changeset 0:4edac0183857

Initial commit from tarball version 1.17

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+# RSEM Galaxy Wrapper #
+
+## Introduction ##
+
+RSEM (RNA-Seq by Expectation-Maximization) is a software package for the
+estimation of gene and isoform abundances from RNA-Seq data. A key feature of
+RSEM is its statistically-principled approach to the handling of RNA-Seq
+reads that map to multiple genes and/or isoforms. In addition, RSEM is
+well-suited to performing quantification with de novo transcriptome
+assemblies, as it does not require a reference genome.
+
+## Installation ##
+
+Follow the [Galaxy Tool Shed
+instructions](http://wiki.g2.bx.psu.edu/Tool_Shed) to add this wrapper from
+the tool shed to your galaxy instance. Once the files are in the tools
+directory you have to have RSEM references installed. This can be done by:
+
+1. Placing the file called `rsem_indices.loc` into the directory
+   `~/galaxy-dist/tool-data` This file tells the RSEM wrapper how to find the
+   reference(s). It is formatted according to galaxy's documentation with the
+   following tab-delimited format:
+
+        unique_build_id    dbkey    display_name    file_base_path
+	
+   For example,
+
+        human_refseq_NM	human_refseq_NM	human_refseq_NM	/opt/galaxy/references/human/1.1.2/NM_refseq_ref
+
+2. Downloaded a pre-built RSEM reference from the [RSEM website](http://deweylab.biostat.wisc.edu/rsem/).
+
+3. Place reference files into the `file_base_path` listed in the
+`rsem_indices.loc` file
+
+If you would rather build your own reference files follow the instructions
+below and then place resulting reference files into the `file_base_path` listed
+in the `rsem_indices.loc` file.
+
+### Building a custom RSEM reference ###
+
+For instructions on how to build the RSEM reference files, first see the [RSEM
+documentation](http://deweylab.biostat.wisc.edu/rsem/README.html).
+
+#### Example ####
+
+Suppose we have mouse RNA-Seq data and want to use the UCSC mm9 version of the
+mouse genome. We have downloaded the UCSC Genes transcript annotations in GTF
+format (as mm9.gtf) using the Table Browser and the knownIsoforms.txt file for
+mm9 from the UCSC Downloads. We also have all chromosome files for mm9 in the
+directory `/data/mm9`. We want to put the generated reference files under
+`/opt/galaxy/references` with name `mouse_125`. We'll add poly(A) tails with
+length 125. Please note that GTF files generated from UCSC's Table Browser do
+not contain isoform-gene relationship information. For the UCSC Genes
+annotation, this information can be obtained from the knownIsoforms.txt file.
+Suppose we want to build Bowtie indices and Bowtie executables are found in
+`/sw/bowtie`.
+
+To build the reference files, first run the command:
+
+    rsem-prepare-reference --gtf mm9.gtf \
+                           --transcript-to-gene-map knownIsoforms.txt \
+                           --bowtie-path /sw/bowtie \                  
+                           /data/mm9/chr1.fa,/data/mm9/chr2.fa,...,/data/mm9/chrM.fa \
+                           /opt/galaxy/references/mouse_125
+
+To add this reference to your galaxy installation, add the following line to
+the the `rsem_indices.loc` file:
+
+    mouse_125	mouse_125	mouse_125	/opt/galaxy/references/mouse_125
+
+Then restart galaxy and you should see the `mouse_125` reference listed in the
+RSEM wrapper.
+
+## References ##
+
+* [RSEM website (stand alone package)](http://deweylab.biostat.wisc.edu/rsem/)
+
+* B. Li and C. Dewey (2011) [RSEM: accurate transcript quantification from
+  RNA-Seq data with or without a reference
+  genome](http://bioinformatics.oxfordjournals.org/content/26/4/493.abstract).
+  BMC Bioinformatics 12:323.
+
+* B. Li, V. Ruotti, R. Stewart, J. Thomson, and C. Dewey (2010) [RNA-Seq gene
+  expression estimation with read mapping
+  uncertainty](http://www.biomedcentral.com/1471-2105/12/323). Bioinformatics
+  26(4): 493-500.
+
+## Contact information ##
+* RSEM galaxy wrapper questions: [e-mail]
+* RSEM stand alone package questions: [e-mail]
+* [RSEM announcements mailing list](http://groups.google.com/group/rsem-announce)
+* [RSEM users mailing list](http://groups.google.com/group/rsem-users)

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rsem/rsem-1.1.17.xml	Mon Mar 05 11:12:34 2012 -0500
@@ -0,0 +1,572 @@
+<tool id="live-rsem-1.1.17" name="RSEM-1.17" version="xml.1.1.17">
+    <description>RNA-Seq by Expectation-Maximization</description>
+  <command interpreter="perl">
+
+## DEFAULT PARAMETERS
+rsem-wrapper-1.1.17.pl --calc-ci $useci.ci --fragment-length-mean $fraglenmean --fragment-length-min 
+$fraglenmin --fragment-length-sd $fraglensd --fragment-length-max $fraglenmax --bowtie-e 
+$bowtie_e --bowtie-m $bowtie_m
+
+   #if $input.format=="fastq"
+        ## IF FASTQ AND SINGLE END READS (DEFAULTS)
+	#if $input.fastqmatepair.matepair=="single" #rsem-wrapper-1.1.17.pl --bam_genome $bam_genome --bamtype $bamtype 
+	--seed-length $seedlength $input.fastq_select --estimate-rspd $rspd --forward-prob 
+	$fprob -p $cpus --bowtie-n $bowtie_mis --output-genome-bam --single_fastq $singlefastq 
+	--output $output --isoformfile $isoforms --bamfile $bam_res --log $log 
+	--sampling-for-bam $sampling_for_bam --reference ${index.fields.path}
+    	#end if
+        ## IF FASTQ AND PAIRED END READS (DEFAULTS)
+        #if $input.fastqmatepair.matepair=="paired" #rsem-wrapper-1.1.17.pl --bam_genome $bam_genome --bamtype $bamtype 
+	--paired-end --seed-length $seedlength --estimate-rspd $rspd $input.fastq_select --forward-prob $fprob -p $cpus 
+        --bowtie-n $bowtie_mis --output-genome-bam --fastq1 $fastq1 --fastq2 $fastq2 --output 
+        $output --isoformfile $isoforms --bamfile $bam_res --log $log --sampling-for-bam 
+        $sampling_for_bam --reference ${index.fields.path} 
+	#end if
+   #end if 
+   #if $input.format=="fasta"
+        ## IF FASTA AND SINGLE END READS (DEFAULTS)
+	#if $input.fastamatepair.matepair=="single" #rsem-wrapper-1.1.17.pl --bam_genome $bam_genome --bamtype $bamtype
+	--no-qualities --seed-length $seedlength --estimate-rspd $rspd --forward-prob $fprob -p $cpus --bowtie-n $bowtie_mis 
+	--output-genome-bam --single_fasta $single_fasta --output $output --isoformfile 
+	$isoforms --bamfile $bam_res --log $log --sampling-for-bam $sampling_for_bam --reference 
+	${index.fields.path}
+        #end if
+        ## IF FASTA AND PAIRED END READS (DEFAULTS)
+        #if $input.fastamatepair.matepair=="paired" #rsem-wrapper-1.1.17.pl --bam_genome $bam_genome --bamtype $bamtype
+	--no-qualities --paired-end --seed-length $seedlength --estimate-rspd $rspd --forward-prob $fprob -p $cpus 
+        --bowtie-n $bowtie_mis --output-genome-bam --fasta1 $fasta1 --fasta2 $fasta2 --output 
+        $output --isoformfile $isoforms --bamfile $bam_res --log $log --sampling-for-bam 
+        $sampling_for_bam --reference ${index.fields.path} 
+	#end if
+    #end if
+
+ </command>
+
+ <inputs>
+ <param name="sample" type="text" format="txt" label="Sample label" />
+ <conditional name="input">
+	<param name="format" type="select" label="Input file type">
+		<option value="fastq">FASTQ</option>
+		<option value="fasta">FASTA</option>
+	</param>
+ 	<when value="fastq">
+                   <param name="fastq_select" size="15" type="select" label="FASTQ type" >
+						<option value="--phred33-quals">phred33 qualities</option>
+						<option value="--solexa-quals">solexa qualities</option>
+						<option value="--phred64-quals">phred64 qualities</option>
+		 </param>
+
+	<conditional name="fastqmatepair">
+        	<when value="single">
+            	<param name="singlefastq" type="data" checked="yes" 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>
+    		<param name="matepair" type="select" label="Library type">
+			<option value="single">Single End Reads</option>
+			<option value="paired">Paired End Reads</option>
+		</param>
+ 	</conditional>
+	</when>
+ 	<when value="fasta">
+	<conditional name="fastamatepair">
+    	<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="single_fasta" type="data" checked="yes" 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>
+	</when>
+	<when>
+	<conditional name="fastamatepair">
+    	<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" checked="yes" 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>
+	</when>
+	</conditional>
+    <param name="fprob" type="select" >
+    	<label>Is the library strand specific?</label>
+		<option value="0.5">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>
+
+	<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>
+	<param name="fraglenmean" size="4" type="text" value="-1" 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 name="fraglensd" size="4" type="text" value="0" 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 name="bamtype" type="select" label="Create genome bam file" 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="no">no</option>
+      <option value="yes">yes</option>
+   </param>
+    <param name="sampling_for_bam" type="select" format="text" help="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)">
+  		<label>Sample Bam File</label>
+			<option value="no">no</option>
+			<option value="yes">yes</option>
+    </param>
+    <param name="rspd" type="select" format="text" help="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)">
+  		<label>Estimate and correct for a non-uniform read start position distribution (RSPD)</label>
+			<option value="no">no</option>
+			<option value="yes">yes</option>
+    </param>
+    
+<!-- <conditional name="fullpar">
+		<param name="fullpar" type="select" label="Full list of parameters" help="use 
+full list for linting all the parameters in RSEM">
+			<option value="default">Default</option>
+			<option value="fullset">Full Set</option>
+		</param>
+	<when value="fullset"> -->
+	 <!-- <param name="testing" size="4" type="text" value="" label="Advanced Parameters" /> 
+-->
+	<conditional name="useci">
+		<param name="ci" type="select" label="Calculate 95% Credibility Intervals">
+	   		<option value="no">no</option>
+	   		<option value="yes">yes</option>
+	   </param>
+       <when value="yes">
+	   	<param name="cimem" size="4" type="text" value="1024" label="Amount of memory in (MB) for computing CI" />
+       </when>
+    </conditional>
+	<param name="fraglenmin" size="4" type="text" value="1" label="Minimum read/insert length. Minimum read/insert length allowed. This is also the value for the bowtie -X option" />
+	<param name="fraglenmax" size="4" type="text" value="1000" label="Maximum read/insert length. Minimum read/insert length allowed. This is also the value for the bowtie -l option" />
+        <param name="bowtie_mis" size="2" type="text" value="2" label="Bowtie mismatches" help="Bowtie parameter max # of mismatches in the seed. (Range: 0-3, Default: 2) "/>
+	<param name="bowtie_e" size="4" type="text" 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 name="bowtie_m" size="4" type="text" value="200" label="Discard alignments for reads with number of alignments greater than" />
+        <param name="seedlength" size="2" type="text" value="25" 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 name="cpus" size="2" type="integer" value="1" label="Number of threads to use" help="Number of threads to use. Both Bowtie and expression estimation will use this many threads.  (Default: 1)" />
+   <!-- </when> --> <!-- </conditional> -->
+  </inputs>
+  <outputs>
+    <data format="tabular" name="output" label="${sample}.gene_abundances"/>
+    <data format="tabular" name="isoforms" label="${sample}.isoform_abundances"/>
+    <data format="bam" name="bam_res" label="${sample}.transcript.bam"/>
+    <data format="bam" name="bam_genome" label="${sample}.genome.bam">
+    	<filter>bamtype == "yes"</filter>
+    </data>
+
+    <data format="txt" name="log" label="${sample}.rsem_log"/>
+  </outputs>
+  <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> 

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rsem/rsem-wrapper-1.1.17.pl	Mon Mar 05 11:12:34 2012 -0500
@@ -0,0 +1,238 @@
+#!/usr/bin/perl 
+
+
+use Data::Dumper;
+use Getopt::Long;
+use Pod::Usage;
+
+
+
+#pod2usage(-verbose => 1) if ($help == 1);
+#if (@ARGV == 0) {
+#	pod2usage(-msg => "Invalid number of arguments!", -exitval => 2, -verbose => 2);
+#}
+
+my $rsem_version = "/opt/rsem-1.1.17";
+my $minL = 1;
+my $maxL = 1000;
+my $NMB = 1024;
+
+# Extra file output #beta
+# --isoformfile $isoforms 
+# --thetafile $theta 
+# --cntfile $cnt 
+# --modelfile $model 
+# --bamfile $bam_res
+
+GetOptions(
+    "log=s"                  => \$log,
+    "bam_genome=s"           => \$bam_genome,
+    "bamtype=s"              => \$bamtype,
+    "isoformfile=s"          => \$isoforms,
+    "reference=s"            => \$dbref,
+    "sampling-for-bam=s"     => \$samplingbam,
+    "thetafile=s"            => \$theta,
+    "cntfile=s"              => \$cnt,
+    "modelfile=s"            => \$model,
+    "bamfile=s"              => \$bamfile,
+    "output=s"               => \$output,
+    "single_fasta=s"         => \$single_fasta,
+    "fasta1=s"               => \$fasta1,
+    "fasta2=s"               => \$fasta2,
+    "single_fastq=s"         => \$single_fastq,
+    "fastq1=s"               => \$fastq1,
+    "fastq2=s"               => \$fastq2,
+    "no-qualities"           => \$no_qual,
+    "paired-end"             => \$paired_end,
+    "sam"                    => \$is_sam,
+    "bam"                    => \$is_bam,
+    "sam-header-info=s"      => \$fn_list,
+    "tag=s"                  => \$tagName,
+    "seed-length=i"          => \$L,
+    "bowtie-path=s"          => \$bowtie_path,
+    "bowtie-n=i"             => \$C,
+    "bowtie-e=i"             => \$E,
+    "bowtie-m=i"             => \$maxHits,
+    "phred33-quals"          => \$phred33,
+    "phred64-quals"          => \$phred64,
+    "solexa-quals"           => \$solexa,
+    "forward-prob=f"         => \$probF,
+    "fragment-length-min=i"  => \$minL,
+    "fragment-length-max=i"  => \$maxL,
+    "fragment-length-mean=f" => \$mean,
+    "fragment-length-sd=f"   => \$sd,
+    "estimate-rspd=s"        => \$estRSPD,
+    "num-rspd-bins=i"        => \$B,
+    "p|num-threads=i"        => \$nThreads,
+    "output-genome-bam"      => \$genBamF,
+    "calc-ci=s"              => \$calcCI,
+    "ci-memory=i"            => \$NMB,
+    "time"                   => \$mTime,
+    "q|quiet"                => \$quiet,
+) or pod2usage( -exitval => 2, -verbose => 2 );
+
+#check parameters and options
+
+if ($is_sam || $is_bam) {
+    pod2usage(-msg => "from rsem-wrapper->Invalid number of arguments!", -exitval => 2, -verbose => 2) if (scalar(@ARGV) != 4);
+    pod2usage(-msg => "--sam and --bam cannot be active at the same time!", -exitval => 2, -verbose => 2) if ($is_sam == 1&& $is_bam == 1);
+    pod2usage(-msg => "--bowtie-path, --bowtie-n, --bowtie-e, --bowtie-m, --phred33-quals, --phred64-quals or --solexa-quals cannot be set if input is SAM/BAM format!", -exitval => 2, -verbose => 2) if ($bowtie_path ne "" || $C != 2 || $E != 99999999 || $maxHits != 200 || $phred33 || $phred64 || $solexa);
+}
+#else {
+#    pod2usage(-msg => "from rsem-wraper->Invalid number of arguments!", -exitval => 2, -verbose => 2) 
+#	if (!$paired_end && scalar(@ARGV) != 1 || $paired_end && scalar(@ARGV) != 1);    
+#    pod2usage(-msg => "Only one of --phred33-quals --phred64-quals/--solexa1.3-quals --solexa-suqls can be active!", -exitval => 2, -verbose => 2) if ($phred33 + $phred64 + $solexa > 1);    
+#    podwusage(-msg => "--sam , --bam or --sam-header-info cannot be set if use bowtie aligner to produce alignments!", -exitval => 2, -verbose => 2) if ($is_sam || $is_bam || $fn_list ne "");
+#}
+
+pod2usage(-msg => "Forward probability should be in [0, 1]!", -exitval => 2, -verbose => 2) if ($probF < 0 || $probF > 1);
+pod2usage(-msg => "Min fragment length should be at least 1!", -exitval => 2, -verbose => 2) if ($minL < 1);
+pod2usage(-msg => "Min fragment length should be smaller or equal to max fragment length!", -exitval => 2, -verbose => 2) if ($minL > $maxL);
+pod2usage(-msg => "The memory allocated for calculating credibility intervals should be at least 1 MB!\n", -exitval => 2, -verbose => 2) if ($NMB < 1);
+pod2usage(-msg => "Number of threads should be at least 1!\n", -exitval => 2, -verbose => 2) if ($nThreads < 1);
+
+# IO Redirection to log file
+use IO::Handle;
+open OUTPUT, '>', $log or die "cant open file $log $!\n";;
+open ERROR,  '>>', $log  or die "cant open file $log $!\n";
+STDOUT->fdopen( \*OUTPUT, 'w' ) or die "cant open file $!\n";
+STDERR->fdopen( \*ERROR,  'w' ) or die "cant open file $!\n";
+# 
+
+my @options;
+
+# generates new output called sample_name.genome.bam 
+# with alignments
+# mapped to genomic coordinates and annotated with their posterior
+# probabilities. In addition, RSEM will call samtools (included in
+# RSEM package) to sort and index the bam file.
+# 'sample_name.genome.sorted.bam' and
+# 'sample_name.genome.sorted.bam.bai' will be generated. (Default: off)
+
+if ($bamtype eq "yes") {
+    my $bam_genome_par = "--output-genome-bam";
+    push @options, $bam_genome_par;
+}
+if ($samplingbam eq "yes") {
+    my $samplingbam = "--sampling-for-bam";
+    push @options, $samplingbam;
+}
+if ($estRSPD eq "yes") {
+    my $rspd = "--estimate-rspd";
+    push @options, $rspd;
+}
+$probF = "--forward-prob $probF";
+push @options, $probF;
+
+if ($calcCI eq "yes") {
+    my $calcCI = "--calc-ci";
+    push @options, $calcCI;
+    my $cimem = "--ci-memory $NMB";
+    push @options, $cimem;
+}
+if ($tagName) {
+    my $tagName = "--tag $tagName";
+    push @options, $tagName;
+}
+if ($L) {
+	my $L = "--seed-length $L";
+	push @options, $L;
+}
+if ($C) {
+    my $C = "--bowtie-n $C";
+    push @options, $C;
+}
+if ($E) {
+    my $E = "--bowtie-e $E";
+    push @options, $E;
+}
+if ($maxHits) {
+    my $maxHits = "--bowtie-m $maxHits";
+    push @options, $maxHits;
+}
+if ($minL != 1) {
+    my $minL = "--fragment-length-min $minL";
+    push @options, $minL;
+}
+if ($maxL != 1000) {
+    my $maxL = "--fragment-length-max $maxL";
+    push @options, $maxL;
+}
+if ($mean) {
+    my $mean = "--fragment-length-mean $mean";
+    push @options, $mean;
+}
+if ($sd) {
+    my $sd = "--fragment-length-sd $sd";
+    push @options, $sd;
+}
+my $options=  join(" ", @options);
+
+#BUILD COMMAND BASED ON PARSED OPTIONS
+if ($no_qual) { 
+        #reads are in fasta file format
+	if ($paired_end) { # reads are in paired end
+	    my $cmd = "$rsem_version/rsem-calculate-expression --quiet --no-qualities --paired-end -p $nThreads $options $fasta1 $fasta2 $dbref $output";
+ 	    print "RSEM Parameters used by Galaxy:\n$cmd\n";
+	    system($cmd);
+	}
+	#run single end with one fasta file
+	else {
+	my $cmd = "$rsem_version/rsem-calculate-expression --quiet --no-qualities -p $nThreads $options $single_fasta $dbref $output";
+ 	print "RSEM Parameters used by Galaxy:\n$cmd\n";
+	system($cmd);
+	}
+}
+else {
+    # reads are in fastq file format
+    # type of fastq file?
+	my $fastqtype;
+	if ($phred33) {
+		$fastqtype = "--phred33-quals";
+	}
+	elsif ($phred64) {
+		$fastqtype = "--phred64-quals";
+	}
+	elsif ($solexa) {
+		$fastqtype = "--solexa-quals";
+	}
+	if ($paired_end) { 
+	#reads in paired end 
+        #run paired end with two fasq files
+	    my $cmd = "$rsem_version/rsem-calculate-expression --quiet --paired-end -p $nThreads $options $fastqtype $fastq1 $fastq2 $dbref $output";
+ 	    print "RSEM Parameters used by Galaxy:\n$cmd\n";
+	    system($cmd);
+	}
+	else { 
+	my $cmd = "$rsem_version/rsem-calculate-expression --quiet -p $nThreads $options $fastqtype $single_fastq $dbref $output";
+ 	print "RSEM Parameters used by Galaxy:\n$cmd\n";
+	system($cmd);
+	}
+}
+
+ #Rename files for galaxy
+my $mv_genes = "mv $output.genes.results $output";
+my $mv_isoforms = "mv $output.isoforms.results $isoforms";
+
+#print "bamtype-parameter=$bamtype\n";
+my $mv_bam_transcript;
+my $mv_bam_genome;
+if ($bamtype eq "yes") {
+  $mv_bam_genome = "mv $output.genome.sorted.bam $bam_genome";
+  system($mv_bam_genome);
+}
+
+$mv_bam_transcript = "mv $output.transcript.sorted.bam $bamfile";
+
+my @rsem_dir = split(/\//, $output);
+my $short_output = $rsem_dir[-1];
+my $mv_theta = "mv $output.stat/$short_output.theta $theta";
+my $mv_cnt = "mv $output.stat/$short_output.cnt $cnt";
+my $mv_model = "mv $output.stat/$short_output.model $model";
+system($mv_genes);
+system($mv_isoforms);
+system($mv_bam_transcript);
+#system($mv_theta);
+#system($mv_cnt);
+#system($mv_model);
+#print "LOG $mv\n";

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rsem/rsem_indices.loc.example	Mon Mar 05 11:12:34 2012 -0500
@@ -0,0 +1,39 @@
+#This is a sample file distributed with Galaxy that enables tools
+#to use a directory of Bowtie indexed sequences data files. You will
+#need to create these data files and then create a bowtie_indices.loc
+#file similar to this one (store it in this directory) that points to
+#the directories in which those files are stored. The bowtie_indices.loc
+#file has this format (longer white space characters are TAB characters):
+#
+#<unique_build_id>   <dbkey>   <display_name>   <file_base_path>
+#
+#So, for example, if you had hg18 indexed stored in 
+#/depot/data2/galaxy/bowtie/hg18/, 
+#then the bowtie_indices.loc entry would look like this:
+#
+#hg18   hg18   hg18   /depot/data2/galaxy/bowtie/hg18/hg18
+human_refseq_NM	human_refseq_NM	human_refseq_NM	/opt/galaxy/references/human/1.1.2/NM_refseq_ref
+
+#
+#and your /depot/data2/galaxy/bowtie/hg18/ directory
+#would contain hg18.*.ebwt files:
+#
+#-rw-r--r--  1 james    universe 830134 2005-09-13 10:12 hg18.1.ebwt
+#-rw-r--r--  1 james    universe 527388 2005-09-13 10:12 hg18.2.ebwt
+#-rw-r--r--  1 james    universe 269808 2005-09-13 10:12 hg18.3.ebwt
+#...etc...
+#
+#Your bowtie_indices.loc file should include an entry per line for each
+#index set you have stored. The "file" in the path does not actually
+#exist, but it is the prefix for the actual index files. For example:
+#
+#hg18canon          hg18   hg18 Canonical   /depot/data2/galaxy/bowtie/hg18/hg18canon
+#hg18full           hg18   hg18 Full        /depot/data2/galaxy/bowtie/hg18/hg18full
+#/orig/path/hg19    hg19   hg19             /depot/data2/galaxy/bowtie/hg19/hg19
+#...etc...
+#
+#Note that for backwards compatibility with workflows, the unique ID of
+#an entry must be the path that was in the original loc file, because that
+#is the value stored in the workflow for that parameter. That is why the
+#hg19 entry above looks odd. New genomes can be better-looking.
+#