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comparison cummerbund_wrapper.xml @ 15:2d7eee38ab5b

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Update to new cuffdiff wrapper, add cuffdb_info.txt to cummerbund html output
author Jim Johnson <jj@umn.edu>
date Fri, 08 Nov 2013 13:28:44 -0600
parents b6427cdbf6d4
children
comparison
equal deleted inserted replaced
14:d10befb0867a 15:2d7eee38ab5b
1 <tool id="cummerbund" name="cummeRbund" version="0.0.6"> 1 <tool id="cummerbund" name="cummeRbund" version="0.0.7">
2
3 <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>
4 3
5 <command interpreter="python"> 4 <command interpreter="python">
6 cummerbund_wrapper.py 5 cummerbund_wrapper.py
7 --r-script ${script_file} 6 --r-script ${script_file}
62 </when> 61 </when>
63 <when value="pca"> 62 <when value="pca">
64 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> 63 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
65 </when> 64 </when>
66 <when value="maplot"> 65 <when value="maplot">
67 <param name="x" type="text" label="Sample name 1"/> 66 <param name="x" type="text" label="Sample name 1" help="Condition1 name used in cuffdiff">
68 <param name="y" type="text" label="Sample name 2"/> 67 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/>
68 </param>
69 <param name="y" type="text" label="Sample name 2" help="Condition2 name used in cuffdiff">
70 <validator type="empty_field" message="A Condition name from the cuffdiff run is required"/>
71 </param>
69 <param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/> 72 <param name="use_count" type="boolean" truevalue="T" falsevalue="F" checked="False" label="Use Count?"/>
70 </when> 73 </when>
71 <when value="dendrogram"> 74 <when value="dendrogram">
72 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/> 75 <param name="replicates" type="boolean" truevalue="T" falsevalue="F" checked="True" label="Replicates?"/>
73 </when> 76 </when>
183 </inputs> 186 </inputs>
184 <stdio> 187 <stdio>
185 <exit_code range="1:" level="fatal" description="CummerBund Error" /> 188 <exit_code range="1:" level="fatal" description="CummerBund Error" />
186 </stdio> 189 </stdio>
187 <outputs> 190 <outputs>
188 <data format="data" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)"> 191 <data format="cuffdatadb" name="output_database" label="${tool.name} on ${on_string}: Database File (sqlite)">
189 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter> 192 <filter>backend_database_source['backend_database_selector'] == "cuffdiff_output"</filter>
190 </data> 193 </data>
191 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/> 194 <data format="html" name="output_html" label="${tool.name} on ${on_string} (HTML)"/>
192 </outputs> 195 </outputs>
193 196
242 #else: 245 #else:
243 dbFile = "${backend_database_source.input_database}", 246 dbFile = "${backend_database_source.input_database}",
244 rebuild = F) 247 rebuild = F)
245 #end if 248 #end if
246 249
250 ## Print out info
251 print(cuff)
252 sink("cuffdb_info.txt")
253 print(cuff)
254 print("SAMPLES:")
255 samples(cuff)
256 print("REPLICATES:")
257 replicates(cuff)
258 print("FEATURES:")
259 print(annotation(genes(cuff)))
260 sink()
261
247 #for $i, $p in enumerate($plots, start=1): 262 #for $i, $p in enumerate($plots, start=1):
248 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type']) 263 #set $filename = "plot%02d-%s.png" % ($i, $p.plot['type'])
249 png(filename = "${filename}", width = ${p.width}, height = ${p.height}) 264 png(filename = "${filename}", width = ${p.width}, height = ${p.height})
250 tryCatch({ 265 tryCatch({
251 ## Density plot ## 266 ## Density plot ##