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comparison rsem_calculate_expression.xml @ 2:f6b8155ab12a

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Add test cases
author Jim Johnson <jj@umn.edu>
date Thu, 06 Feb 2014 11:46:40 -0600
parents 1ff2fc8da328
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1:1ff2fc8da328 2:f6b8155ab12a
183 </macros> 183 </macros>
184 184
185 <inputs> 185 <inputs>
186 <param name="sample" type="text" value="rsem_sample" label="Sample name" /> 186 <param name="sample" type="text" value="rsem_sample" label="Sample name" />
187 <conditional name="reference"> 187 <conditional name="reference">
188 <param name="refSrc" type="select" label="RSEM Reference"> 188 <param name="refSrc" type="select" label="RSEM Reference Source">
189 <option value="cached">Locally cached</option> 189 <option value="cached">Locally cached</option>
190 <option value="history">From your history</option> 190 <option value="history">From your history</option>
191 </param> 191 </param>
192 <when value="cached"> 192 <when value="cached">
193 <param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference"> 193 <param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference">
207 <option value="fasta">FASTA</option> 207 <option value="fasta">FASTA</option>
208 <option value="sam">SAM/BAM</option> 208 <option value="sam">SAM/BAM</option>
209 </param> 209 </param>
210 <when value="fastq"> 210 <when value="fastq">
211 <param name="fastq_select" size="15" type="select" label="FASTQ type" > 211 <param name="fastq_select" size="15" type="select" label="FASTQ type" >
212 <option value="--phred33-quals">phred33 qualities (default for sanger)</option> 212 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
213 <option value="--solexa-quals">solexa qualities</option> 213 <option value="--solexa-quals">solexa qualities</option>
214 <option value="--phred64-quals">phred64 qualities</option> 214 <option value="--phred64-quals">phred64 qualities</option>
215 </param> 215 </param>
216 <conditional name="fastq"> 216 <conditional name="fastq">
217 <param name="matepair" type="select" label="Library type"> 217 <param name="matepair" type="select" label="Library type">
272 </inputs> 272 </inputs>
273 <stdio> 273 <stdio>
274 <exit_code range="1:" level="fatal" description="Error Running RSEM" /> 274 <exit_code range="1:" level="fatal" description="Error Running RSEM" />
275 </stdio> 275 </stdio>
276 <outputs> 276 <outputs>
277 <data format="tabular" name="output" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/> 277 <data format="tabular" name="gene_abundances" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/>
278 <data format="tabular" name="isoforms" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/> 278 <data format="tabular" name="isoform_abundances" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/>
279 <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" > 279 <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" >
280 <filter>rsem_outputs['result_bams'] != "none"</filter> 280 <filter>rsem_outputs['result_bams'] != "none"</filter>
281 </data> 281 </data>
282 <data format="bam" name="transcript__sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" > 282 <data format="bam" name="transcript_sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
283 <filter>rsem_outputs['result_bams'] != "none"</filter> 283 <filter>rsem_outputs['result_bams'] != "none"</filter>
284 </data> 284 </data>
285 <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam"> 285 <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam">
286 <filter>rsem_outputs['result_bams'] == "both"</filter> 286 <filter>rsem_outputs['result_bams'] == "both"</filter>
287 </data> 287 </data>
288 <data format="bam" name="genome_sorted_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam"> 288 <data format="bam" name="genome_sorted_bam" label="${sample}.genome.sorted.bam" from_work_dir="rsem_output.genome.sorted.bam">
289 <filter>rsem_outputs['result_bams'] == "both"</filter> 289 <filter>rsem_outputs['result_bams'] == "both"</filter>
290 </data> 290 </data>
291 <data format="txt" name="log" label="${sample}.rsem_log"/> 291 <data format="txt" name="log" label="${sample}.rsem_log"/>
292 </outputs> 292 </outputs>
293 <tests>
294 <test>
295 <param name="sample" value="rsem_sample"/>
296 <param name="refSrc" value="history"/>
297 <param name="rsem_ref" value="RSEM_ref_reference.zip" ftype="rsem_ref"/>
298 <param name="format" value="fastq"/>
299 <param name="matepair" value="single"/>
300 <param name="singlefastq" value="test.fastq" ftype="fastqsanger"/>
301 <param name="result_bams" value="none"/>
302 <output name="gene_abundances">
303 <assert_contents>
304 <has_text text="ENST00000423562,ENST00000438504,ENST00000488147,ENST00000538476,ENST00000541675" />
305 </assert_contents>
306 </output>
307 <output name="isoform_abundances">
308 <assert_contents>
309 <has_text text="ENST00000332831" />
310 </assert_contents>
311 </output>
312 <output name="log">
313 <assert_contents>
314 <has_text text="Expression Results are written" />
315 </assert_contents>
316 </output>
317 </test>
318 </tests>
293 <help> 319 <help>
294 320
295 321
296 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/ 322 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
297 323