diff rsem_calculate_expression.xml @ 0:ca988deacfd1

Uploaded

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+++ b/rsem_calculate_expression.xml	Fri Feb 07 08:07:29 2014 -0500
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+<tool id="rsem_calculate_expression" name="RSEM calculate expression" version="1.1.17">
+  <description>RNA-Seq by Expectation-Maximization</description>
+  <requirements>
+    <requirement type="package" version="1.1.17">rsem</requirement>
+    <requirement type="package" version="0.1.19">samtools</requirement>
+    <requirement type="package" version="1.0.0">bowtie</requirement>
+  </requirements>
+  <command>
+    rsem-calculate-expression 
+    ## --tag string
+    #if $seedlength:
+      --seed-length $seedlength 
+    #end if
+    --forward-prob $forward_prob
+    #if $rsem_options.fullparams == 'fullset':
+      ## Fragment info
+      #if $rsem_options.fragment_length_mean:
+        --fragment-length-mean $rsem_options.fragment_length_mean
+      #end if
+      #if $rsem_options.fragment_length_min:
+        --fragment-length-min $rsem_options.fragment_length_min
+      #end if
+      #if $rsem_options.fragment_length_sd:
+        --fragment-length-sd $rsem_options.fragment_length_sd
+      #end if
+      #if $rsem_options.fragment_length_max:
+        --fragment-length-max $rsem_options.fragment_length_max
+      #end if
+      ## RSPD
+      #if $rsem_options.rspd.estimate == 'yes':
+        --estimate-rspd
+        #if $rsem_options.rspd.num_rspd_bins:
+          --num-rspd-bins $rsem_options.rspd.num_rspd_bins
+        #end if
+      #end if
+      ## Calculate 95% credibility intervals and posterior mean estimates. 
+      #if $rsem_options.useci.ci == 'yes':
+        --calc-ci
+        #if $rsem_options.useci.cimem:
+          --ci-memory $rsem_options.useci.cimem
+        #end if
+      #end if
+    #end if
+    ## --num-threads $GALAXY_SLOTS
+    #if $input.format != 'bam' and $input.bowtie_options.fullparams == 'fullset':
+      ## Bowtie params
+      #if $bowtie_options.bowtie_e:
+      --bowtie-e $bowtie_options.bowtie_e
+      #end if
+      #if $bowtie_options.bowtie_m:
+      --bowtie-m $bowtie_options.bowtie_m
+      #end if
+      #if $bowtie_options.bowtie_n:
+      --bowtie-n $bowtie_options.bowtie_n
+      #end if
+    #end if
+    ## Outputs
+    #if $rsem_outputs.result_bams == 'none':
+      --no-bam-output
+    #else
+      #if $rsem_outputs.result_bams == 'both':
+        --output-genome-bam
+      #end if
+      $rsem_outputs.sampling_for_bam
+    #end if
+    ## Input data
+    #if $input.format=="fastq"
+      $input.fastq_select
+      #if $input.fastq.matepair=="single": 
+        $input.fastq.singlefastq
+      #elif $input.fastq.matepair=="paired":
+        --paired-end
+        $input.fastq.fastq1
+        $input.fastq.fastq2
+      #end if
+    #elif $input.format=="fasta"
+      --no-qualities
+      #if $input.fasta.matepair=="single": 
+        $input.fasta.singlefasta
+      #elif $input.fasta.matepair=="paired":
+        --paired-end
+        $input.fasta.fasta1
+        $input.fasta.fasta2
+      #end if
+    #elif $input.format=="sam"
+      #if $input.matepair=="paired":
+        --paired-end
+      #end if
+      #if $input.rsem_sam._extension == 'sam':
+        --sam
+      #elif $input.rsem_sam._extension == 'bam':
+        --bam
+      #end if
+      $input.rsem_sam
+    #end if
+    ## RSEM reference
+    #if $reference.refSrc == 'history':
+      ${reference.rsem_ref.extra_files_path}/${reference.rsem_ref.metadata.reference_name}
+    #elif $reference.refSrc == 'cached':
+      ${reference.index.fields.path}
+    #end if
+    ## sample_name: use a hard coded name so we can pull out galaxy outputs
+    rsem_output
+    ## direct output into logfile
+    > $log
+  </command>
+  <macros>
+    <macro name="rsem_options">
+        <param name="seedlength" type="integer" value="25" optional="true" label="Seed length used by the read aligner" help="Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads. RSEM uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default:25)">
+        </param>
+        <param name="forward_prob" type="select" label="Is the library strand specific?">
+          <option value="0.5" selected="true">No</option>
+          <option value="1">Yes, the reads (or first reads from paired-end libraries) are only in the forward orientation</option>
+          <option value="0">Yes, the reads (or first reads from paired-end libraries) are only in the reverse orientation</option>
+        </param>
+        <conditional name="rsem_options">
+          <param name="fullparams" type="select" label="Additional RSEM options">
+            <option value="default">Use RSEM Defaults</option>
+            <option value="fullset">Set Additional RSEM Options</option>
+          </param>
+          <when value="default"/>
+          <when value="fullset">
+            <param name="fragment_length_min" type="integer" value="1" optional="true" label="Minimum read/insert length." help=" This is also the value for the bowtie -I option">
+              <validator type="in_range" message="0 or greater" min="0" />
+            </param>
+            <param name="fragment_length_max" type="integer" value="1000" optional="true" label="Maximum read/insert length." help=" This is also the value for the bowtie -X option">
+              <validator type="in_range" message="0 or greater" min="0" max="1000000"/>
+            </param>
+            <param name="fragment_length_mean" type="float" value="" optional="true" label="Fragment length mean (single-end data only)" help="The mean of the fragment length distribution, which is assumed to be a Gaussian. (Default: -1, which disables use of the fragment length distribution)">
+            </param>
+            <param name="fragment_length_sd" type="float" value="" optional="true" label="The standard deviation of the fragment length distribution (single-end data only)" help="Default 0, which assumes that all fragments are of the same length, given by the rounded value of fragment length mean. ">
+            </param>
+            <conditional name="rspd">
+              <param name="estimate" type="select" lanel="Read Start Position Distribution (RSPD)" 
+                  help="Set this option if you want to estimate the read start position distribution (RSPD) from data. Otherwise, RSEM will use a uniform RSPD.">
+                <option value="no" selected="true">Use a uniform RSPD</option>
+                <option value="yes">Estimate and correct for a non-uniform RSPD</option>
+              </param>
+              <when value="no"/>
+              <when value="yes"> 
+                <param name="num_rspd_bins" type="integer" value="20" optional="true" label="Number of bins in the RSPD." help="Use of the default setting of 20 is recommended.">
+                   <validator type="in_range" message="" min="0" max="100"/>
+                </param>
+              </when>
+            </conditional>
+            <conditional name="useci">
+              <param name="ci" type="select" label="Calculate 95% Credibility Intervals">
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+              </param>
+              <when value="no"/>
+              <when value="yes">
+                <param name="cimem" size="4" type="text" value="1024" label="Amount of memory in (MB) for computing CI" />
+              </when>
+            </conditional>
+          </when>
+        </conditional>
+    </macro>
+    <macro name="bowtie_options">
+        <conditional name="bowtie_options">
+          <param name="fullparams" type="select" label="bowtie settings">
+            <option value="default">use bowtie defaults</option>
+            <option value="fullset">set bowtie options</option>
+          </param>
+          <when value="default"/>
+          <when value="fullset">
+            <param name="bowtie_n" type="integer" value="2" optional="true" label="Bowtie mismatches" help="Bowtie parameter max # of mismatches in the seed. (Range: 0-3, Default: 2) ">
+              <validator type="in_range" message="max # of mismatches in the seed between 0 and 3" min="0" max="3"/>
+            </param>
+            <param name="bowtie_e" type="integer" value="99999999" label="Maximum sum of quality scores at mismatched positions in read alignments.  This is also the value for the Bowtie -e option">
+            </param>
+            <param name="bowtie_m" type="integer" value="200" label="Discard alignments for reads with number of alignments greater than">
+            </param>
+          </when>
+        </conditional>
+    </macro>
+    <macro name="sampling_for_bam">
+        <param name="sampling_for_bam" type="boolean" truevalue="--sampling-for-bam" falsevalue="" checked="false" label="Use sampling for BAM">
+          <help> When RSEM generates a BAM file, instead of outputing all alignments a read has with their posterior probabilities, one alignment is sampled according to the posterior probabilities. The sampling procedure includes the alignment to the "noise" transcript, which does not appear in the BAM file. Only the sampled alignment has a weight of 1. All other alignments have weight 0. If the "noise" transcript is sampled, all alignments appeared in the BAM file should have weight 0. (Default: off)
+          </help>
+        </param>
+    </macro>
+  </macros>
+
+  <inputs>
+    <param name="sample" type="text" value="rsem_sample" label="Sample name" />
+    <conditional name="reference">
+      <param name="refSrc" type="select" label="RSEM Reference Source">
+        <option value="cached">Locally cached</option>
+        <option value="history">From your history</option>
+      </param>
+      <when value="cached">
+        <param name="index" type="select" label="Select RSEM reference" help="Select from a list of pre-indexed references. If you don't see anything consult the wrapper's documentation on how to create or download a reference">
+          <options from_data_table="rsem_indexes">
+            <filter type="sort_by" column="2" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="rsem_ref" type="data" format="rsem_ref" label="RSEM reference" />
+      </when>
+    </conditional>
+    <conditional name="input">
+      <param name="format" type="select" label="RSEM Input file type">
+        <option value="fastq">FASTQ</option>
+        <option value="fasta">FASTA</option>
+        <option value="sam">SAM/BAM</option>
+      </param>
+      <when value="fastq">
+        <param name="fastq_select" size="15" type="select" label="FASTQ type" >
+          <option value="--phred33-quals" selected="true">phred33 qualities (default for sanger)</option>
+          <option value="--solexa-quals">solexa qualities</option>
+          <option value="--phred64-quals">phred64 qualities</option>
+        </param>
+        <conditional name="fastq">
+          <param name="matepair" type="select" label="Library type">
+            <option value="single">Single End Reads</option>
+            <option value="paired">Paired End Reads</option>
+          </param>
+          <when value="single">
+            <param name="singlefastq" type="data" format="fastq" label="FASTQ file" />
+          </when>
+          <when value="paired">
+            <param name="fastq1" type="data" format="fastq" label="Read 1 fastq file" />
+            <param name="fastq2" type="data" format="fastq" label="Read 2 fastq file" />
+          </when>
+        </conditional>
+        <expand macro="bowtie_options"/>
+      </when>
+      <when value="fasta">
+        <conditional name="fasta">
+          <param name="matepair" type="select" label="Library Type">
+            <option value="single">Single End Reads</option>
+            <option value="paired">Paired End Reads</option>
+          </param>
+          <when value="single">
+            <param name="singlefasta" type="data" format="fasta" label="fasta file" />
+          </when>
+          <when value="paired">
+            <param name="fasta1" type="data" format="fasta" label="Read 1 fasta file" />
+            <param name="fasta2" type="data" format="fasta" label="Read 2 fasta file" />
+          </when>
+        </conditional>
+        <expand macro="bowtie_options"/>
+      </when>
+      <when value="sam">
+          <!-- convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam -->
+          <param name="matepair" type="select" label="Library Type">
+            <option value="single">Single End Reads</option>
+            <option value="paired">Paired End Reads</option>
+          </param>
+          <param name="rsem_sam" type="data" format="rsem_sam" label="RSEM formatted SAM file" />
+      </when>
+    </conditional>
+    <expand macro="rsem_options"/>
+    <conditional name="rsem_outputs">
+      <param name="result_bams" type="select" label="Create bam results files" 
+             help="In addition to the transcript-coordinate-based BAM file output, also output a BAM file with the read alignments in genomic coordinates" >
+        <option value="none">No BAM results files</option>
+        <option value="default" selected="true">Transcript BAM results file</option>
+        <option value="both">Transcript and genome BAM results files</option>
+      </param>
+      <when value="none"/>
+      <when value="default">
+        <expand macro="sampling_for_bam"/>
+      </when>
+      <when value="both">
+        <expand macro="sampling_for_bam"/>
+      </when>
+    </conditional>
+  </inputs>
+  <stdio>
+    <exit_code range="1:"  level="fatal" description="Error Running RSEM" />
+  </stdio>
+  <outputs>
+    <data format="tabular" name="gene_abundances" label="${sample}.gene_abundances" from_work_dir="rsem_output.genes.results"/>
+    <data format="tabular" name="isoform_abundances" label="${sample}.isoform_abundances" from_work_dir="rsem_output.isoforms.results"/>
+    <data format="bam" name="transcript_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.bam" >
+      <filter>rsem_outputs['result_bams'] != "none"</filter>
+    </data>
+    <data format="bam" name="transcript_sorted_bam" label="${sample}.transcript.bam" from_work_dir="rsem_output.transcript.sorted.bam" >
+      <filter>rsem_outputs['result_bams'] != "none"</filter>
+    </data>
+    <data format="bam" name="genome_bam" label="${sample}.genome.bam" from_work_dir="rsem_output.genome.bam">
+      <filter>rsem_outputs['result_bams'] == "both"</filter>
+    </data>
+    <data format="bam" name="genome_sorted_bam" label="${sample}.genome.sorted.bam" from_work_dir="rsem_output.genome.sorted.bam">
+      <filter>rsem_outputs['result_bams'] == "both"</filter>
+    </data>
+    <data format="txt" name="log" label="${sample}.rsem_log"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="sample" value="rsem_sample"/>
+      <param name="refSrc" value="history"/>
+      <param name="rsem_ref" value="RSEM_ref_reference.zip" ftype="rsem_ref"/>
+      <param name="format" value="fastq"/>
+      <param name="matepair" value="single"/>
+      <param name="singlefastq" value="test.fastq" ftype="fastqsanger"/>
+      <param name="result_bams" value="none"/>
+      <output name="gene_abundances"> 
+        <assert_contents>
+          <has_text text="ENST00000423562,ENST00000438504,ENST00000488147,ENST00000538476,ENST00000541675" />
+        </assert_contents>
+      </output>
+      <output name="isoform_abundances"> 
+        <assert_contents>
+          <has_text text="ENST00000332831" />
+        </assert_contents>
+      </output>
+      <output name="log"> 
+        <assert_contents>
+          <has_text text="Expression Results are written" />
+        </assert_contents>
+      </output>
+    </test>
+  </tests>
+  <help>
+  
+
+RSEM HOME PAGE - http://deweylab.biostat.wisc.edu/rsem/
+
+NAME
+    rsem-calculate-expression
+
+SYNOPSIS
+         rsem-calculate-expression [options] upstream_read_file(s) reference_name sample_name
+         rsem-calculate-expression [options] --paired-end upstream_read_file/s downstream_read_file/s reference_name sample_name
+         rsem-calculate-expression [options] --sam/--bam [--paired-end] input reference_name sample_name
+
+ARGUMENTS
+    upstream_read_files/s
+        Comma-separated list of files containing single-end reads or
+        upstream reads for paired-end data. By default, these files are
+        assumed to be in FASTQ format. If the --no-qualities option is
+        specified, then FASTA format is expected.
+
+    downstream_read_file/s
+        Comma-separated list of files containing downstream reads which are
+        paired with the upstream reads. By default, these files are assumed
+        to be in FASTQ format. If the --no-qualities option is specified,
+        then FASTA format is expected.
+
+    input
+        SAM/BAM formatted input file. If "-" is specified for the filename,
+        SAM/BAM input is instead assumed to come from standard input. RSEM
+        requires all alignments of the same read group together. For
+        paired-end reads, RSEM also requires the two mates of any alignment
+        be adjacent. See Description section for how to make input file obey
+        RSEM's requirements.
+
+    reference_name
+        The name of the reference used. The user must have run
+        'rsem-prepare-reference' with this reference_name before running
+        this program.
+
+    sample_name
+        The name of the sample analyzed. All output files are prefixed by
+        this name (e.g., sample_name.genes.results)
+
+OPTIONS
+
+    --paired-end
+        Input reads are paired-end reads. (Default: off)
+
+    --no-qualities
+        Input reads do not contain quality scores. (Default: off)
+
+    --strand-specific
+        The RNA-Seq protocol used to generate the reads is strand specific,
+        i.e., all (upstream) reads are derived from the forward strand. This
+        option is equivalent to --forward-prob=1.0. With this option set, if
+        RSEM runs the Bowtie aligner, the '--norc' Bowtie option will be
+        used, which disables alignment to the reverse strand of transcripts.
+        (Default: off)
+
+    --sam
+        Input file is in SAM format. (Default: off)
+
+    --bam
+        Input file is in BAM format. (Default: off)
+
+    --sam-header-info [file]
+        RSEM reads header information from input by default. If this option
+        is on, header information is read from the specified file. For the
+        format of the file, please see SAM official website. (Default: "")
+
+    -p/--num-threads [int]
+        Number of threads to use. Both Bowtie and expression estimation will
+        use this many threads. (Default: 1)
+
+    --no-bam-output
+        Do not output any BAM file. (Default: off)
+
+    --output-genome-bam
+        Generate a BAM file, 'sample_name.genome.bam', with alignments
+        mapped to genomic coordinates and annotated with their posterior
+        probabilities. In addition, RSEM will call samtools (included in
+        RSEM package) to sort and index the bam file.
+        'sample_name.genome.sorted.bam' and
+        'sample_name.genome.sorted.bam.bai' will be generated. (Default:
+        off)
+
+    --sampling-for-bam
+        When RSEM generates a BAM file, instead of outputing all alignments
+        a read has with their posterior probabilities, one alignment is
+        sampled and outputed according to the posterior probabilities. If
+        the sampling result is that the read comes from the "noise"
+        transcript, nothing is outputed. (Default: off)
+
+    --calc-ci
+        Calculate 95% credibility intervals and posterior mean estimates.
+        (Default: off)
+
+    --seed-length [int]
+        Seed length used by the read aligner. Providing the correct value is
+        important for RSEM. If RSEM runs Bowtie, it uses this value for
+        Bowtie's seed length parameter. Any read with its or at least one of
+        its mates' (for paired-end reads) length less than this value will
+        be ignored. If the references are not added poly(A) tails, the
+        minimum allowed value is 5, otherwise, the minimum allowed value is
+        25. Note that this script will only check if the value less or equal than
+        5 and give a warning message if the value less than 25 but greter or equal than
+        5. (Default: 25)
+
+    --tag [string]
+        The name of the optional field used in the SAM input for identifying
+        a read with too many valid alignments. The field should have the
+        format [tagName]:i:[value], where a [value] bigger than 0 indicates
+        a read with too many alignments. (Default: "")
+
+    --bowtie-path [path]
+        The path to the bowtie executables. (Default: the path to the bowtie
+        executables is assumed to be in the user's PATH environment
+        variable)
+
+    --bowtie-n [int]
+        (Bowtie parameter) max # of mismatches in the seed. (Range: 0-3,
+        Default: 2)
+
+    --bowtie-e [int]
+        (Bowtie parameter) max sum of mismatch quality scores across the
+        alignment. (Default: 99999999)
+
+    --bowtie-m [int]
+        (Bowtie parameter) suppress all alignments for a read if greater then [int]
+        valid alignments exist. (Default: 200)
+
+    --bowtie-chunkmbs [int]
+        (Bowtie parameter) memory allocated for best first alignment
+        calculation (Default: 0 - use bowtie's default)
+
+    --phred33-quals
+        Input quality scores are encoded as Phred+33. (Default: on)
+
+    --phred64-quals
+        Input quality scores are encoded as Phred+64 (default for GA
+        Pipeline ver. less than  1.3). (Default: off)
+
+    --solexa-quals
+        Input quality scores are solexa encoded (from GA Pipeline ver. less
+        than 1.3). (Default: off)
+
+    --forward-prob [double]
+        Probability of generating a read from the forward strand of a
+        transcript. Set to 1 for a strand-specific protocol where all
+        (upstream) reads are derived from the forward strand, 0 for a
+        strand-specific protocol where all (upstream) read are derived from
+        the reverse strand, or 0.5 for a non-strand-specific protocol.
+        (Default: 0.5)
+
+    --fragment-length-min [int]
+        Minimum read/insert length allowed. This is also the value for the
+        bowtie -I option. (Default: 1)
+
+    --fragment-length-max [int]
+        Maximum read/insert length allowed. This is also the value for the
+        bowtie -X option. (Default: 1000)
+
+    --fragment-length-mean [double]
+        (single-end data only) The mean of the fragment length distribution,
+        which is assumed to be a Gaussian. (Default: -1, which disables use
+        of the fragment length distribution)
+
+    --fragment-length-sd [double]
+        (single-end data only) The standard deviation of the fragment length
+        distribution, which is assumed to be a Gaussian. (Default: 0, which
+        assumes that all fragments are of the same length, given by the
+        rounded value of --fragment-length-mean)
+
+    --estimate-rspd
+        Set this option if you want to estimate the read start position
+        distribution (RSPD) from data. Otherwise, RSEM will use a uniform
+        RSPD. (Default: off)
+
+    --num-rspd-bins [int]
+        Number of bins in the RSPD. Only relevant when '--estimate-rspd' is
+        specified. Use of the default setting is recommended. (Default: 20)
+
+    --ci-memory [int]
+        Maximum size (in memory, MB) of the auxiliary buffer used for
+        computing credibility intervals (CI). Set it larger for a faster CI
+        calculation. However, leaving 2 GB memory free for other usage is
+        recommended. (Default: 1024)
+
+    --keep-intermediate-files
+        Keep temporary files generated by RSEM. RSEM creates a temporary
+        directory, 'sample_name.temp', into which it puts all intermediate
+        output files. If this directory already exists, RSEM overwrites all
+        files generated by previous RSEM runs inside of it. By default,
+        after RSEM finishes, the temporary directory is deleted. Set this
+        option to prevent the deletion of this directory and the
+        intermediate files inside of it. (Default: off)
+
+    --time
+        Output time consumed by each step of RSEM to 'sample_name.time'.
+        (Default: off)
+
+    -q/--quiet
+        Suppress the output of logging information. (Default: off)
+
+    -h/--help
+        Show help information.
+
+DESCRIPTION
+    In its default mode, this program aligns input reads against a reference
+    transcriptome with Bowtie and calculates expression values using the
+    alignments. RSEM assumes the data are single-end reads with quality
+    scores, unless the '--paired-end' or '--no-qualities' options are
+    specified. Users may use an alternative aligner by specifying one of the
+    --sam and --bam options, and providing an alignment file in the
+    specified format. However, users should make sure that they align
+    against the indices generated by 'rsem-prepare-reference' and the
+    alignment file satisfies the requirements mentioned in ARGUMENTS
+    section.
+
+    One simple way to make the alignment file satisfying RSEM's requirements
+    (assuming the aligner used put mates in a paired-end read adjacent) is
+    to use 'convert-sam-for-rsem' script. This script only accept SAM format
+    files as input. If a BAM format file is obtained, please use samtools to
+    convert it to a SAM file first. For example, if '/ref/mouse_125' is the
+    'reference_name' and the SAM file is named 'input.sam', you can run the
+    following command:
+
+      convert-sam-for-rsem /ref/mouse_125 input.sam -o input_for_rsem.sam
+
+    For details, please refer to 'convert-sam-for-rsem's documentation page.
+
+    The SAM/BAM format RSEM uses is v1.4. However, it is compatible with old
+    SAM/BAM format. However, RSEM cannot recognize 0x100 in the FLAG field.
+    In addition, RSEM requires SEQ and QUAL are not '*'.
+
+    The user must run 'rsem-prepare-reference' with the appropriate
+    reference before using this program.
+
+    For single-end data, it is strongly recommended that the user provide
+    the fragment length distribution parameters (--fragment-length-mean and
+    --fragment-length-sd). For paired-end data, RSEM will automatically
+    learn a fragment length distribution from the data.
+
+    Please note that some of the default values for the Bowtie parameters
+    are not the same as those defined for Bowtie itself.
+
+    The temporary directory and all intermediate files will be removed when
+    RSEM finishes unless '--keep-intermediate-files' is specified.
+
+    With the '--calc-ci' option, 95% credibility intervals and posterior
+    mean estimates will be calculated in addition to maximum likelihood
+    estimates.
+
+OUTPUT
+    sample_name.genes.results
+        File containing gene level expression estimates. The format of each
+        line in this file is:
+
+        gene_id expected_counts tau_value [pmc_value tau_pme_value
+        tau_ci_lower_bound tau_ci_upper_bound] transcript_id_list
+
+        Fields are separated by the tab character. Fields within "[]" are
+        only presented if '--calc-ci' is set. pme stands for posterior mean
+        estimation. pmc stands for posterior mean counts. ci_lower_bound(l)
+        means the lower bound of the credibility intervals,
+        ci_upper_bound(u) means the upper bound of the credibility
+        intervals. So the credibility interval is [l, u].
+        'transcript_id_list' is a space-separated list of transcript_ids
+        belonging to the gene. If no gene information is provided, this file
+        has the same content as 'sample_name.isoforms.results'.
+
+    sample_name.isoforms.results
+        File containing isoform level expression values. The format of each
+        line in this file is:
+
+        transcript_id expected_counts tau_value [pmc_value tau_pme_value
+        tau_ci_lower_bound tau_ci_upper_bound] gene_id
+
+        Fields are separated by the tab character. 'gene_id' is the gene_id
+        of the gene which this transcript belongs to. If no gene information
+        is provided, 'gene_id' and 'transcript_id' are the same.
+
+    sample_name.transcript.bam, sample_name.transcript.sorted.bam and
+    sample_name.transcript.sorted.bam.bai
+        Only generated when --no-bam-output is not specified.
+
+        'sample_name.transcript.bam' is a BAM-formatted file of read
+        alignments in transcript coordinates. The MAPQ field of each
+        alignment is set to min(100, floor(-10 * log10(1.0 - w) + 0.5)),
+        where w is the posterior probability of that alignment being the
+        true mapping of a read. In addition, RSEM pads a new tag ZW:f:value,
+        where value is a single precision floating number representing the
+        posterior probability.
+
+        'sample_name.transcript.sorted.bam' and
+        'sample_name.transcript.sorted.bam.bai' are the sorted BAM file and
+        indices generated by samtools (included in RSEM package).
+
+    sample_name.genome.bam, sample_name.genome.sorted.bam and
+    sample_name.genome.sorted.bam.bai
+        Only generated when --no-bam-output is not specified and
+        --output-genome-bam is specified.
+
+        'sample_name.genome.bam' is a BAM-formatted file of read alignments
+        in genomic coordinates. Alignments of reads that have identical
+        genomic coordinates (i.e., alignments to different isoforms that
+        share the same genomic region) are collapsed into one alignment. The
+        MAPQ field of each alignment is set to min(100, floor(-10 *
+        log10(1.0 - w) + 0.5)), where w is the posterior probability of that
+        alignment being the true mapping of a read. In addition, RSEM pads a
+        new tag ZW:f:value, where value is a single precision floating
+        number representing the posterior probability. If an alignment is
+        spliced, a XS:A:value tag is also added, where value is either '+'
+        or '-' indicating the strand of the transcript it aligns to.
+
+        'sample_name.genome.sorted.bam' and
+        'sample_name.genome.sorted.bam.bai' are the sorted BAM file and
+        indices generated by samtools (included in RSEM package).
+
+    sample_name.sam.gz
+        Only generated when the input files are raw reads instead of SAM/BAM
+        format files
+
+        It is the gzipped SAM output produced by bowtie aligner.
+
+    sample_name.time
+        Only generated when --time is specified.
+
+        It contains time (in seconds) consumed by aligning reads, estimating
+        expression levels and calculating credibility intervals.
+
+    sample_name.stat
+        This is a folder instead of a file. All model related statistics are
+        stored in this folder. Use 'rsem-plot-model' can generate plots
+        using this folder.
+
+EXAMPLES
+    Assume the path to the bowtie executables is in the user's PATH
+    environment variable. Reference files are under '/ref' with name
+    'mouse_125'.
+
+    1) '/data/mmliver.fq', single-end reads with quality scores. Quality
+    scores are encoded as for 'GA pipeline version >= 1.3'. We want to use 8
+    threads and generate a genome BAM file:
+
+     rsem-calculate-expression --phred64-quals \
+                               -p 8 \
+                               --output-genome-bam \
+                               /data/mmliver.fq \
+                               /ref/mouse_125 \
+                               mmliver_single_quals
+
+    2) '/data/mmliver_1.fq' and '/data/mmliver_2.fq', paired-end reads with
+    quality scores. Quality scores are in SANGER format. We want to use 8
+    threads and do not generate a genome BAM file:
+
+     rsem-calculate-expression -p 8 \
+                               --paired-end \
+                               /data/mmliver_1.fq \
+                               /data/mmliver_2.fq \
+                               /ref/mouse_125 \
+                               mmliver_paired_end_quals
+
+    3) '/data/mmliver.fa', single-end reads without quality scores. We want
+    to use 8 threads:
+
+     rsem-calculate-expression -p 8 \
+                               --no-qualities \
+                               /data/mmliver.fa \
+                               /ref/mouse_125 \
+                               mmliver_single_without_quals
+
+    4) Data are the same as 1). We want to take a fragment length
+    distribution into consideration. We set the fragment length mean to 150
+    and the standard deviation to 35. In addition to a BAM file, we also
+    want to generate credibility intervals. We allow RSEM to use 1GB of
+    memory for CI calculation:
+
+     rsem-calculate-expression --bowtie-path /sw/bowtie \
+                               --phred64-quals \
+                               --fragment-length-mean 150.0 \
+                               --fragment-length-sd 35.0 \
+                               -p 8 \
+                               --output-genome-bam \
+                               --calc-ci \
+                               --ci-memory 1024 \
+                               /data/mmliver.fq \
+                               /ref/mouse_125 \
+                               mmliver_single_quals
+
+    5) '/data/mmliver_paired_end_quals.bam', paired-end reads with quality
+    scores. We want to use 8 threads:
+
+     rsem-calculate-expression --paired-end \
+                               --bam \
+                               -p 8 \
+                               /data/mmliver_paired_end_quals.bam \
+                               /ref/mouse_125 \
+                               mmliver_paired_end_quals
+  </help> 
+</tool>