Mercurial > repos > artbio > rsem
comparison rsem-bwt2.xml @ 2:9fa602bc29ec draft
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 |
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| 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" |