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comparison rsem.xml @ 3:26ead8419b63 draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 36c2780df597aa4b14ae9c620457f7460166aaa5
author artbio
date Tue, 03 Apr 2018 18:25:39 -0400
parents 9fa602bc29ec
children 1823c8e07d96
comparison
equal deleted inserted replaced
2:9fa602bc29ec 3:26ead8419b63
146 #elif $run_rsem.input.fasta.matepair=="paired": 146 #elif $run_rsem.input.fasta.matepair=="paired":
147 --paired-end 147 --paired-end
148 $run_rsem.input.fasta.fasta1 148 $run_rsem.input.fasta.fasta1
149 $run_rsem.input.fasta.fasta2 149 $run_rsem.input.fasta.fasta2
150 #end if 150 #end if
151 #elif $run_rsem.input.format=="sam"
152 #if $run_rsem.input.matepair=="paired":
153 --paired-end
154 #end if
155 #if $run_rsem.input.rsem_sam.is_of_type('sam'):
156 --sam
157 #elif $run_rsem.input.rsem_sam.is_of_type('bam'):
158 --bam
159 #end if
160 $run_rsem.input.rsem_sam
161 #end if 151 #end if
162 ## RSEM reference 152 ## RSEM reference
163 #if $run_rsem.reference.refSrc == 'history': 153 #if $run_rsem.reference.refSrc == 'history':
164 ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name} 154 ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name}
165 #elif $run_rsem.reference.refSrc == 'self': 155 #elif $run_rsem.reference.refSrc == 'self':
255 </conditional> 245 </conditional>
256 <conditional name="input"> 246 <conditional name="input">
257 <param name="format" type="select" label="RSEM Input file type"> 247 <param name="format" type="select" label="RSEM Input file type">
258 <option value="fastq">FASTQ</option> 248 <option value="fastq">FASTQ</option>
259 <option value="fasta">FASTA</option> 249 <option value="fasta">FASTA</option>
260 <option value="sam">SAM/BAM</option>
261 </param> 250 </param>
262 <when value="fastq"> 251 <when value="fastq">
263 <param name="fastq_select" size="15" type="select" label="FASTQ type" > 252 <param name="fastq_select" size="15" type="select" label="FASTQ type" >
264 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option> 253 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
265 <option value="--solexa-quals">solexa qualities</option> 254 <option value="--solexa-quals">solexa qualities</option>
293 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" /> 282 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
294 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" /> 283 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
295 </when> 284 </when>
296 </conditional> 285 </conditional>
297 <expand macro="bowtie_options"/> 286 <expand macro="bowtie_options"/>
298 </when>
299 <when value="sam">
300 <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
301 <param name="matepair" type="select" label="Library Type">
302 <option value="single">Single End Reads</option>
303 <option value="paired">Paired End Reads</option>
304 </param>
305 <param name="rsem_sam" type="data" format="sam,bam" label="RSEM formatted SAM file" />
306 </when> 287 </when>
307 </conditional> 288 </conditional>
308 <expand macro="rsem_options"/> 289 <expand macro="rsem_options"/>
309 <conditional name="rsem_outputs"> 290 <conditional name="rsem_outputs">
310 <param name="result_bams" type="select" label="Create bam results files" 291 <param name="result_bams" type="select" label="Create bam results files"