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comparison cummerbund_wrapper.xml @ 3:f109453ecfa2

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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
author Jim Johnson <jj@umn.edu>
date Fri, 15 Nov 2013 13:39:14 -0600
parents fdf01b3c1841
children 137aab1d9ac1
comparison
equal deleted inserted replaced
2:fdf01b3c1841 3:f109453ecfa2
1 <tool id="cummerbund" name="cummeRbund" version="0.0.7"> 1 <tool id="cummerbund" name="cummeRbund" version="0.0.7">
2 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description> 2 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description>
3 3 <!--
4 <requirements>
5 <requirement type="package" version="3.0.1">R_3_0_1</requirement>
6 </requirements>
7 -->
4 <command interpreter="python"> 8 <command interpreter="python">
5 cummerbund_wrapper.py 9 cummerbund_wrapper.py
6 --r-script ${script_file} 10 --r-script ${script_file}
7 --html-report-from-directory "${output_html}" "${output_html.files_path}" 11 --html-report-from-directory "${output_html}" "${output_html.files_path}"
8 </command> 12 </command>
24 <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/> 28 <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/>
25 <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential expression testing"/> 29 <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential expression testing"/>
26 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/> 30 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/>
27 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/> 31 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/>
28 <param name="rebuild" type="hidden" value="TRUE"/> 32 <param name="rebuild" type="hidden" value="TRUE"/>
33 <conditional name="reference">
34 <param name="include" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Include genome reference and Feature file"/>`
35 <when value="yes">
36 <param name="gtf_file" type="data" format="gtf,gff3" label="Transcripts" help="A transcript GFF3 or GTF file produced by cufflinks, cuffcompare, or other source."/>
37 <conditional name="genome">
38 <param name="source" type="select" label="Reference sequence data">
39 <option value="cached">Locally cached</option>
40 <option value="history">History</option>
41 </param>
42 <when value="cached">
43 <param name="ref_fasta" type="select" label="Select the reference genome that was used for cuffdiff">
44 <options from_data_table="all_fasta">
45 <filter type="sort_by" column="2" />
46 <validator type="no_options" message="No reference fasta files are available" />
47 </options>
48 </param>
49 </when>
50 <when value="history">
51 <param name="ref_file" type="data" format="fasta" label="Using reference file" />
52 </when>
53 </conditional>
54 </when>
55 <when value="no"/>
56 </conditional>
29 </when> 57 </when>
30 <when value="history"> 58 <when value="history">
31 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/> 59 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/>
32 </when> 60 </when>
33 </conditional> 61 </conditional>
225 253
226 ## Load cummeRbund library 254 ## Load cummeRbund library
227 library("cummeRbund") 255 library("cummeRbund")
228 256
229 ## Initialize cuff object 257 ## Initialize cuff object
258 #if $backend_database_source.backend_database_selector == "cuffdiff_output":
259 ## Check if gtfFIle and genome are includes
260 #set $gtf_link = None
261 #if $backend_database_source.reference.include:
262 #set $gtf_link = '.'.join(['cuff',$backend_database_source.reference.gtf_file.extension])
263 system('ln -s $backend_database_source.reference.gtf_file $gtf_link')
264 #if $backend_database_source.reference.genome.source == 'cached':
265 #set $ref_file = $backend_database_source.reference.genome.ref_fasta
266 #else
267 #set $ref_file = $backend_database_source.reference.genome.ref_file
268 #end if
269 #end if
230 cuff &lt;- readCufflinks(dir = "", 270 cuff &lt;- readCufflinks(dir = "",
231 #if $backend_database_source.backend_database_selector == "cuffdiff_output":
232 dbFile = "${output_database}", 271 dbFile = "${output_database}",
233 geneFPKM = "${genes_fpkm_tracking}", 272 geneFPKM = "${genes_fpkm_tracking}",
234 geneDiff = "${genes_exp}", 273 geneDiff = "${genes_exp}",
235 isoformFPKM = "${isoforms_fpkm_tracking}", 274 isoformFPKM = "${isoforms_fpkm_tracking}",
236 isoformDiff = "${isoforms_exp}", 275 isoformDiff = "${isoforms_exp}",
239 CDSFPKM = "${cds_fpkm_tracking}", 278 CDSFPKM = "${cds_fpkm_tracking}",
240 CDSExpDiff = "${cds_exp_diff}", 279 CDSExpDiff = "${cds_exp_diff}",
241 CDSDiff = "${cds_diff}", 280 CDSDiff = "${cds_diff}",
242 promoterFile = "${promoters_diff}", 281 promoterFile = "${promoters_diff}",
243 splicingFile = "${splicing_diff}", 282 splicingFile = "${splicing_diff}",
283 #if $gtf_link:
284 gtfFile = "${gtf_link}",
285 genome = "${ref_file}",
286 #end if
244 rebuild = T) 287 rebuild = T)
245 #else: 288 #else:
289 cuff &lt;- readCufflinks(dir = "",
246 dbFile = "${backend_database_source.input_database}", 290 dbFile = "${backend_database_source.input_database}",
247 rebuild = F) 291 rebuild = F)
248 #end if 292 #end if
249 293
250 ## Print out info 294 ## Print out info