label="${tool.name} on ${on_string}: dynamic HTML" />
102 <data name="summarizeQueryRegions" format="tsv" from_work_dir="summarizeQueryRegions.data.tsv" label="${tool.name} on ${on_string}: Query regions summary">
103 <filter>run_anot == True</filter>
104 </data>
105 <data name="query_gene_types" format="tsv" from_work_dir="query_gene_types.data.tsv" label="${tool.name} on ${on_string}: Query gene types">
106 <filter>run_anot == True</filter>
107 </data>
108 <data name="transcriptBoundaryCoverage.fiveprime" format="tsv" from_work_dir="transcriptBoundaryCoverage.fiveprime.data.tsv" label="${tool.name} on ${on_string}: Transcript boundary coverage (5')">
109 <filter>run_anot == True</filter>
110 </data>
111 <data name="transcriptBoundaryCoverage.threeprime" format="tsv" from_work_dir="transcriptBoundaryCoverage.threeprime.data.tsv" label="${tool.name} on ${on_string}: Transcript boundary coverage (3')">
112 <filter>run_anot == True</filter>
113 </data>
114 <data name="exonIntronBoundaryCoverage.fiveprime" format="tsv" from_work_dir="exonIntronBoundaryCoverage.fiveprime.data.tsv" label="${tool.name} on ${on_string}: Exon-intron boundary coverage (5')">
115 <filter>run_anot == True</filter>
116 </data>
117 <data name="exonIntronBoundaryCoverage.threeprime" format="tsv" from_work_dir="exonIntronBoundaryCoverage.threeprime.data.tsv" label="${tool.name} on ${on_string}: Exon-intron boundary coverage (3')">
118 <filter>run_anot == True</filter>
119 </data>
120 <data name="coverageprofilelist" format="tsv" from_work_dir="coverageprofilelist.data.tsv" label="${tool.name} on ${on_string}: Coverage profile list">
121 <filter>run_anot == True</filter>
122 </data>
123 <data name="getTargetedGenesTable" format="tsv" from_work_dir="getTargetedGenesTable.data.tsv" label="${tool.name} on ${on_string}: Targeted genes">
124 <filter>run_anot == True</filter>
125 </data>
126 <data name="goCC" format="tsv" from_work_dir="goCC.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (cellular compartments)">
127 <filter>run_GOrich == True</filter>
128 </data>
129 <data name="goBP" format="tsv" from_work_dir="goBP.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (biological processes)">
130 <filter>run_GOrich == True</filter>
131 </data>
132 <data name="goMF" format="tsv" from_work_dir="goMF.data.tsv" label="${tool.name} on ${on_string}: GO term enrichment (molecular functions)">
133 <filter>run_GOrich == True</filter>
134 </data>
135 <data name="GSEA" format="tsv" from_work_dir="GSEA.data.tsv" label="${tool.name} on ${on_string}: Gene set enrichment analysis">
136 <filter>choice['run_PATHrich'] == "TRUE"</filter>
137 </data>
138 <data name="motif" format="tsv" from_work_dir="motif_analysis_table.data.tsv" label="${tool.name} on ${on_string}: Motif">
139 <filter>run_motif == True</filter>
140 </data>
141 </outputs>
142 <tests>
143 <test>
144 <param name="input_BED" value="input.TIA1.bed" />
145 <param name="input_GTF" value="input.Homo_sapiens.GRCh37-chr1-f10k.75.gtf" />
146 <param name="input_human_msigdb_gmt" value="input.msigdb_test.gmt" />
147 <param name="run_anot" value="TRUE" />
148 <param name="run_GOrich" value="TRUE" />
149 <param name="run_PATHrich" value="TRUE" />
150 <param name="run_motif" value="TRUE" />
151 <param name="genomeVersion" value="hg19" />
152 <output name="report" file="output.TIA1.bed.RCAS.report.html" ftype="html" compare="sim_size" />
153 <output name="summarizeQueryRegions" file="summarizeQueryRegions.data.tsv" ftype="tsv" />
154 <output name="query_gene_types" file="query_gene_types.data.tsv" ftype="tsv" />
155 <output name="transcriptBoundaryCoverage.fiveprime" file="transcriptBoundaryCoverage.fiveprime.data.tsv" ftype="tsv" />
156 <output name="transcriptBoundaryCoverage.threeprime" file="transcriptBoundaryCoverage.threeprime.data.tsv" ftype="tsv" />
157 <output name="exonIntronBoundaryCoverage.fiveprime" file="exonIntronBoundaryCoverage.fiveprime.data.tsv" ftype="tsv" />
158 <output name="exonIntronBoundaryCoverage.threeprime" file="exonIntronBoundaryCoverage.threeprime.data.tsv" ftype="tsv" />
159 <output name="coverageprofilelist" file="coverageprofilelist.data.tsv" ftype="tsv" />
160 <output name="getTargetedGenesTable" file="getTargetedGenesTable.data.tsv" ftype="tsv" />
161 <output name="goCC" file="goCC.data.tsv" ftype="tsv" compare="sim_size"/>
162 <output name="goBP" file="goBP.data.tsv" ftype="tsv" compare="sim_size"/>
163 <output name="goMF" file="goMF.data.tsv" ftype="tsv" compare="sim_size"/>
164 <output name="GSEA" file="GSEA.data.tsv" ftype="tsv" />
165 <output name="motif" file="motif_analysis_table.data.tsv" ftype="tsv" compare="sim_size" />
166 </test>
167 </tests>
168 <help><![CDATA[.. class:: infomark
169
170 **Purpose**
171
172 RNA Centric Annotation System (RCAS) automatically generates
173 dynamic annotations for custom input files
174 that contain transcriptomic target regions.
175 RCAS automatically summarizes annotated features
176 that overlap with targets in the BED file,
177 and perform enrichment analysis of
178 Gene Ontology (GO) terms, gene set and motifs.
179
180 -----
181
182 .. class:: infomark
183
184 **Inputs**
185
186 1. A target region file in BED format
187 2. A reference annotation file in GTF format
188 3. A Human Molecular Signatures Database (MSigDB) (only needed for gene set enrichment)
189
190 -----
191
192 .. class:: infomark
193
194 **Outputs**
195
196 The outputs consist of a dynamic HTML file and
197 a dozen of tabular files.
198 The dynamic HTML file is composed of the interactive tables and figures,
199 which can be downloaded and viewed with a web browser.
200
201 The tabular files correspond to the respective figures in the HTML file,
202 which are the results
203 of different RCAS analysis, as following:
204
205 1. Annotation summary for query regions
206
207 * Query regions summary
208 * Query gene types
209 * Transcript boundary coverage (5')
210 * Transcript boundary coverage (3')
211 * Exon-intron boundary coverage (5')
212 * Exon-intron boundary coverage (3')
213 * Coverage profile list
214 * Targeted genes
215
216 2. GO term analysis results
217
218 * GO term enrichment (cellular compartments)
219 * GO term enrichment (biological processes)
220 * GO term enrichment (molecular functions)
221
222 3. Gene set enrichment analysis results
223
224 4. Motif analysis results]]></help>
225 <citations>
226 <citation type="doi">10.1093/nar/gkx120</citation>
227 </citations>
228 </tool>