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comparison rsem.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
46 && 46 &&
47 #end if 47 #end if
48 48
49 #if $run_rsem.select == "Yes": 49 #if $run_rsem.select == "Yes":
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' &&
150 #end if 150 #end if
151 #elif $run_rsem.input.format=="sam" 151 #elif $run_rsem.input.format=="sam"
152 #if $run_rsem.input.matepair=="paired": 152 #if $run_rsem.input.matepair=="paired":
153 --paired-end 153 --paired-end
154 #end if 154 #end if
155 #if $run_rsem.input.rsem_sam._extension == 'sam': 155 #if $run_rsem.input.rsem_sam.is_of_type('sam'):
156 --sam 156 --sam
157 #elif $run_rsem.input.rsem_sam._extension == 'bam': 157 #elif $run_rsem.input.rsem_sam.is_of_type('bam'):
158 --bam 158 --bam
159 #end if 159 #end if
160 $run_rsem.input.rsem_sam 160 $run_rsem.input.rsem_sam
161 #end if 161 #end if
162 ## RSEM reference 162 ## RSEM reference
300 <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.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"> 301 <param name="matepair" type="select" label="Library Type">
302 <option value="single">Single End Reads</option> 302 <option value="single">Single End Reads</option>
303 <option value="paired">Paired End Reads</option> 303 <option value="paired">Paired End Reads</option>
304 </param> 304 </param>
305 <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" /> 305 <param name="rsem_sam" type="data" format="sam,bam" label="RSEM formatted SAM file" />
306 </when> 306 </when>
307 </conditional> 307 </conditional>
308 <expand macro="rsem_options"/> 308 <expand macro="rsem_options"/>
309 <conditional name="rsem_outputs"> 309 <conditional name="rsem_outputs">
310 <param name="result_bams" type="select" label="Create bam results files" 310 <param name="result_bams" type="select" label="Create bam results files"