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comparison rsem-bwt2.xml @ 2:9fa602bc29ec draft

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planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 0d726dfe7f500b597a3b102f101cc2e12c58b279
author artbio
date Mon, 02 Apr 2018 13:23:17 -0400
parents 49795544dac7
children 26ead8419b63
comparison
equal deleted inserted replaced
1:49795544dac7 2:9fa602bc29ec
44 44
45 #if $job.select_job == "index" and $run_rsem.select == "Yes": 45 #if $job.select_job == "index" and $run_rsem.select == "Yes":
46 && 46 &&
47 #end if 47 #end if
48 48
49 #if $run_rsem.select == "Yes": 49 #if $run_rsem.select == "Yes" and $run_rsem.input.format == 'fastq':
50 ## uncompress fastq.gz or fastqsanger.gz if needed 50 ## uncompress fastq.gz or fastqsanger.gz if needed
51 #if $run_rsem.input.fastq.matepair=="single": 51 #if $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="single":
52 #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'): 52 #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'):
53 gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq && 53 gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq &&
54 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'): 54 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
55 ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' && 55 ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' &&
56 #end if 56 #end if
57 #elif $run_rsem.input.fastq.matepair=="paired": 57 #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired":
58 #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'): 58 #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'):
59 gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq && 59 gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq &&
60 gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq && 60 gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq &&
61 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'): 61 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
62 ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' && 62 ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' &&
143 #end if 143 #end if
144 #elif $run_rsem.input.format=="sam" 144 #elif $run_rsem.input.format=="sam"
145 #if $run_rsem.input.matepair=="paired": 145 #if $run_rsem.input.matepair=="paired":
146 --paired-end 146 --paired-end
147 #end if 147 #end if
148 #if $run_rsem.input.rsem_sam._extension == 'sam': 148 #if $run_rsem.input.rsem_sam.is_of_type('sam'):
149 --sam 149 --sam
150 #elif $run_rsem.input.rsem_sam._extension == 'bam': 150 #elif $run_rsem.input.rsem_sam.is_of_type('bam'):
151 --bam 151 --bam
152 #end if 152 #end if
153 $run_rsem.input.rsem_sam 153 $run_rsem.input.rsem_sam
154 #end if 154 #end if
155 ## RSEM reference 155 ## RSEM reference
293 <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.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"> 294 <param name="matepair" type="select" label="Library Type">
295 <option value="single">Single End Reads</option> 295 <option value="single">Single End Reads</option>
296 <option value="paired">Paired End Reads</option> 296 <option value="paired">Paired End Reads</option>
297 </param> 297 </param>
298 <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" /> 298 <param name="rsem_sam" type="data" format="sam,bam" label="RSEM formatted SAM file" />
299 </when> 299 </when>
300 </conditional> 300 </conditional>
301 <expand macro="rsem_options"/> 301 <expand macro="rsem_options"/>
302 <conditional name="rsem_outputs"> 302 <conditional name="rsem_outputs">
303 <param name="result_bams" type="select" label="Create bam results files" 303 <param name="result_bams" type="select" label="Create bam results files"