rsem: rsem.xml annotate

annotate rsem.xml @ 7:585c6120dca0 draft

planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 8e5c580d93b413f4a0b2ef41218a38f4d27f1e42

author	artbio
date	Thu, 30 Aug 2018 12:34:13 -0400
parents	45a30e216fec
children	f6fc9b92d629

rev	line source
1 49795544dac7 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 62e8088d5f73cbb9b2f93e23a74636c77a06b492 artbio parents: 0 diff changeset	1 <tool id="rsembowtie" name="RSEM-Bowtie" version="@WRAPPER_VERSION@">
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	2 <description></description>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	3 <macros>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	4 <import>macros.xml</import>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	5 </macros>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	6 <requirements>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	7 <requirement type="package" version="1.3.0">rsem</requirement>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	8 <requirement type="package" version="1.2.2=py27pl5.22.0_0">bowtie</requirement>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	9 </requirements>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	10 <stdio>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	11 <exit_code range="1:" level="warning" description="Tool exception" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	12 </stdio>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	14 #if $job.select_job == "index":
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	15 echo ${job.reference_name} " " \| tee $reference_file &&
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	16 mkdir $reference_file.files_path &&
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	17 rsem-prepare-reference
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	18 #if $job.polya.polya_use == 'add':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	19 #if $job.polya.polya_length:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	20 --polyA-length $job.polya.polya_length
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	21 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	22 #elif $job.polya.polya_use == 'subset':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	23 --no-polyA-subset $job.polya.no_polya_subset
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	24 #if $job.polya.polya_length:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	25 --polyA-length $job.polya.polya_length
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	26 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	27 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	28 $job.ntog
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	29 #if $job.transcript_to_gene_map:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	30 --transcript-to-gene-map $job.transcript_to_gene_map
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	31 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	32 --bowtie
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	33 #if $job.self_reference.ref_type == 'transcripts':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	34 $job.self_reference.reference_fasta_file
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	35 #else:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	36 --gtf $job.self_reference.gtf
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	37 $job.self_reference.reference_fasta_file
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	38 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	39 ${reference_file.files_path}/${job.reference_name}
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	40 > ${reference_file.files_path}/${job.reference_name}.log
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	41 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	42
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	43 #if $job.select_job == "index" and $run_rsem.select == "Yes":
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	44 &&
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	45 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	46
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	47 #if $run_rsem.select == "Yes":
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	48 ## uncompress fastq.gz or fastqsanger.gz if needed
2 9fa602bc29ec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 0d726dfe7f500b597a3b102f101cc2e12c58b279 artbio parents: 1 diff changeset	49 #if $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="single":
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	50 #if $run_rsem.input.fastq.singlefastq.is_of_type('fastq.gz') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger.gz'):
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	51 gunzip < '$run_rsem.input.fastq.singlefastq' > uncomp_single.fastq &&
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	52 #elif $run_rsem.input.fastq.singlefastq.is_of_type('fastq') or $run_rsem.input.fastq.singlefastq.is_of_type('fastqsanger'):
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	53 ln -f -s '$run_rsem.input.fastq.singlefastq' 'uncomp_single.fastq' &&
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	54 #end if
2 9fa602bc29ec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 0d726dfe7f500b597a3b102f101cc2e12c58b279 artbio parents: 1 diff changeset	55 #elif $run_rsem.input.format == 'fastq' and $run_rsem.input.fastq.matepair=="paired":
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	56 #if $run_rsem.input.fastq.fastq1.is_of_type('fastq.gz') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger.gz'):
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	57 gunzip < '$run_rsem.input.fastq.fastq1' > uncomp_pair1.fastq &&
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	58 gunzip < '$run_rsem.input.fastq.fastq2' > uncomp_pair2.fastq &&
4 1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	59 #elif $run_rsem.input.fastq.fastq1.is_of_type('fastq') or $run_rsem.input.fastq.fastq1.is_of_type('fastqsanger'):
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	60 ln -f -s '$run_rsem.input.fastq.fastq1' 'uncomp_pair1.fastq' &&
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	61 ln -f -s '$run_rsem.input.fastq.fastq2' 'uncomp_pair2.fastq' &&
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	62 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	63 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	64 rsem-calculate-expression
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	65 ## --tag string
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	66 #if $run_rsem.seedlength:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	67 --seed-length $run_rsem.seedlength
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	68 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	69 --forward-prob $run_rsem.forward_prob
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	70 #if $run_rsem.rsem_options.fullparams == 'fullset':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	71 ## Fragment info
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	72 #if $run_rsem.rsem_options.fragment_length_mean:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	73 --fragment-length-mean $run_rsem.rsem_options.fragment_length_mean
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	74 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	75 #if $run_rsem.rsem_options.fragment_length_min:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	76 --fragment-length-min $run_rsem.rsem_options.fragment_length_min
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	77 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	78 #if $run_rsem.rsem_options.fragment_length_sd:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	79 --fragment-length-sd $run_rsem.rsem_options.fragment_length_sd
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	80 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	81 #if $run_rsem.rsem_options.fragment_length_max:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	82 --fragment-length-max $run_rsem.rsem_options.fragment_length_max
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	83 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	84 ## RSPD
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	85 #if $run_rsem.rsem_options.rspd.estimate == 'yes':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	86 --estimate-rspd
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	87 #if $run_rsem.rsem_options.rspd.num_rspd_bins:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	88 --num-rspd-bins $run_rsem.rsem_options.rspd.num_rspd_bins
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	89 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	90 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	91 ## Calculate 95% credibility intervals and posterior mean estimates.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	92 #if $run_rsem.rsem_options.useci.ci == 'yes':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	93 --calc-ci
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	94 #if $run_rsem.rsem_options.useci.cimem:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	95 --ci-memory $run_rsem.rsem_options.useci.cimem
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	96 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	97 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	98 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	99 --num-threads \${GALAXY_SLOTS:-4}
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	100 #if $run_rsem.input.format == 'fasta' and $run_rsem.input.bowtie_options.fullparams == 'fullset':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	101 ## Bowtie params
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	102 #if $run_rsem.input.bowtie_options.bowtie_e:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	103 --bowtie-e $run_rsem.input.bowtie_options.bowtie_e
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	104 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	105 #if $run_rsem.input.bowtie_options.bowtie_m:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	106 --bowtie-m $run_rsem.input.bowtie_options.bowtie_m
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	107 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	108 --bowtie-n $run_rsem.input.bowtie_options.bowtie_n
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	109 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	110 #if $run_rsem.input.format == 'fastq' and $run_rsem.input.bowtie_options.fullparams == 'fullset':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	111 ## Bowtie params
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	112 #if $run_rsem.input.bowtie_options.bowtie_e:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	113 --bowtie-e $run_rsem.input.bowtie_options.bowtie_e
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	114 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	115 #if $run_rsem.input.bowtie_options.bowtie_m:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	116 --bowtie-m $run_rsem.input.bowtie_options.bowtie_m
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	117 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	118 --bowtie-n $run_rsem.input.bowtie_options.bowtie_n
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	119 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	120 ## Outputs
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	121 #if $run_rsem.rsem_outputs.result_bams == 'none':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	122 --no-bam-output
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	123 #elif $run_rsem.rsem_outputs.result_bams == 'default':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	124 --sort-bam-by-coordinate
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	125 #else
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	126 --sort-bam-by-coordinate
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	127 --output-genome-bam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	128 $run_rsem.rsem_outputs.sampling_for_bam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	129 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	130 ## Input data
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	131 #if $run_rsem.input.format=="fastq"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	132 $run_rsem.input.fastq_select
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	133 #if $run_rsem.input.fastq.matepair=="single":
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	134 uncomp_single.fastq
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	135 #elif $run_rsem.input.fastq.matepair=="paired":
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	136 --paired-end
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	137 uncomp_pair1.fastq
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	138 uncomp_pair2.fastq
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	139 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	140 #elif $run_rsem.input.format=="fasta"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	141 --no-qualities
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	142 #if $run_rsem.input.fasta.matepair=="single":
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	143 $run_rsem.input.fasta.singlefasta
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	144 #elif $run_rsem.input.fasta.matepair=="paired":
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	145 --paired-end
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	146 $run_rsem.input.fasta.fasta1
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	147 $run_rsem.input.fasta.fasta2
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	148 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	149 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	150 ## RSEM reference
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	151 #if $run_rsem.reference.refSrc == 'history':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	152 ${run_rsem.reference.rsem_ref.extra_files_path}/${run_rsem.reference.rsem_ref.metadata.reference_name}
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	153 #elif $run_rsem.reference.refSrc == 'self':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	154 ${reference_file.files_path}/${job.reference_name}
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	155 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	156 ## sample_name: use a hard coded name so we can pull out galaxy outputs
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	157 rsem_output
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	158 ## direct output into logfile
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	159 > $log
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	160 #end if
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	161 ]]></command>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	162
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	163 <inputs>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	164 <conditional name="job">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	165 <param name="select_job" type="select" label="rsem reference">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	166 <option value="index">Build rsem reference</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	167 <option value="no-index" selected="true">rsem reference available from history</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	168 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	169 <when value="index">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	170 <conditional name="self_reference">
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	171 <param name="ref_type" type="select" label="Reference source">
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	172 <option value="transcripts">transcript fasta</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	173 <option value="genomic">reference genome and gtf</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	174 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	175 <when value="transcripts">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	176 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	177 help="The files should contain the sequences of transcripts."/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	178 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	179 <when value="genomic">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	180 <param name="reference_fasta_file" type="data" format="fasta" label="reference fasta file"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	181 help="The file should contain the sequence of an entire genome."/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	182 <param name="gtf" type="data" format="gtf" label="gtf"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	183 help="extract transcript reference sequences using the gene annotations specified in this GTF" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	184 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	185 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	186 <param name="transcript_to_gene_map" type="data" format="tabular" optional="true" label="Map of gene ids to transcript (isoform) ids" >
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	187 <help>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	188 Each line of should be of the form: gene_id transcript_id ( with the two fields separated by a tab character )
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	189 The map can be obtained from the UCSC table browser
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	190 group: Genes and Gene Prediction Tracks
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	191 table: knownIsoforms
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	192 Without a map:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	193 If a reference genome and gtf is used, then RSEM uses the "gene_id" and "transcript_id" attributes in the GTF file.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	194 Otherwise, RSEM assumes that each sequence in the reference sequence files is a separate gene.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	195 </help>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	196 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	197 <param name="reference_name" type="text" value="rsem_ref_name" label="reference name">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	198 <help>A one word name for this RSEM reference containing only letters, digits, and underscore characters</help>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	199 <validator type="regex" message="Use only letters, digits, and underscore characters">^\w+$</validator>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	200 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	201 <conditional name="polya">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	202 <param name="polya_use" type="select" label="PolyA ">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	203 <option value="add" selected="true">Add poly(A) tails to all transcripts</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	204 <option value="subset">Exclude poly(A) tails from selected transcripts</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	205 <option value="none">Do not add poly(A) tails to any transcripts</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	206 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	207 <when value="add">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	208 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	209 <validator type="in_range" message="must be positive " min="1"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	210 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	211 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	212 <when value="subset">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	213 <param name="no_polya_subset" type="data" format="tabular" optional="true" label="List of transcript IDs (one per line) that should should not have polyA tails added."/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	214 <param name="polya_length" type="integer" value="125" optional="true" label="The length of the poly(A) tails to be added. (Default: 125)">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	215 <validator type="in_range" message="must be positive " min="1"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	216 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	217 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	218 <when value="none"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	219 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	220 <param name="ntog" type="boolean" truevalue="--no-ntog" falsevalue="" checked="false" label="Disable the conversion of 'N' characters to 'G' characters in the reference sequences" help="Bowtie uses the automatic N to G conversion to align against all positions in the reference."/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	221 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	222 <when value="no-index">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	223 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	224 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	225
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	226 <conditional name="run_rsem">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	227 <param name="select" type="select" label="calculate expression with rsem">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	228 <option value="No">Just build rsem reference for latter rsem profiling</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	229 <option value="Yes" selected="true">profile expression with rsem</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	230 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	231 <when value="Yes">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	232 <param name="sample" type="text" value="rsem_sample" label="Sample name" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	233 <conditional name="reference">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	234 <param name="refSrc" type="select" label="RSEM Reference Source">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	235 <option value="history">From your history</option>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	236 <option value="self">RSEM Reference prepared with this tool</option>
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	237 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	238 <when value="history">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	239 <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	240 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	241 <when value="self">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	242 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	243 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	244 <conditional name="input">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	245 <param name="format" type="select" label="RSEM Input file type">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	246 <option value="fastq">FASTQ</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	247 <option value="fasta">FASTA</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	248 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	249 <when value="fastq">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	250 <param name="fastq_select" size="15" type="select" label="FASTQ type" >
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	251 <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	252 <option value="--solexa-quals">solexa qualities</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	253 <option value="--phred64-quals">phred64 qualities</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	254 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	255 <conditional name="fastq">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	256 <param name="matepair" type="select" label="Library type">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	257 <option value="single">Single End Reads</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	258 <option value="paired">Paired End Reads</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	259 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	260 <when value="single">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	261 <param name="singlefastq" type="data" format="fastq,fastq.gz" label="FASTQ file" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	262 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	263 <when value="paired">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	264 <param name="fastq1" type="data" format="fastq,fastq.gz" label="Read 1 fastq file" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	265 <param name="fastq2" type="data" format="fastq,fastq.gz" label="Read 2 fastq file" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	266 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	267 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	268 <expand macro="bowtie_options"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	269 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	270 <when value="fasta">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	271 <conditional name="fasta">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	272 <param name="matepair" type="select" label="Library Type">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	273 <option value="single">Single End Reads</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	274 <option value="paired">Paired End Reads</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	275 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	276 <when value="single">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	277 <param name="singlefasta" type="data" format="fasta" label="fasta file" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	278 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	279 <when value="paired">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	280 <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	281 <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	282 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	283 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	284 <expand macro="bowtie_options"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	285 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	286 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	287 <expand macro="rsem_options"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	288 <conditional name="rsem_outputs">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	289 <param name="result_bams" type="select" label="Create bam results files"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	290 help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" >
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	291 <option value="none">No BAM results files</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	292 <option value="default" selected="true">Transcript BAM results file</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	293 <option value="both">Transcript and genome BAM results files</option>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	294 </param>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	295 <when value="none"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	296 <when value="default">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	297 <expand macro="sampling_for_bam"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	298 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	299 <when value="both">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	300 <expand macro="sampling_for_bam"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	301 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	302 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	303 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	304 <when value="No">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	305 </when>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	306 </conditional>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	307 </inputs>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	308
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	309 <outputs>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	310 <data format="rsem_ref" name="reference_file" label="RSEM ${job.reference_name} reference">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	311 <filter>job['select_job'] == "index"</filter>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	312 </data>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	313 <data format="tabular" name="gene_abundances" label="${run_rsem.sample}.gene_abundances" from_work_dir="rsem_output.genes.results">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	314 <filter>run_rsem['select'] == "Yes"</filter>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	315 </data>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	316 <data format="tabular" name="isoform_abundances" label="${run_rsem.sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	317 <filter>run_rsem['select'] == "Yes"</filter>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	318 </data>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	319 <data format="bam" name="transcript_sorted_bam" label="${run_rsem.sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	320 <filter>run_rsem['select'] == "Yes" and run_rsem['rsem_outputs']['result_bams'] != "none"</filter>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	321 </data>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	322 <data format="bam" name="genome_sorted_bam" label="${run_rsem.sample}.genome.bam" from_work_dir="rsem_output.genome.sorted.bam">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	323 <filter>run_rsem['select'] == "Yes" and run_rsem['rsem_outputs']['result_bams'] == "both"</filter>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	324 </data>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	325 <data format="txt" name="log" label="${run_rsem.sample}.rsem_log">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	326 <filter>run_rsem['select'] == "Yes"</filter>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	327 </data>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	328 </outputs>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	329
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	330 <tests>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	331 <test>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	332 <param name="select_job" value="index"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	333 <param name="ref_type" value="genomic"/>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	334 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	335 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	336 <param name="reference_name" value="ebola"/>
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	337 <param name="select" value="Yes"/>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	338 <param name="sample" value="ebola_RNAseq"/>
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	339 <param name="refSrc" value="self"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	340 <param name="format" value="fastq"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	341 <param name="matepair" value="single"/>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	342 <param name="singlefastq" value="Ebola_forward.fastqsanger" ftype="fastqsanger"/>
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	343 <param name="result_bams" value="none"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	344 <output name="reference_file">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	345 <assert_contents>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	346 <has_text text="ebola" />
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	347 </assert_contents>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	348 </output>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	349 <output name="gene_abundances" value="refgen_gene_abundances.bt.tab"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	350 <output name="isoform_abundances" value="refgen_isoform_abundances.bt.tab" />
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	351 <output name="log">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	352 <assert_contents>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	353 <has_text text="Expression Results are written" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	354 </assert_contents>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	355 </output>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	356 </test>
4 1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	357 <test>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	358 <!-- test fastqsanger paired end Ebola genome-->
4 1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	359 <param name="select_job" value="index"/>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	360 <param name="ref_type" value="genomic"/>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	361 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	362 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	363 <param name="reference_name" value="ebola"/>
4 1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	364 <param name="select" value="Yes"/>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	365 <param name="sample" value="rsem_sample"/>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	366 <param name="refSrc" value="self"/>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	367 <param name="format" value="fastq"/>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	368 <param name="matepair" value="paired"/>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	369 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	370 <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	371 <param name="result_bams" value="both" />
4 1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	372 <output name="reference_file">
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	373 <assert_contents>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	374 <has_text text="ebola" />
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	375 </assert_contents>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	376 </output>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	377 <output name="gene_abundances" value="paired_refgen_gene_abundances.bt.tab"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	378 <output name="isoform_abundances" value="paired_refgen_isoform_abundances.bt.tab" />
6 45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6 artbio parents: 5 diff changeset	379 <output name="transcript_sorted_bam" value="paired_refgen_transcripts.bt.bam" ftype="bam" lines_diff="4" />
45a30e216fec planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 4bc762d0932b87d4e91ce76bc3eeb52f0b8d3bc6 artbio parents: 5 diff changeset	380 <output name="genome_sorted_bam" value="paired_refgen_isoform_abundances.bt.bam" ftype="bam" lines_diff="4" />
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	381 <output name="log">
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	382 <assert_contents>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	383 <has_text text="Expression Results are written" />
4 1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	384 </assert_contents>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	385 </output>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	386 </test>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	387 <test>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	388 <!-- test fastqsanger paired end Ebola transcripts -->
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	389 <param name="select_job" value="index"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	390 <param name="ref_type" value="transcripts"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	391 <param name="reference_fasta_file" value="Ebola_transcripts.fa" ftype="fasta"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	392 <param name="transcript_to_gene_map" value="ebola_gene_transcript_table.txt" ftype="tabular"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	393 <param name="reference_name" value="ebola"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	394 <param name="select" value="Yes"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	395 <param name="sample" value="rsem_sample"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	396 <param name="refSrc" value="self"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	397 <param name="format" value="fastq"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	398 <param name="matepair" value="paired"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	399 <param name="fastq1" value="Ebola_forward.fastqsanger.gz" ftype="fastqsanger"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	400 <param name="fastq2" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	401 <param name="result_bams" value="default" />
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	402 <output name="reference_file">
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	403 <assert_contents>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	404 <has_text text="ebola" />
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	405 </assert_contents>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	406 </output>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	407 <output name="gene_abundances" value="paired_reftrans_gene_abundances.bt.tab"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	408 <output name="isoform_abundances" value="paired_reftrans_isoform_abundances.bt.tab" />
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	409 <output name="transcript_sorted_bam" value="paired_reftrans_transcripts.bt.bam" ftype="bam" lines_diff="2" />
4 1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	410 <output name="log">
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	411 <assert_contents>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	412 <has_text text="Expression Results are written" />
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	413 </assert_contents>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	414 </output>
1823c8e07d96 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit a3df058f7bb29ae3d42b85d6e911b68679150c9f artbio parents: 3 diff changeset	415 </test>
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	416 <test>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	417 <param name="select_job" value="index"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	418 <param name="ref_type" value="genomic"/>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	419 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	420 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	421 <param name="reference_name" value="ebola"/>
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	422 <param name="select" value="Yes"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	423 <param name="sample" value="rsem_sample"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	424 <param name="refSrc" value="self"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	425 <param name="format" value="fastq"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	426 <param name="matepair" value="single"/>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	427 <param name="singlefastq" value="Ebola_reverse.fastqsanger.gz" ftype="fastqsanger.gz"/>
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	428 <param name="result_bams" value="none"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	429 <output name="reference_file">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	430 <assert_contents>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	431 <has_text text="ebola" />
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	432 </assert_contents>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	433 </output>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	434 <output name="gene_abundances" value="single_refgen_gene_abundances.bt.tab"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	435 <output name="isoform_abundances" value="single_refgen_isoform_abundances.bt.tab" />
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	436 <output name="log">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	437 <assert_contents>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	438 <has_text text="Expression Results are written" />
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	439 </assert_contents>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	440 </output>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	441 </test>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	442 <test>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	443 <param name="select_job" value="index"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	444 <param name="ref_type" value="genomic"/>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	445 <param name="reference_fasta_file" value="eboVir3.fa" ftype="fasta"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	446 <param name="gtf" value="eboVir3.gtf" ftype="gtf"/>
835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	447 <param name="reference_name" value="alone"/>
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	448 <param name="select" value="No"/>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	449 <output name="reference_file">
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	450 <assert_contents>
5 835a2f3372b5 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit 5bb908607e13ccad44d768e786253ce7b5c626f8 artbio parents: 4 diff changeset	451 <has_text text="alone" />
0 e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	452 </assert_contents>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	453 </output>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	454 </test>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	455 </tests>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	456
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	457 <help>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	458 .. class:: infomark
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	459
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	460 RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	461
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	462 NAME
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	463 rsem-prepare-reference
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	464
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	465 SYNOPSIS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	466 rsem-prepare-reference [options] reference_fasta_file(s) reference_name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	467
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	468 DESCRIPTION
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	469 The rsem-prepare-reference program extracts/preprocesses the reference sequences and builds Bowtie indices using default parameters.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	470 This program is used in conjunction with the 'rsem-calculate-expression' program.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	471
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	472 INPUTS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	473 A fasta file of transcripts
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	474 or
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	475 A genome sequence fasta file and a GTF gene annotation file. (When using UCSC data, include the related knownIsoforms.txt)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	476
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	477 ---
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	478
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	479 NAME
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	480 rsem-calculate-expression - Estimate gene and isoform expression from
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	481 RNA-Seq data.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	482
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	483 SYNOPSIS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	484 rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	485 rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	486 rsem-calculate-expression [options] --alignments [--paired-end] input reference_name sample_name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	487
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	488 ARGUMENTS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	489 upstream_read_files(s)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	490 Comma-separated list of files containing single-end reads or
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	491 upstream reads for paired-end data. By default, these files are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	492 assumed to be in FASTQ format. If the --no-qualities option is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	493 specified, then FASTA format is expected.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	494
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	495 downstream_read_file(s)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	496 Comma-separated list of files containing downstream reads which are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	497 paired with the upstream reads. By default, these files are assumed
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	498 to be in FASTQ format. If the --no-qualities option is specified,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	499 then FASTA format is expected.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	500
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	501 input
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	502 SAM/BAM/CRAM formatted input file. If "-" is specified for the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	503 filename, the input is instead assumed to come from standard input.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	504 RSEM requires all alignments of the same read group together. For
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	505 paired-end reads, RSEM also requires the two mates of any alignment
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	506 be adjacent. In addition, RSEM does not allow the SEQ and QUAL
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	507 fields to be empty. See Description section for how to make input
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	508 file obey RSEM's requirements.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	509
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	510 reference_name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	511 The name of the reference used. The user must have run
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	512 'rsem-prepare-reference' with this reference_name before running
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	513 this program.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	514
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	515 sample_name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	516 The name of the sample analyzed. All output files are prefixed by
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	517 this name (e.g., sample_name.genes.results)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	518
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	519 BASIC OPTIONS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	520 --paired-end
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	521 Input reads are paired-end reads. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	522
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	523 --no-qualities
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	524 Input reads do not contain quality scores. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	525
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	526 --strandedness <none\|forward\|reverse>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	527 This option defines the strandedness of the RNA-Seq reads. It
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	528 recognizes three values: 'none', 'forward', and 'reverse'. 'none'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	529 refers to non-strand-specific protocols. 'forward' means all
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	530 (upstream) reads are derived from the forward strand. 'reverse'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	531 means all (upstream) reads are derived from the reverse strand. If
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	532 'forward'/'reverse' is set, the '--norc'/'--nofw' Bowtie/Bowtie 2
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	533 option will also be enabled to avoid aligning reads to the opposite
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	534 strand. For Illumina TruSeq Stranded protocols, please use
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	535 'reverse'. (Default: 'none')
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	536
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	537 -p/--num-threads <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	538 Number of threads to use. Both Bowtie/Bowtie2, expression estimation
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	539 and 'samtools sort' will use this many threads. (Default: 1)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	540
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	541 --alignments
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	542 Input file contains alignments in SAM/BAM/CRAM format. The exact
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	543 file format will be determined automatically. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	544
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	545 --fai <file>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	546 If the header section of input alignment file does not contain
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	547 reference sequence information, this option should be turned on.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	548 <file> is a FAI format file containing each reference sequence's
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	549 name and length. Please refer to the SAM official website for the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	550 details of FAI format. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	551
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	552 --bowtie2
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	553 Use Bowtie 2 instead of Bowtie to align reads. Since currently RSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	554 does not handle indel, local and discordant alignments, the Bowtie2
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	555 parameters are set in a way to avoid those alignments. In
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	556 particular, we use options '--sensitive --dpad 0 --gbar 99999999
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	557 --mp 1,1 --np 1 --score-min L,0,-0.1' by default. The last parameter
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	558 of '--score-min', '-0.1', is the negative of maximum mismatch rate.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	559 This rate can be set by option '--bowtie2-mismatch-rate'. If reads
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	560 are paired-end, we additionally use options '--no-mixed' and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	561 '--no-discordant'. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	562
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	563 --star
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	564 Use STAR to align reads. Alignment parameters are from ENCODE3's
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	565 STAR-RSEM pipeline. To save computational time and memory resources,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	566 STAR's Output BAM file is unsorted. It is stored in RSEM's temporary
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	567 directory with name as 'sample_name.bam'. Each STAR job will have
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	568 its own private copy of the genome in memory. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	569
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	570 --append-names
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	571 If gene_name/transcript_name is available, append it to the end of
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	572 gene_id/transcript_id (separated by '_') in files
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	573 'sample_name.isoforms.results' and 'sample_name.genes.results'.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	574 (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	575
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	576 --seed <uint32>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	577 Set the seed for the random number generators used in calculating
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	578 posterior mean estimates and credibility intervals. The seed must be
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	579 a non-negative 32 bit integer. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	580
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	581 --single-cell-prior
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	582 By default, RSEM uses Dirichlet(1) as the prior to calculate
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	583 posterior mean estimates and credibility intervals. However, much
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	584 less genes are expressed in single cell RNA-Seq data. Thus, if you
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	585 want to compute posterior mean estimates and/or credibility
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	586 intervals and you have single-cell RNA-Seq data, you are recommended
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	587 to turn on this option. Then RSEM will use Dirichlet(0.1) as the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	588 prior which encourage the sparsity of the expression levels.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	589 (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	590
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	591 --calc-pme
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	592 Run RSEM's collapsed Gibbs sampler to calculate posterior mean
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	593 estimates. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	594
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	595 --calc-ci
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	596 Calculate 95% credibility intervals and posterior mean estimates.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	597 The credibility level can be changed by setting
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	598 '--ci-credibility-level'. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	599
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	600 -q/--quiet
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	601 Suppress the output of logging information. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	602
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	603 -h/--help
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	604 Show help information.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	605
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	606 --version
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	607 Show version information.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	608
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	609 OUTPUT OPTIONS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	610 --sort-bam-by-read-name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	611 Sort BAM file aligned under transcript coordidate by read name.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	612 Setting this option on will produce deterministic maximum likelihood
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	613 estimations from independent runs. Note that sorting will take long
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	614 time and lots of memory. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	615
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	616 --no-bam-output
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	617 Do not output any BAM file. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	618
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	619 --sampling-for-bam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	620 When RSEM generates a BAM file, instead of outputting all alignments
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	621 a read has with their posterior probabilities, one alignment is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	622 sampled according to the posterior probabilities. The sampling
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	623 procedure includes the alignment to the "noise" transcript, which
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	624 does not appear in the BAM file. Only the sampled alignment has a
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	625 weight of 1. All other alignments have weight 0. If the "noise"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	626 transcript is sampled, all alignments appeared in the BAM file
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	627 should have weight 0. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	628
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	629 --output-genome-bam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	630 Generate a BAM file, 'sample_name.genome.bam', with alignments
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	631 mapped to genomic coordinates and annotated with their posterior
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	632 probabilities. In addition, RSEM will call samtools (included in
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	633 RSEM package) to sort and index the bam file.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	634 'sample_name.genome.sorted.bam' and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	635 'sample_name.genome.sorted.bam.bai' will be generated. (Default:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	636 off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	637
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	638 --sort-bam-by-coordinate
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	639 Sort RSEM generated transcript and genome BAM files by coordinates
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	640 and build associated indices. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	641
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	642 --sort-bam-memory-per-thread <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	643 Set the maximum memory per thread that can be used by 'samtools
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	644 sort'. <string> represents the memory and accepts suffices 'K/M/G'.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	645 RSEM will pass <string> to the '-m' option of 'samtools sort'. Note
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	646 that the default used here is different from the default used by
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	647 samtools. (Default: 1G)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	648
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	649 ALIGNER OPTIONS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	650 --seed-length <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	651 Seed length used by the read aligner. Providing the correct value is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	652 important for RSEM. If RSEM runs Bowtie, it uses this value for
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	653 Bowtie's seed length parameter. Any read with its or at least one of
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	654 its mates' (for paired-end reads) length less than this value will
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	655 be ignored. If the references are not added poly(A) tails, the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	656 minimum allowed value is 5, otherwise, the minimum allowed value is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	657 25. Note that this script will only check if the value >= 5 and give
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	658 a warning message if the value < 25 but >= 5. (Default: 25)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	659
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	660 --phred33-quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	661 Input quality scores are encoded as Phred+33. (Default: on)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	662
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	663 --phred64-quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	664 Input quality scores are encoded as Phred+64 (default for GA
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	665 Pipeline ver. >= 1.3). (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	666
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	667 --solexa-quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	668 Input quality scores are solexa encoded (from GA Pipeline ver. <
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	669 1.3). (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	670
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	671 --bowtie-path <path>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	672 The path to the Bowtie executables. (Default: the path to the Bowtie
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	673 executables is assumed to be in the user's PATH environment
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	674 variable)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	675
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	676 --bowtie-n <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	677 (Bowtie parameter) max # of mismatches in the seed. (Range: 0-3,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	678 Default: 2)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	679
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	680 --bowtie-e <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	681 (Bowtie parameter) max sum of mismatch quality scores across the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	682 alignment. (Default: 99999999)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	683
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	684 --bowtie-m <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	685 (Bowtie parameter) suppress all alignments for a read if > <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	686 valid alignments exist. (Default: 200)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	687
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	688 --bowtie-chunkmbs <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	689 (Bowtie parameter) memory allocated for best first alignment
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	690 calculation (Default: 0 - use Bowtie's default)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	691
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	692 --bowtie2-path <path>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	693 (Bowtie 2 parameter) The path to the Bowtie 2 executables. (Default:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	694 the path to the Bowtie 2 executables is assumed to be in the user's
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	695 PATH environment variable)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	696
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	697 --bowtie2-mismatch-rate <double>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	698 (Bowtie 2 parameter) The maximum mismatch rate allowed. (Default:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	699 0.1)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	700
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	701 --bowtie2-k <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	702 (Bowtie 2 parameter) Find up to <int> alignments per read. (Default:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	703 200)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	704
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	705 --bowtie2-sensitivity-level <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	706 (Bowtie 2 parameter) Set Bowtie 2's preset options in --end-to-end
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	707 mode. This option controls how hard Bowtie 2 tries to find
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	708 alignments. <string> must be one of "very_fast", "fast", "sensitive"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	709 and "very_sensitive". The four candidates correspond to Bowtie 2's
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	710 "--very-fast", "--fast", "--sensitive" and "--very-sensitive"
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	711 options. (Default: "sensitive" - use Bowtie 2's default)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	712
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	713 --star-path <path>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	714 The path to STAR's executable. (Default: the path to STAR executable
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	715 is assumed to be in user's PATH environment variable)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	716
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	717 --star-gzipped-read-file
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	718 (STAR parameter) Input read file(s) is compressed by gzip. (Default:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	719 off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	720
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	721 --star-bzipped-read-file
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	722 (STAR parameter) Input read file(s) is compressed by bzip2.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	723 (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	724
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	725 --star-output-genome-bam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	726 (STAR parameter) Save the BAM file from STAR alignment under genomic
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	727 coordinate to 'sample_name.STAR.genome.bam'. This file is NOT sorted
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	728 by genomic coordinate. In this file, according to STAR's manual,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	729 'paired ends of an alignment are always adjacent, and multiple
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	730 alignments of a read are adjacent as well'. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	731
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	732 ADVANCED OPTIONS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	733 --tag <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	734 The name of the optional field used in the SAM input for identifying
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	735 a read with too many valid alignments. The field should have the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	736 format <tagName>:i:<value>, where a <value> bigger than 0 indicates
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	737 a read with too many alignments. (Default: "")
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	738
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	739 --fragment-length-min <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	740 Minimum read/insert length allowed. This is also the value for the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	741 Bowtie/Bowtie2 -I option. (Default: 1)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	742
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	743 --fragment-length-max <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	744 Maximum read/insert length allowed. This is also the value for the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	745 Bowtie/Bowtie 2 -X option. (Default: 1000)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	746
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	747 --fragment-length-mean <double>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	748 (single-end data only) The mean of the fragment length distribution,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	749 which is assumed to be a Gaussian. (Default: -1, which disables use
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	750 of the fragment length distribution)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	751
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	752 --fragment-length-sd <double>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	753 (single-end data only) The standard deviation of the fragment length
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	754 distribution, which is assumed to be a Gaussian. (Default: 0, which
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	755 assumes that all fragments are of the same length, given by the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	756 rounded value of --fragment-length-mean)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	757
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	758 --estimate-rspd
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	759 Set this option if you want to estimate the read start position
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	760 distribution (RSPD) from data. Otherwise, RSEM will use a uniform
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	761 RSPD. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	762
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	763 --num-rspd-bins <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	764 Number of bins in the RSPD. Only relevant when '--estimate-rspd' is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	765 specified. Use of the default setting is recommended. (Default: 20)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	766
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	767 --gibbs-burnin <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	768 The number of burn-in rounds for RSEM's Gibbs sampler. Each round
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	769 passes over the entire data set once. If RSEM can use multiple
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	770 threads, multiple Gibbs samplers will start at the same time and all
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	771 samplers share the same burn-in number. (Default: 200)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	772
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	773 --gibbs-number-of-samples <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	774 The total number of count vectors RSEM will collect from its Gibbs
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	775 samplers. (Default: 1000)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	776
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	777 --gibbs-sampling-gap <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	778 The number of rounds between two succinct count vectors RSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	779 collects. If the count vector after round N is collected, the count
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	780 vector after round N + <int> will also be collected. (Default: 1)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	781
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	782 --ci-credibility-level <double>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	783 The credibility level for credibility intervals. (Default: 0.95)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	784
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	785 --ci-memory <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	786 Maximum size (in memory, MB) of the auxiliary buffer used for
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	787 computing credibility intervals (CI). (Default: 1024)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	788
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	789 --ci-number-of-samples-per-count-vector <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	790 The number of read generating probability vectors sampled per
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	791 sampled count vector. The crebility intervals are calculated by
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	792 first sampling P(C \| D) and then sampling P(Theta \| C) for each
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	793 sampled count vector. This option controls how many Theta vectors
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	794 are sampled per sampled count vector. (Default: 50)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	795
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	796 --keep-intermediate-files
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	797 Keep temporary files generated by RSEM. RSEM creates a temporary
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	798 directory, 'sample_name.temp', into which it puts all intermediate
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	799 output files. If this directory already exists, RSEM overwrites all
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	800 files generated by previous RSEM runs inside of it. By default,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	801 after RSEM finishes, the temporary directory is deleted. Set this
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	802 option to prevent the deletion of this directory and the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	803 intermediate files inside of it. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	804
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	805 --temporary-folder <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	806 Set where to put the temporary files generated by RSEM. If the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	807 folder specified does not exist, RSEM will try to create it.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	808 (Default: sample_name.temp)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	809
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	810 --time
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	811 Output time consumed by each step of RSEM to 'sample_name.time'.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	812 (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	813
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	814 PRIOR-ENHANCED RSEM OPTIONS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	815 --run-pRSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	816 Running prior-enhanced RSEM (pRSEM). Prior parameters, i.e.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	817 isoform's initial pseudo-count for RSEM's Gibbs sampling, will be
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	818 learned from input RNA-seq data and an external data set. When pRSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	819 needs and only needs ChIP-seq peak information to partition isoforms
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	820 (e.g. in pRSEM's default partition model), either ChIP-seq peak file
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	821 (with the '--chipseq-peak-file' option) or ChIP-seq FASTQ files for
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	822 target and input and the path for Bowtie executables are required
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	823 (with the '--chipseq-target-read-files <string>',
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	824 '--chipseq-control-read-files <string>', and '--bowtie-path <path>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	825 options), otherwise, ChIP-seq FASTQ files for target and control and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	826 the path to Bowtie executables are required. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	827
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	828 --chipseq-peak-file <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	829 Full path to a ChIP-seq peak file in ENCODE's narrowPeak, i.e.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	830 BED6+4, format. This file is used when running prior-enhanced RSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	831 in the default two-partition model. It partitions isoforms by
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	832 whether they have ChIP-seq overlapping with their transcription
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	833 start site region or not. Each partition will have its own prior
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	834 parameter learned from a training set. This file can be either
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	835 gzipped or ungzipped. (Default: "")
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	836
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	837 --chipseq-target-read-files <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	838 Comma-separated full path of FASTQ read file(s) for ChIP-seq target.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	839 This option is used when running prior-enhanced RSEM. It provides
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	840 information to calculate ChIP-seq peaks and signals. The file(s) can
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	841 be either ungzipped or gzipped with a suffix '.gz' or '.gzip'. The
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	842 options '--bowtie-path <path>' and '--chipseq-control-read-files
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	843 <string>' must be defined when this option is specified. (Default:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	844 "")
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	845
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	846 --chipseq-control-read-files <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	847 Comma-separated full path of FASTQ read file(s) for ChIP-seq conrol.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	848 This option is used when running prior-enhanced RSEM. It provides
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	849 information to call ChIP-seq peaks. The file(s) can be either
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	850 ungzipped or gzipped with a suffix '.gz' or '.gzip'. The options
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	851 '--bowtie-path <path>' and '--chipseq-target-read-files <string>'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	852 must be defined when this option is specified. (Default: "")
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	853
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	854 --chipseq-read-files-multi-targets <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	855 Comma-separated full path of FASTQ read files for multiple ChIP-seq
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	856 targets. This option is used when running prior-enhanced RSEM, where
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	857 prior is learned from multiple complementary data sets. It provides
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	858 information to calculate ChIP-seq signals. All files can be either
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	859 ungzipped or gzipped with a suffix '.gz' or '.gzip'. When this
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	860 option is specified, the option '--bowtie-path <path>' must be
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	861 defined and the option '--partition-model <string>' will be set to
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	862 'cmb_lgt' automatically. (Default: "")
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	863
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	864 --chipseq-bed-files-multi-targets <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	865 Comma-separated full path of BED files for multiple ChIP-seq
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	866 targets. This option is used when running prior-enhanced RSEM, where
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	867 prior is learned from multiple complementary data sets. It provides
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	868 information of ChIP-seq signals and must have at least the first six
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	869 BED columns. All files can be either ungzipped or gzipped with a
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	870 suffix '.gz' or '.gzip'. When this option is specified, the option
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	871 '--partition-model <string>' will be set to 'cmb_lgt' automatically.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	872 (Default: "")
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	873
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	874 --cap-stacked-chipseq-reads
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	875 Keep a maximum number of ChIP-seq reads that aligned to the same
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	876 genomic interval. This option is used when running prior-enhanced
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	877 RSEM, where prior is learned from multiple complementary data sets.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	878 This option is only in use when either
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	879 '--chipseq-read-files-multi-targets <string>' or
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	880 '--chipseq-bed-files-multi-targets <string>' is specified. (Default:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	881 off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	882
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	883 --n-max-stacked-chipseq-reads <int>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	884 The maximum number of stacked ChIP-seq reads to keep. This option is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	885 used when running prior-enhanced RSEM, where prior is learned from
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	886 multiple complementary data sets. This option is only in use when
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	887 the option '--cap-stacked-chipseq-reads' is set. (Default: 5)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	888
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	889 --partition-model <string>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	890 A keyword to specify the partition model used by prior-enhanced
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	891 RSEM. It must be one of the following keywords:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	892
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	893 - pk
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	894 Partitioned by whether an isoform has a ChIP-seq peak overlapping
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	895 with its transcription start site (TSS) region. The TSS region is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	896 defined as [TSS-500bp, TSS+500bp]. For simplicity, we refer this
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	897 type of peak as 'TSS peak' when explaining other keywords.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	898
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	899 - pk_lgtnopk
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	900 First partitioned by TSS peak. Then, for isoforms in the 'no TSS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	901 peak' set, a logistic model is employed to further classify them
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	902 into two partitions.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	903
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	904 - lm3, lm4, lm5, or lm6
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	905 Based on their ChIP-seq signals, isoforms are classified into 3,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	906 4, 5, or 6 partitions by a linear regression model.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	907
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	908 - nopk_lm2pk, nopk_lm3pk, nopk_lm4pk, or nopk_lm5pk
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	909 First partitioned by TSS peak. Then, for isoforms in the 'with TSS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	910 peak' set, a linear regression model is employed to further
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	911 classify them into 2, 3, 4, or 5 partitions.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	912
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	913 - pk_lm2nopk, pk_lm3nopk, pk_lm4nopk, or pk_lm5nopk
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	914 First partitioned by TSS peak. Then, for isoforms in the 'no TSS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	915 peak' set, a linear regression model is employed to further
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	916 classify them into 2, 3, 4, or 5 partitions.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	917
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	918 - cmb_lgt
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	919 Using a logistic regression to combine TSS signals from multiple
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	920 complementary data sets and partition training set isoform into
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	921 'expressed' and 'not expressed'. This partition model is only in
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	922 use when either '--chipseq-read-files-multi-targets <string>' or
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	923 '--chipseq-bed-files-multi-targets <string> is specified.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	924
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	925 Parameters for all the above models are learned from a training set.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	926 For detailed explanations, please see prior-enhanced RSEM's paper.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	927 (Default: 'pk')
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	928
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	929 DEPRECATED OPTIONS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	930 The options in this section are deprecated. They are here only for
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	931 compatibility reasons and may be removed in future releases.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	932
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	933 --sam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	934 Inputs are alignments in SAM format. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	935
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	936 --bam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	937 Inputs are alignments in BAM format. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	938
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	939 --strand-specific
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	940 Equivalent to '--strandedness forward'. (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	941
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	942 --forward-prob <double>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	943 Probability of generating a read from the forward strand of a
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	944 transcript. Set to 1 for a strand-specific protocol where all
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	945 (upstream) reads are derived from the forward strand, 0 for a
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	946 strand-specific protocol where all (upstream) read are derived from
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	947 the reverse strand, or 0.5 for a non-strand-specific protocol.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	948 (Default: off)
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	949
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	950 DESCRIPTION
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	951 In its default mode, this program aligns input reads against a reference
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	952 transcriptome with Bowtie and calculates expression values using the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	953 alignments. RSEM assumes the data are single-end reads with quality
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	954 scores, unless the '--paired-end' or '--no-qualities' options are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	955 specified. Alternatively, users can use STAR to align reads using the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	956 '--star' option. RSEM has provided options in 'rsem-prepare-reference'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	957 to prepare STAR's genome indices. Users may use an alternative aligner
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	958 by specifying '--alignments', and providing an alignment file in
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	959 SAM/BAM/CRAM format. However, users should make sure that they align
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	960 against the indices generated by 'rsem-prepare-reference' and the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	961 alignment file satisfies the requirements mentioned in ARGUMENTS
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	962 section.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	963
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	964 One simple way to make the alignment file satisfying RSEM's requirements
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	965 is to use the 'convert-sam-for-rsem' script. This script accepts
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	966 SAM/BAM/CRAM files as input and outputs a BAM file. For example, type
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	967 the following command to convert a SAM file, 'input.sam', to a
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	968 ready-for-use BAM file, 'input_for_rsem.bam':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	969
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	970 convert-sam-for-rsem input.sam input_for_rsem
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	971
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	972 For details, please refer to 'convert-sam-for-rsem's documentation page.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	973
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	974 NOTES
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	975 1. Users must run 'rsem-prepare-reference' with the appropriate
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	976 reference before using this program.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	977
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	978 2. For single-end data, it is strongly recommended that the user provide
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	979 the fragment length distribution parameters (--fragment-length-mean and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	980 --fragment-length-sd). For paired-end data, RSEM will automatically
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	981 learn a fragment length distribution from the data.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	982
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	983 3. Some aligner parameters have default values different from their
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	984 original settings.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	985
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	986 4. With the '--calc-pme' option, posterior mean estimates will be
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	987 calculated in addition to maximum likelihood estimates.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	988
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	989 5. With the '--calc-ci' option, 95% credibility intervals and posterior
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	990 mean estimates will be calculated in addition to maximum likelihood
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	991 estimates.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	992
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	993 6. The temporary directory and all intermediate files will be removed
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	994 when RSEM finishes unless '--keep-intermediate-files' is specified.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	995
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	996 With the '--run-pRSEM' option and associated options (see section
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	997 'PRIOR-ENHANCED RSEM OPTIONS' above for details), prior-enhanced RSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	998 will be running. Prior parameters will be learned from supplied external
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	999 data set(s) and assigned as initial pseudo-counts for isoforms in the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1000 corresponding partition for Gibbs sampling.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1001
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1002 OUTPUT
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1003 sample_name.isoforms.results
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1004 File containing isoform level expression estimates. The first line
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1005 contains column names separated by the tab character. The format of
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1006 each line in the rest of this file is:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1007
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1008 transcript_id gene_id length effective_length expected_count TPM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1009 FPKM IsoPct [posterior_mean_count
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1010 posterior_standard_deviation_of_count pme_TPM pme_FPKM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1011 IsoPct_from_pme_TPM TPM_ci_lower_bound TPM_ci_upper_bound
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1012 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1013 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1014
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1015 Fields are separated by the tab character. Fields within "[]" are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1016 optional. They will not be presented if neither '--calc-pme' nor
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1017 '--calc-ci' is set.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1018
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1019 'transcript_id' is the transcript name of this transcript. 'gene_id'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1020 is the gene name of the gene which this transcript belongs to
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1021 (denote this gene as its parent gene). If no gene information is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1022 provided, 'gene_id' and 'transcript_id' are the same.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1023
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1024 'length' is this transcript's sequence length (poly(A) tail is not
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1025 counted). 'effective_length' counts only the positions that can
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1026 generate a valid fragment. If no poly(A) tail is added,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1027 'effective_length' is equal to transcript length - mean fragment
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1028 length + 1. If one transcript's effective length is less than 1,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1029 this transcript's both effective length and abundance estimates are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1030 set to 0.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1031
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1032 'expected_count' is the sum of the posterior probability of each
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1033 read comes from this transcript over all reads. Because 1) each read
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1034 aligning to this transcript has a probability of being generated
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1035 from background noise; 2) RSEM may filter some alignable low quality
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1036 reads, the sum of expected counts for all transcript are generally
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1037 less than the total number of reads aligned.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1038
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1039 'TPM' stands for Transcripts Per Million. It is a relative measure
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1040 of transcript abundance. The sum of all transcripts' TPM is 1
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1041 million. 'FPKM' stands for Fragments Per Kilobase of transcript per
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1042 Million mapped reads. It is another relative measure of transcript
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1043 abundance. If we define l_bar be the mean transcript length in a
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1044 sample, which can be calculated as
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1045
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1046 l_bar = \sum_i TPM_i / 10^6 * effective_length_i (i goes through
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1047 every transcript),
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1048
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1049 the following equation is hold:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1050
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1051 FPKM_i = 10^3 / l_bar * TPM_i.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1052
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1053 We can see that the sum of FPKM is not a constant across samples.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1054
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1055 'IsoPct' stands for isoform percentage. It is the percentage of this
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1056 transcript's abandunce over its parent gene's abandunce. If its
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1057 parent gene has only one isoform or the gene information is not
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1058 provided, this field will be set to 100.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1059
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1060 'posterior_mean_count', 'pme_TPM', 'pme_FPKM' are posterior mean
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1061 estimates calculated by RSEM's Gibbs sampler.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1062 'posterior_standard_deviation_of_count' is the posterior standard
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1063 deviation of counts. 'IsoPct_from_pme_TPM' is the isoform percentage
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1064 calculated from 'pme_TPM' values.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1065
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1066 'TPM_ci_lower_bound', 'TPM_ci_upper_bound', 'FPKM_ci_lower_bound'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1067 and 'FPKM_ci_upper_bound' are lower(l) and upper(u) bounds of 95%
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1068 credibility intervals for TPM and FPKM values. The bounds are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1069 inclusive (i.e. [l, u]).
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1070
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1071 'TPM_coefficient_of_quartile_variation' and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1072 'FPKM_coefficient_of_quartile_variation' are coefficients of
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1073 quartile variation (CQV) for TPM and FPKM values. CQV is a robust
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1074 way of measuring the ratio between the standard deviation and the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1075 mean. It is defined as
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1076
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1077 CQV := (Q3 - Q1) / (Q3 + Q1),
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1078
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1079 where Q1 and Q3 are the first and third quartiles.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1080
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1081 sample_name.genes.results
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1082 File containing gene level expression estimates. The first line
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1083 contains column names separated by the tab character. The format of
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1084 each line in the rest of this file is:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1085
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1086 gene_id transcript_id(s) length effective_length expected_count TPM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1087 FPKM [posterior_mean_count posterior_standard_deviation_of_count
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1088 pme_TPM pme_FPKM TPM_ci_lower_bound TPM_ci_upper_bound
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1089 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1090 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1091
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1092 Fields are separated by the tab character. Fields within "[]" are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1093 optional. They will not be presented if neither '--calc-pme' nor
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1094 '--calc-ci' is set.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1095
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1096 'transcript_id(s)' is a comma-separated list of transcript_ids
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1097 belonging to this gene. If no gene information is provided,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1098 'gene_id' and 'transcript_id(s)' are identical (the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1099 'transcript_id').
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1100
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1101 A gene's 'length' and 'effective_length' are defined as the weighted
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1102 average of its transcripts' lengths and effective lengths (weighted
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1103 by 'IsoPct'). A gene's abundance estimates are just the sum of its
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1104 transcripts' abundance estimates.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1105
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1106 sample_name.alleles.results
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1107 Only generated when the RSEM references are built with
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1108 allele-specific transcripts.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1109
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1110 This file contains allele level expression estimates for
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1111 allele-specific expression calculation. The first line contains
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1112 column names separated by the tab character. The format of each line
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1113 in the rest of this file is:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1114
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1115 allele_id transcript_id gene_id length effective_length
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1116 expected_count TPM FPKM AlleleIsoPct AlleleGenePct
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1117 [posterior_mean_count posterior_standard_deviation_of_count pme_TPM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1118 pme_FPKM AlleleIsoPct_from_pme_TPM AlleleGenePct_from_pme_TPM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1119 TPM_ci_lower_bound TPM_ci_upper_bound
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1120 TPM_coefficient_of_quartile_variation FPKM_ci_lower_bound
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1121 FPKM_ci_upper_bound FPKM_coefficient_of_quartile_variation]
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1122
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1123 Fields are separated by the tab character. Fields within "[]" are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1124 optional. They will not be presented if neither '--calc-pme' nor
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1125 '--calc-ci' is set.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1126
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1127 'allele_id' is the allele-specific name of this allele-specific
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1128 transcript.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1129
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1130 'AlleleIsoPct' stands for allele-specific percentage on isoform
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1131 level. It is the percentage of this allele-specific transcript's
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1132 abundance over its parent transcript's abundance. If its parent
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1133 transcript has only one allele variant form, this field will be set
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1134 to 100.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1135
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1136 'AlleleGenePct' stands for allele-specific percentage on gene level.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1137 It is the percentage of this allele-specific transcript's abundance
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1138 over its parent gene's abundance.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1139
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1140 'AlleleIsoPct_from_pme_TPM' and 'AlleleGenePct_from_pme_TPM' have
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1141 similar meanings. They are calculated based on posterior mean
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1142 estimates.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1143
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1144 Please note that if this file is present, the fields 'length' and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1145 'effective_length' in 'sample_name.isoforms.results' should be
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1146 interpreted similarly as the corresponding definitions in
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1147 'sample_name.genes.results'.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1148
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1149 sample_name.transcript.bam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1150 Only generated when --no-bam-output is not specified.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1151
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1152 'sample_name.transcript.bam' is a BAM-formatted file of read
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1153 alignments in transcript coordinates. The MAPQ field of each
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1154 alignment is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)),
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1155 where w is the posterior probability of that alignment being the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1156 true mapping of a read. In addition, RSEM pads a new tag ZW:f:value,
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1157 where value is a single precision floating number representing the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1158 posterior probability. Because this file contains all alignment
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1159 lines produced by bowtie or user-specified aligners, it can also be
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1160 used as a replacement of the aligner generated BAM/SAM file.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1161
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1162 sample_name.transcript.sorted.bam and sample_name.transcript.sorted.bam.bai
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1163 Only generated when --no-bam-output is not specified and --sort-bam-by-coordinate is specified.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1164
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1165 'sample_name.transcript.sorted.bam' and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1166 'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1167 indices generated by samtools (included in RSEM package).
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1168
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1169 sample_name.genome.bam
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1170 Only generated when --no-bam-output is not specified and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1171 --output-genome-bam is specified.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1172
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1173 'sample_name.genome.bam' is a BAM-formatted file of read alignments
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1174 in genomic coordinates. Alignments of reads that have identical
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1175 genomic coordinates (i.e., alignments to different isoforms that
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1176 share the same genomic region) are collapsed into one alignment. The
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1177 MAPQ field of each alignment is set to min(100, floor(-10 *
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1178 log10(1.0 - w) + 0.5)), where w is the posterior probability of that
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1179 alignment being the true mapping of a read. In addition, RSEM pads a
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1180 new tag ZW:f:value, where value is a single precision floating
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1181 number representing the posterior probability. If an alignment is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1182 spliced, a XS:A:value tag is also added, where value is either '+'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1183 or '-' indicating the strand of the transcript it aligns to.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1184
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1185 sample_name.genome.sorted.bam and sample_name.genome.sorted.bam.bai
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1186 Only generated when --no-bam-output is not specified, and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1187 --sort-bam-by-coordinate and --output-genome-bam are specified.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1188
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1189 'sample_name.genome.sorted.bam' and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1190 'sample_name.genome.sorted.bam.bai' are the sorted BAM file and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1191 indices generated by samtools (included in RSEM package).
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1192
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1193 sample_name.time
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1194 Only generated when --time is specified.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1195
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1196 It contains time (in seconds) consumed by aligning reads, estimating
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1197 expression levels and calculating credibility intervals.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1198
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1199 sample_name.stat
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1200 This is a folder instead of a file. All model related statistics are
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1201 stored in this folder. Use 'rsem-plot-model' can generate plots
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1202 using this folder.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1203
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1204 'sample_name.stat/sample_name.cnt' contains alignment statistics.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1205 The format and meanings of each field are described in
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1206 'cnt_file_description.txt' under RSEM directory.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1207
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1208 'sample_name.stat/sample_name.model' stores RNA-Seq model parameters
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1209 learned from the data. The format and meanings of each filed of this
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1210 file are described in 'model_file_description.txt' under RSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1211 directory.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1212
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1213 The following four output files will be generated only by
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1214 prior-enhanced RSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1215
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1216 - 'sample_name.stat/sample_name_prsem.all_tr_features'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1217 It stores isofrom features for deriving and assigning pRSEM prior.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1218 The first line is a header and the rest is one isoform per line.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1219 The description for each column is:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1220
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1221 * trid: transcript ID from input annotation
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1222
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1223 * geneid: gene ID from input anntation
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1224
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1225 * chrom: isoform's chromosome name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1226
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1227 * strand: isoform's strand name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1228
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1229 * start: isoform's end with the lowest genomic loci
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1230
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1231 * end: isoform's end with the highest genomic loci
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1232
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1233 * tss_mpp: average mappability of [TSS-500bp, TSS+500bp], where
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1234 TSS is isoform's transcription start site, i.e. 5'-end
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1235
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1236 * body_mpp: average mappability of (TSS+500bp, TES-500bp), where
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1237 TES is isoform's transcription end site, i.e. 3'-end
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1238
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1239 * tes_mpp: average mappability of [TES-500bp, TES+500bp]
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1240
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1241 * pme_count: isoform's fragment or read count from RSEM's
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1242 posterior mean estimates
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1243
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1244 * tss: isoform's TSS loci
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1245
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1246 * tss_pk: equal to 1 if isoform's [TSS-500bp, TSS+500bp] region
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1247 overlaps with a RNA Pol II peak; 0 otherwise
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1248
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1249 * is_training: equal to 1 if isoform is in the training set where
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1250 Pol II prior is learned; 0 otherwise
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1251
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1252 - 'sample_name.stat/sample_name_prsem.all_tr_prior'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1253 It stores prior parameters for every isoform. This file does not
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1254 have a header. Each line contains a prior parameter and an
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1255 isoform's transcript ID delimited by " # ".
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1256
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1257 - 'sample_name.stat/sample_name_uniform_prior_1.isoforms.results'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1258 RSEM's posterior mean estimates on the isoform level with an
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1259 initial pseudo-count of one for every isoform. It is in the same
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1260 format as the 'sample_name.isoforms.results'.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1261
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1262 - 'sample_name.stat/sample_name_uniform_prior_1.genes.results'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1263 RSEM's posterior mean estimates on the gene level with an initial
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1264 pseudo-count of one for every isoform. It is in the same format as
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1265 the 'sample_name.genes.results'.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1266
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1267 When learning prior from multiple external data sets in
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1268 prior-enhanced RSEM, two additional output files will be generated.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1269
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1270 - 'sample_name.stat/sample_name.pval_LL'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1271 It stores a p-value and a log-likelihood. The p-value indicates
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1272 whether the combination of multiple complementary data sets is
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1273 informative for RNA-seq quantification. The log-likelihood shows
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1274 how well pRSEM's Dirichlet-multinomial model fits the read counts
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1275 of partitioned training set isoforms.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1276
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1277 - 'sample_name.stat/sample_name.lgt_mdl.RData'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1278 It stores an R object named 'glmmdl', which is a logistic
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1279 regression model on the training set isoforms and multiple
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1280 external data sets.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1281
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1282 In addition, extra columns will be added to
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1283 'sample_name.stat/all_tr_features'
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1284
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1285 * is_expr: equal to 1 if isoform has an abundance >= 1 TPM and a
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1286 non-zero read count from RSEM's posterior mean estimates; 0
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1287 otherwise
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1288
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1289 * "$external_data_set_basename": log10 of external data's signal at
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1290 [TSS-500, TSS+500]. Signal is the number of reads aligned within
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1291 that interval and normalized to RPKM by read depth and interval
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1292 length. It will be set to -4 if no read aligned to that interval.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1293
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1294 There are multiple columns like this one, where each represents an
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1295 external data set.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1296
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1297 * prd_expr_prob: predicted probability from logistic regression
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1298 model on whether this isoform is expressed or not. A probability
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1299 higher than 0.5 is considered as expressed
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1300
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1301 * partition: group index, to which this isoforms is partitioned
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1302
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1303 * prior: prior parameter for this isoform
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1304
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1305 EXAMPLES
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1306 Assume the path to the bowtie executables is in the user's PATH
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1307 environment variable. Reference files are under '/ref' with name
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1308 'mouse_125'.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1309
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1310 1) '/data/mmliver.fq', single-end reads with quality scores. Quality
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1311 scores are encoded as for 'GA pipeline version >= 1.3'. We want to use 8
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1312 threads and generate a genome BAM file. In addition, we want to append
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1313 gene/transcript names to the result files:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1314
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1315 rsem-calculate-expression --phred64-quals \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1316 -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1317 --append-names \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1318 --output-genome-bam \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1319 /data/mmliver.fq \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1320 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1321 mmliver_single_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1322
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1323 2) '/data/mmliver_1.fq' and '/data/mmliver_2.fq', stranded paired-end
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1324 reads with quality scores. Suppose the library is prepared using TruSeq
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1325 Stranded Kit, which means the first mate should map to the reverse
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1326 strand. Quality scores are in SANGER format. We want to use 8 threads
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1327 and do not generate a genome BAM file:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1328
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1329 rsem-calculate-expression -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1330 --paired-end \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1331 --strandedness reverse \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1332 /data/mmliver_1.fq \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1333 /data/mmliver_2.fq \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1334 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1335 mmliver_paired_end_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1336
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1337 3) '/data/mmliver.fa', single-end reads without quality scores. We want
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1338 to use 8 threads:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1339
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1340 rsem-calculate-expression -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1341 --no-qualities \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1342 /data/mmliver.fa \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1343 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1344 mmliver_single_without_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1345
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1346 4) Data are the same as 1). This time we assume the bowtie executables
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1347 are under '/sw/bowtie'. We want to take a fragment length distribution
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1348 into consideration. We set the fragment length mean to 150 and the
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1349 standard deviation to 35. In addition to a BAM file, we also want to
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1350 generate credibility intervals. We allow RSEM to use 1GB of memory for
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1351 CI calculation:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1352
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1353 rsem-calculate-expression --bowtie-path /sw/bowtie \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1354 --phred64-quals \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1355 --fragment-length-mean 150.0 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1356 --fragment-length-sd 35.0 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1357 -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1358 --output-genome-bam \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1359 --calc-ci \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1360 --ci-memory 1024 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1361 /data/mmliver.fq \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1362 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1363 mmliver_single_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1364
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1365 5) '/data/mmliver_paired_end_quals.bam', BAM-formatted alignments for
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1366 paired-end reads with quality scores. We want to use 8 threads:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1367
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1368 rsem-calculate-expression --paired-end \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1369 --alignments \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1370 -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1371 /data/mmliver_paired_end_quals.bam \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1372 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1373 mmliver_paired_end_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1374
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1375 6) '/data/mmliver_1.fq.gz' and '/data/mmliver_2.fq.gz', paired-end reads
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1376 with quality scores and read files are compressed by gzip. We want to
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1377 use STAR to aligned reads and assume STAR executable is '/sw/STAR'.
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1378 Suppose we want to use 8 threads and do not generate a genome BAM file:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1379
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1380 rsem-calculate-expression --paired-end \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1381 --star \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1382 --star-path /sw/STAR \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1383 --gzipped-read-file \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1384 --paired-end \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1385 -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1386 /data/mmliver_1.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1387 /data/mmliver_2.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1388 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1389 mmliver_paired_end_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1390
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1391 7) In the above example, suppose we want to run prior-enhanced RSEM
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1392 instead. Assuming we want to learn priors from a ChIP-seq peak file
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1393 '/data/mmlive.narrowPeak.gz':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1394
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1395 rsem-calculate-expression --star \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1396 --star-path /sw/STAR \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1397 --gzipped-read-file \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1398 --paired-end \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1399 --calc-pme \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1400 --run-pRSEM \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1401 --chipseq-peak-file /data/mmliver.narrowPeak.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1402 -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1403 /data/mmliver_1.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1404 /data/mmliver_2.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1405 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1406 mmliver_paired_end_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1407
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1408 8) Similar to the example in 7), suppose we want to use the partition
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1409 model 'pk_lm2nopk' (partitioning isoforms by Pol II TSS peak first and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1410 then partitioning 'no TSS peak' isoforms into two bins by a linear
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1411 regression model), and we want to partition isoforms by RNA Pol II's
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1412 ChIP-seq read files '/data/mmliver_PolIIRep1.fq.gz' and
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1413 '/data/mmliver_PolIIRep2.fq.gz', and the control ChIP-seq read files
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1414 '/data/mmliver_ChIPseqCtrl.fq.gz'. Also, assuming Bowtie's executables
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1415 are under '/sw/bowtie/':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1416
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1417 rsem-calculate-expression --star \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1418 --star-path /sw/STAR \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1419 --gzipped-read-file \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1420 --paired-end \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1421 --calc-pme \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1422 --run-pRSEM \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1423 --chipseq-target-read-files /data/mmliver_PolIIRep1.fq.gz,/data/mmliver_PolIIRep2.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1424 --chipseq-control-read-files /data/mmliver_ChIPseqCtrl.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1425 --partition-model pk_lm2nopk \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1426 --bowtie-path /sw/bowtie \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1427 -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1428 /data/mmliver_1.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1429 /data/mmliver_2.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1430 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1431 mmliver_paired_end_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1432
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1433 9) Similar to the example in 8), suppose we want to derive prior from
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1434 four histone modification ChIP-seq read data sets:
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1435 '/data/H3K27Ac.fastq.gz', '/data/H3K4me1.fastq.gz',
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1436 '/data/H3K4me2.fastq.gz', and '/data/H3K4me3.fastq.gz'. Also, assuming
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1437 Bowtie's executables are under '/sw/bowtie/':
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1438
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1439 rsem-calculate-expression --star \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1440 --star-path /sw/STAR \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1441 --gzipped-read-file \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1442 --paired-end \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1443 --calc-pme \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1444 --run-pRSEM \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1445 --partition-model cmb_lgt \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1446 --chipseq-read-files-multi-targets /data/H3K27Ac.fastq.gz,/data/H3K4me1.fastq.gz,/data/H3K4me2.fastq.gz,/data/H3K4me3.fastq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1447 --bowtie-path /sw/bowtie \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1448 -p 8 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1449 /data/mmliver_1.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1450 /data/mmliver_2.fq.gz \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1451 /ref/mouse_125 \
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1452 mmliver_paired_end_quals
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1453
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1454 </help>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1455 <citations>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1456 <citation type="doi">10.1186/1471-2105-12-323</citation>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1457 </citations>
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1458
e5e836936d60 planemo upload for repository https://github.com/artbio/tools-artbio/tree/master/tools/rsem commit d84a0359354698a4b29df12ab581c2618bffcf80 artbio parents: diff changeset	1459 </tool>

Mercurial > repos > artbio > rsem

annotate rsem.xml @ 7:585c6120dca0 draft