Mercurial > repos > jjohnson > cummerbund
annotate cummerbund_wrapper.xml @ 9:532a336a14c1 default tip
Need all_fasta.loc for cummerbund
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 13 Oct 2014 09:39:39 -0500 |
parents | 137aab1d9ac1 |
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rev | line source |
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1 <tool id="cummerbund" name="cummeRbund" version="0.0.7"> |
0 | 2 <description>R package designed to aid and simplify the task of analyzing Cufflinks RNA-Seq output</description> |
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3 <!-- |
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4 <requirements> |
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5 <requirement type="package" version="3.0.1">R_3_0_1</requirement> |
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6 </requirements> |
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7 --> |
0 | 8 <command interpreter="python"> |
9 cummerbund_wrapper.py | |
10 --r-script ${script_file} | |
11 --html-report-from-directory "${output_html}" "${output_html.files_path}" | |
12 </command> | |
13 | |
14 <inputs> | |
15 <conditional name="backend_database_source"> | |
16 <param name="backend_database_selector" type="select" label="Will you select a backend database file from the history or do you want to build a new one using cuffdiff output?"> | |
17 <option value="history" selected="true">Use backend database from the history</option> | |
18 <option value="cuffdiff_output">Build backend database using cuffdiff output</option> | |
19 </param> | |
20 <when value="cuffdiff_output"> | |
21 <param format="tabular" name="isoforms_fpkm_tracking" type="data" label="Transcript FPKM tracking"/> | |
22 <param format="tabular" name="isoforms_exp" type="data" label="Transcript differential expression testing"/> | |
23 <param format="tabular" name="genes_fpkm_tracking" type="data" label="Gene FPKM tracking"/> | |
24 <param format="tabular" name="genes_exp" type="data" label="Gene differential expression testing"/> | |
25 <param format="tabular" name="tss_groups_fpkm_tracking" type="data" label="TSS groups FPKM tracking"/> | |
26 <param format="tabular" name="tss_groups_exp" type="data" label="TSS groups differential expression testing"/> | |
27 <param format="tabular" name="cds_fpkm_tracking" type="data" label="CDS FPKM tracking"/> | |
28 <param format="tabular" name="cds_exp_diff" type="data" label="CDS FPKM differential expression testing"/> | |
29 <param format="tabular" name="cds_diff" type="data" label="CDS overloading diffential expression testing"/> | |
30 <param format="tabular" name="promoters_diff" type="data" label="Promoters differential expression testing"/> | |
31 <param format="tabular" name="splicing_diff" type="data" label="Splicing differential expression testing"/> | |
32 <param name="rebuild" type="hidden" value="TRUE"/> | |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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33 <conditional name="reference"> |
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34 <param name="include" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Include genome reference and Feature file"/>` |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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35 <when value="yes"> |
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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."/> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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37 <conditional name="genome"> |
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38 <param name="source" type="select" label="Reference sequence data"> |
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39 <option value="cached">Locally cached</option> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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40 <option value="history">History</option> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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41 </param> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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42 <when value="cached"> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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43 <param name="ref_fasta" type="select" label="Select the reference genome that was used for cuffdiff"> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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44 <options from_data_table="all_fasta"> |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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45 <filter type="sort_by" column="2" /> |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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46 <validator type="no_options" message="No reference fasta files are available" /> |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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47 </options> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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parents:
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48 </param> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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49 </when> |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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50 <when value="history"> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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parents:
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51 <param name="ref_file" type="data" format="fasta" label="Using reference file" /> |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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52 </when> |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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53 </conditional> |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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54 </when> |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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parents:
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55 <when value="no"/> |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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parents:
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56 </conditional> |
0 | 57 </when> |
58 <when value="history"> | |
59 <param name="input_database" type="data" format="cuffdatadb" label="Select backend database (sqlite)"/> | |
60 </when> | |
61 </conditional> | |
62 <repeat name="plots" title="Plots"> | |
63 <param name="width" type="text" value="1280" label="The width of the image"/> | |
64 <param name="height" type="text" value="960" label="The height of the image"/> | |
65 <conditional name="plot"> | |
66 <param name="type" type="select" label="Plot type"> | |
67 <option value="density" selected="true">Density</option> | |
68 <option value="dispersion">Dispersion</option> | |
69 <option value="fpkmSCV">Squared Coefficient of Variation</option> | |
70 <option value="scatterMatrix">Scatter Matrix</option> | |
71 <option value="boxplot">Boxplot</option> | |
72 <option value="scatter">Scatter</option> | |
73 <option value="volcano">Volcano</option> | |
74 <option value="heatmap">Heatmap</option> | |
75 <option value="cluster">Cluster</option> | |
76 <option value="expressionplot">Expression Plot</option> | |
77 <option value="expressionbarplot">Expression Bar Plot</option> | |
78 <option value="mds">MultiDimentional Scaling (MDS) Plot</option> | |
79 <option value="pca">Principal Component Analysis (PCA) Plot</option> | |
80 <option value="maplot">Intensity vs Fold-change (MvaA) Plot</option> | |
81 <option value="dendrogram">Dendrogram</option> | |
82 </param> | |
83 <when value="density"> | |
84 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
85 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Replicates?"/> | |
86 </when> | |
87 <when value="mds"> | |
88 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> | |
89 </when> | |
90 <when value="pca"> | |
91 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> | |
92 </when> | |
93 <when value="maplot"> | |
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94 <param name="x" type="text" label="Sample name 1" help="Condition1 name used in cuffdiff"> |
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95 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/> |
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96 </param> |
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97 <param name="y" type="text" label="Sample name 2" help="Condition2 name used in cuffdiff"> |
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98 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/> |
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parents:
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99 </param> |
0 | 100 <param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/> |
101 </when> | |
102 <when value="dendrogram"> | |
103 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> | |
104 </when> | |
105 <when value="dispersion"> | |
106 </when> | |
107 <when value="fpkmSCV"> | |
108 </when> | |
109 <when value="scatterMatrix"> | |
110 </when> | |
111 <when value="boxplot"> | |
112 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
113 </when> | |
114 <when value="scatter"> | |
115 <param name="x" type="text" label="Sample name for x axis"/> | |
116 <param name="y" type="text" label="Sample name for y axis"/> | |
117 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
118 <param name="smooth" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Add a smooth-fit regression line"/> | |
119 <conditional name="multiple_genes"> | |
120 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
121 <when value="T"> | |
122 <param name="features" type="select" label="Expression levels to plot?"> | |
123 <option value="gene" selected="true">Genes</option> | |
124 <option value="isoforms">Isoforms</option> | |
125 <option value="tss">TSS</option> | |
126 <option value="cds">CDS</option> | |
127 </param> | |
128 <repeat name="genes" title="Genes"> | |
129 <param name="gene_id" type="text" label="Gene ID"/> | |
130 </repeat> | |
131 </when> | |
132 <when value="F"/> | |
133 </conditional> | |
134 </when> | |
135 <when value="volcano"> | |
136 <param name="x" type="text" label="First sample name for comparison"/> | |
137 <param name="y" type="text" label="Second sample name for comparison"/> | |
138 <conditional name="multiple_genes"> | |
139 <param name="multiple_genes_selector" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Limit plot to a group of genes?"/> | |
140 <when value="T"> | |
141 <param name="features" type="select" label="Expression levels to plot?"> | |
142 <option value="gene" selected="true">Genes</option> | |
143 <option value="isoforms">Isoforms</option> | |
144 <option value="tss">TSS</option> | |
145 <option value="cds">CDS</option> | |
146 </param> | |
147 <repeat name="genes" title="Genes"> | |
148 <param name="gene_id" type="text" label="Gene ID"/> | |
149 </repeat> | |
150 </when> | |
151 <when value="F"/> | |
152 </conditional> | |
153 </when> | |
154 <when value="heatmap"> | |
155 <param name="features" type="select" label="Expression levels to plot?"> | |
156 <option value="gene" selected="true">Genes</option> | |
157 <option value="isoforms">Isoforms</option> | |
158 <option value="tss">TSS</option> | |
159 <option value="cds">CDS</option> | |
160 </param> | |
161 <repeat name="genes" title="Genes"> | |
162 <param name="gene_id" type="text" label="Gene ID"/> | |
163 </repeat> | |
164 <param name="clustering" type="select" label="Cluster by"> | |
165 <option value="row">Row</option> | |
166 <option value="column">Column</option> | |
167 <option value="both" selected="true">Both</option> | |
168 <option value="none">None</option> | |
169 </param> | |
170 <param name="labcol" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
171 <param name="labrow" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Display column labels?"/> | |
172 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
173 <param name="border" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw border around plot?"/> | |
174 </when> | |
175 <when value="cluster"> | |
176 <param name="features" type="select" label="Expression levels to plot?"> | |
177 <option value="gene" selected="true">Genes</option> | |
178 <option value="isoforms">Isoforms</option> | |
179 <option value="tss">TSS</option> | |
180 <option value="cds">CDS</option> | |
181 </param> | |
182 <repeat name="genes" title="Genes"> | |
183 <param name="gene_id" type="text" label="Gene ID"/> | |
184 </repeat> | |
185 <param name="k" type="text" label="Number of pre-defined clusters to attempt to find."/> | |
186 <param name="iter_max" type="text" value="100" label="Max iterations"/> | |
187 </when> | |
188 <when value="expressionplot"> | |
189 <param name="features" type="select" label="Expression levels to plot?"> | |
190 <option value="gene" selected="true">Genes</option> | |
191 <option value="isoforms">Isoforms</option> | |
192 <option value="tss">TSS</option> | |
193 <option value="cds">CDS</option> | |
194 </param> | |
195 <param name="gene_id" type="text" label="Gene ID"/> | |
196 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
197 <param name="draw_summary" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Draw a 'summary' line with mean FPKM | |
198 values for each condition?"/> | |
199 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
200 </when> | |
201 <when value="expressionbarplot"> | |
202 <param name="features" type="select" label="Expression levels to plot?"> | |
203 <option value="gene" selected="true">Genes</option> | |
204 <option value="isoforms">Isoforms</option> | |
205 <option value="tss">TSS</option> | |
206 <option value="cds">CDS</option> | |
207 </param> | |
208 <param name="gene_id" type="text" label="Gene ID"/> | |
209 <param name="log_mode" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Apply log10 transformation on FPKM values?"/> | |
210 <param name="show_error_bars" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Draw error bars?"/> | |
211 </when> | |
212 </conditional> | |
213 </repeat> | |
214 </inputs> | |
215 <stdio> | |
216 <exit_code range="1:" level="fatal" description="CummerBund Error" /> | |
217 </stdio> | |
218 <outputs> | |
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Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
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219 <data format="cuffdatadb" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)"> |
0 | 220 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter> |
221 </data> | |
222 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/> | |
223 </outputs> | |
224 | |
225 <requirements> | |
226 <requirement type="binary">R</requirement> | |
227 </requirements> | |
228 | |
229 <!--> | |
230 <tests> | |
231 <test> | |
232 <param name="" value=""/> | |
233 <output name="" file=""/> | |
234 </test> | |
235 </tests> | |
236 --> | |
237 <configfiles> | |
238 <configfile name="script_file"> | |
239 | |
240 ## Feature Selection ## | |
241 get_features <- function(myGenes, f="gene") { | |
242 if (f == "isoforms") | |
243 return(isoforms(myGenes)) | |
244 else if (f == "tss") | |
245 return(TSS(myGenes)) | |
246 else if (f == "cds") | |
247 return(CDS(myGenes)) | |
248 else | |
249 return(myGenes) | |
250 } | |
251 | |
252 ## Main Function ## | |
253 | |
254 ## Load cummeRbund library | |
255 library("cummeRbund") | |
256 | |
257 ## Initialize cuff object | |
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readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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258 #if $backend_database_source.backend_database_selector == "cuffdiff_output": |
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259 ## Check if gtfFIle and genome are includes |
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260 #set $gtf_link = None |
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261 #if $backend_database_source.reference.include: |
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262 #set $gtf_link = '.'.join(['cuff',$backend_database_source.reference.gtf_file.extension]) |
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263 system('ln -s $backend_database_source.reference.gtf_file $gtf_link') |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
Jim Johnson <jj@umn.edu>
parents:
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264 #if $backend_database_source.reference.genome.source == 'cached': |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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parents:
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265 #set $ref_file = $backend_database_source.reference.genome.ref_fasta |
f109453ecfa2
readCufflinks() parses feature file based on file extension: .gtf/.gff3 Also added gtfFile and genome input to cummerbund_wrapper.xml
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266 #else |
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267 #set $ref_file = $backend_database_source.reference.genome.ref_file |
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268 #end if |
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269 #end if |
0 | 270 cuff <- readCufflinks(dir = "", |
271 dbFile = "${output_database}", | |
272 geneFPKM = "${genes_fpkm_tracking}", | |
273 geneDiff = "${genes_exp}", | |
274 isoformFPKM = "${isoforms_fpkm_tracking}", | |
275 isoformDiff = "${isoforms_exp}", | |
276 TSSFPKM = "${tss_groups_fpkm_tracking}", | |
277 TSSDiff = "${tss_groups_exp}", | |
278 CDSFPKM = "${cds_fpkm_tracking}", | |
279 CDSExpDiff = "${cds_exp_diff}", | |
280 CDSDiff = "${cds_diff}", | |
281 promoterFile = "${promoters_diff}", | |
282 splicingFile = "${splicing_diff}", | |
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283 #if $gtf_link: |
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284 gtfFile = "${gtf_link}", |
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285 genome = "${ref_file}", |
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286 #end if |
0 | 287 rebuild = T) |
288 #else: | |
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289 cuff <- readCufflinks(dir = "", |
0 | 290 dbFile = "${backend_database_source.input_database}", |
291 rebuild = F) | |
292 #end if | |
293 | |
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294 ## Print out info |
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295 print(cuff) |
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296 sink("cuffdb_info.txt") |
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297 print(cuff) |
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298 print("SAMPLES:") |
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299 samples(cuff) |
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300 print("REPLICATES:") |
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301 replicates(cuff) |
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302 print("FEATURES:") |
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303 print(annotation(genes(cuff))) |
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304 cat(annotation(genes(cuff))[[1]],sep=",") |
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305 sink() |
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306 |
0 | 307 #for $i, $p in enumerate($plots, start=1): |
308 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) | |
309 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) | |
310 tryCatch({ | |
311 ## Density plot ## | |
312 #if $p.plot['type'] == "density": | |
313 csDensity(genes(cuff),replicates=$p.plot.replicates) | |
314 | |
315 ## Dispersion plot ## | |
316 #elif $p.plot['type'] == "dispersion": | |
317 dispersionPlot(genes(cuff)) | |
318 | |
319 ## Squared Coefficient of Variation plot ## | |
320 #elif $p.plot['type'] == "fpkmSCV": | |
321 fpkmSCVPlot(genes(cuff)) | |
322 | |
323 ## Scatter Matrix ## | |
324 #elif $p.plot['type'] == "scatterMatrix": | |
325 csScatterMatrix(genes(cuff)) | |
326 | |
327 ## Boxplot ## | |
328 #elif $p.plot['type'] == "boxplot": | |
329 csBoxplot(genes(cuff)) | |
330 | |
331 ## Scatter ## | |
332 #elif $p.plot['type'] == "scatter": | |
333 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
334 myGeneIds <- c() | |
335 #for $g in $p.plot.multiple_genes['genes']: | |
336 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
337 #end for | |
338 myGenes <- getGenes(cuff, myGeneIds) | |
339 csScatter(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
340 #else | |
341 csScatter(genes(cuff), "${p.plot.x}", "${p.plot.y}", smooth=${p.plot.smooth}) | |
342 #end if | |
343 | |
344 ## Volcano ## | |
345 #elif $p.plot['type'] == "volcano": | |
346 #if $p.plot.multiple_genes['multiple_genes_selector']: | |
347 myGeneIds <- c() | |
348 #for $g in $p.plot.multiple_genes['genes']: | |
349 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
350 #end for | |
351 myGenes <- getGenes(cuff, myGeneIds) | |
352 csVolcano(get_features(myGenes, "$p.plot.multiple_genes['features']"), "${p.plot.x}", "${p.plot.y}") | |
353 #else | |
354 csVolcano(genes(cuff), "${p.plot.x}", "${p.plot.y}") | |
355 #end if | |
356 | |
357 ## Heatmap ## | |
358 #elif $p.plot['type'] == "heatmap": | |
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359 #if $p.plot.genes and len($p.plot.genes) > 0: |
0 | 360 myGeneIds <- c() |
361 #for $g in $p.plot.genes: | |
362 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
363 #end for | |
364 myGenes <- getGenes(cuff, myGeneIds) | |
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365 #else |
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366 myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]]) |
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367 #end if |
0 | 368 csHeatmap(get_features(myGenes, "${p.plot.features}"), clustering="${p.plot.clustering}", labCol="${p.plot.labcol}", labRow="${p.plot.labrow}", border="${p.plot.border}") |
369 | |
370 ## Cluster ## | |
371 #elif $p.plot['type'] == "cluster": | |
372 myGeneIds <- c() | |
373 #for $g in $p.plot.genes: | |
374 myGeneIds <- c(myGeneIds, "$g['gene_id']") | |
375 #end for | |
376 myGenes <- getGenes(cuff, myGeneIds) | |
377 csCluster(get_features(myGenes, "${p.plot.features}"), k=${p.plot.k}, iter.max="${p.plot.iter_max}") | |
378 | |
379 ## Expression Plot ## | |
380 #elif $p.plot['type'] == "expressionplot": | |
381 myGeneId <- "$p.plot.gene_id" | |
382 myGenes <- getGenes(cuff, myGeneId) | |
383 expressionPlot(get_features(myGenes, "${p.plot.features}"), drawSummary=${p.plot.draw_summary}, iter.max="${p.plot.show_error_bars}") | |
384 | |
385 ## Expression Bar Plot ## | |
386 #elif $p.plot['type'] == "expressionbarplot": | |
387 myGeneId <- "$p.plot.gene_id" | |
388 myGenes <- getGenes(cuff, myGeneId) | |
389 expressionBarplot(get_features(myGenes, "${p.plot.features}"), iter.max="${p.plot.show_error_bars}") | |
390 | |
391 ## MDS plot ## | |
392 #elif $p.plot['type'] == "mds": | |
393 MDSplot(genes(cuff),replicates=$p.plot.replicates) | |
394 | |
395 ## PCA plot ## | |
396 #elif $p.plot['type'] == "pca": | |
397 PCAplot(genes(cuff),"PC1","PC2",replicates=$p.plot.replicates) | |
398 | |
399 ## MAplot plot ## | |
400 #elif $p.plot['type'] == "maplot": | |
401 MAplot(genes(cuff), "${p.plot.x}", "${p.plot.y}", useCount=${p.plot.use_count}) | |
402 | |
403 ## Dendogram plot ## | |
404 #elif $p.plot['type'] == "dendrogram": | |
405 csDendro(genes(cuff),replicates=$p.plot.replicates) | |
406 #end if | |
407 | |
408 },error = function(e) {paste("$p.plot['type'] failed: ", e)}) | |
409 devname = dev.off() | |
410 | |
411 #end for | |
412 </configfile> | |
413 </configfiles> | |
414 | |
415 <help> | |
416 This tool allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations. | |
417 </help> | |
418 | |
419 </tool> |