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comparison rsem-bwt2.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
139 #elif $run_rsem.input.fasta.matepair=="paired": 139 #elif $run_rsem.input.fasta.matepair=="paired":
140 --paired-end 140 --paired-end
141 $run_rsem.input.fasta.fasta1 141 $run_rsem.input.fasta.fasta1
142 $run_rsem.input.fasta.fasta2 142 $run_rsem.input.fasta.fasta2
143 #end if 143 #end if
144 #elif $run_rsem.input.format=="sam"
145 #if $run_rsem.input.matepair=="paired":
146 --paired-end
147 #end if
148 #if $run_rsem.input.rsem_sam.is_of_type('sam'):
149 --sam
150 #elif $run_rsem.input.rsem_sam.is_of_type('bam'):
151 --bam
152 #end if
153 $run_rsem.input.rsem_sam
154 #end if 144 #end if
155 ## RSEM reference 145 ## RSEM reference
156 #if $run_rsem.reference.refSrc == 'history': 146 #if $run_rsem.reference.refSrc == 'history':
157 ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name} 147 ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name}
158 #elif $run_rsem.reference.refSrc == 'self': 148 #elif $run_rsem.reference.refSrc == 'self':
248 </conditional> 238 </conditional>
249 <conditional name="input"> 239 <conditional name="input">
250 <param name="format" type="select" label="RSEM Input file type"> 240 <param name="format" type="select" label="RSEM Input file type">
251 <option value="fastq">FASTQ</option> 241 <option value="fastq">FASTQ</option>
252 <option value="fasta">FASTA</option> 242 <option value="fasta">FASTA</option>
253 <option value="sam">SAM/BAM</option>
254 </param> 243 </param>
255 <when value="fastq"> 244 <when value="fastq">
256 <param name="fastq_select" size="15" type="select" label="FASTQ type" > 245 <param name="fastq_select" size="15" type="select" label="FASTQ type" >
257 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option> 246 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
258 <option value="--solexa-quals">solexa qualities</option> 247 <option value="--solexa-quals">solexa qualities</option>
286 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" /> 275 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
287 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" /> 276 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
288 </when> 277 </when>
289 </conditional> 278 </conditional>
290 <expand macro="bowtie2_options"/> 279 <expand macro="bowtie2_options"/>
291 </when>
292 <when value="sam">
293 <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
294 <param name="matepair" type="select" label="Library Type">
295 <option value="single">Single End Reads</option>
296 <option value="paired">Paired End Reads</option>
297 </param>
298 <param name="rsem_sam" type="data" format="sam,bam" label="RSEM formatted SAM file" />
299 </when> 280 </when>
300 </conditional> 281 </conditional>
301 <expand macro="rsem_options"/> 282 <expand macro="rsem_options"/>
302 <conditional name="rsem_outputs"> 283 <conditional name="rsem_outputs">
303 <param name="result_bams" type="select" label="Create bam results files" 284 <param name="result_bams" type="select" label="Create bam results files"