# HG changeset patch
# User bgruening
# Date 1492085985 14400
# Node ID 536873982e52db73cebc7575ddee9434bf0f0b52
# Parent  c778eb2f721bd396ed06d95a1ed1f6f5c93d2cf1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sailfish commit 359ddec398e18d3e2a534239b1202691595d1243

diff -r c778eb2f721b -r 536873982e52 README.rst
--- a/README.rst	Tue Nov 15 11:23:48 2016 -0500
+++ b/README.rst	Thu Apr 13 08:19:45 2017 -0400
@@ -1,16 +1,15 @@
-Galaxy wrappers for salmon
+Galaxy wrappers for sailfish
 =====================================
 
-These wrappers are copyright 2014, updated 2016 by Björn Grüning, Mhd Ramez Alrawas and additional contributors.
+These wrappers are copyright 2014 by Björn Grüning, Mhd Ramez Alrawas and additional contributors. 
 All rights reserved. See the licence text below.
 
-Currently tested with salmon 0.7.2.
-
+Currently tested with sailfish 0.10.1
 
 Automated Installation
 ======================
 
-Galaxy should be able to automatically install the salmon for you.
+Galaxy should be able to automatically install the sailfish for you.
 
 
 History
@@ -21,8 +20,7 @@
 -------- ----------------------------------------------------------------------
 v0.6.3.0  - First release
 -------- ----------------------------------------------------------------------
-v0.7.2    - Second release
-
+v0.10.1   - Second release
 ======== ======================================================================
 
 
diff -r c778eb2f721b -r 536873982e52 sailfish.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/sailfish.xml	Thu Apr 13 08:19:45 2017 -0400
@@ -0,0 +1,464 @@
+<tool id="sailfish" name="Sailfish" version="0.10.1.1">
+    <description>transcript quantification from RNA-seq data</description>
+    <macros>
+        <xml name="strandedness">
+            <param name="strandedness" type="select" label="Specify the strandedness of the reads">
+                <option value="U" selected="True">Not stranded (U)</option>
+                <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
+                <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
+            </param>
+        </xml>
+    </macros>
+    <requirements>
+        <requirement type="package" version="1.0.6">bzip2</requirement>
+        <requirement type="package" version="0.10.1">sailfish</requirement>
+    </requirements>
+    <stdio>
+        <exit_code range="1:" />
+        <exit_code range=":-1" />
+        <regex match="Error:" />
+        <regex match="Exception:" />
+        <regex match="Exception :" />
+    </stdio>
+    <version_command>sailfish -version</version_command>
+    <command>
+<![CDATA[
+        #if $refTranscriptSource.TranscriptSource == "history":
+            sailfish index
+                --transcripts $refTranscriptSource.ownFile
+                --kmerSize $refTranscriptSource.kmerSize
+                --out ./index_dir
+                --threads "\${GALAXY_SLOTS:-4}"
+            #set $index_path = './index_dir'
+        #else:
+            #set $index_path = $refTranscriptSource.index.fields.path
+        #end if
+        &&
+        #set compressed = 'no'
+        #if $single_or_paired.single_or_paired_opts == 'single':
+            #if $single_or_paired.input_singles.ext == 'fasta':
+                #set $ext = 'fasta'
+            #else:
+                #if $single_or_paired.input_singles.is_of_type("fastq.gz"):
+                    #set compressed = 'GZ'
+                #else if $single_or_paired.input_singles.is_of_type("fastq.bz2"):
+                    #set compressed = 'BZ2'
+                #end if
+                #set $ext = 'fastq'
+            #end if
+            ln -s $single_or_paired.input_singles ./single.$ext &&
+        #else:
+            #if $single_or_paired.input_mate1.ext == 'fasta':
+                #set $ext = 'fasta'
+            #else:
+                #if $single_or_paired.input_mate1.is_of_type("fastq.gz"):
+                    #set compressed = 'GZ'
+                #else if $single_or_paired.input_mate1.is_of_type("fastq.bz2"):
+                    #set compressed = 'BZ2'
+                #end if
+                #set $ext = 'fastq'
+            #end if
+            ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
+            ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
+        #end if
+        #if $geneMap:
+            ln -s "$geneMap" ./geneMap.$geneMap.ext &&
+        #end if
+        sailfish quant
+            --index $index_path
+            #if $single_or_paired.single_or_paired_opts == 'single':
+                --libType ${single_or_paired.strandedness}
+                #if $compressed == 'GZ':
+                    --unmatedReads <(zcat ./single.$ext)
+                #else if $compressed == 'BZ2':
+                    --unmatedReads <(bzcat ./single.$ext)
+                #else:
+                    --unmatedReads ./single.$ext
+                #end if
+            #else:
+                #if $compressed == 'GZ':
+                    --mates1 <(zcat ./mate1.$ext)
+                    --mates2 <(zcat ./mate2.$ext)
+                #else if $compressed == 'BZ2':
+                    --mates1 <(bzcat ./mate1.$ext)
+                    --mates2 <(bzcat ./mate2.$ext)
+                #else:
+                    --mates1 ./mate1.$ext
+                    --mates2 ./mate2.$ext
+                #end if
+                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
+            #end if
+            --output ./results
+            $biasCorrect
+            $gcBiasCorrect
+            --threads "\${GALAXY_SLOTS:-4}"
+            $dumpEq
+            #if str($gcSizeSamp):
+                --gcSizeSamp $gcSizeSamp
+            #end if
+            #if str($gcSpeedSamp):
+                --gcSpeedSamp $gcSpeedSamp
+            #end if
+            #if str($fldMean):
+                --fldMean $fldMean
+            #end if
+            #if str($fldSD):
+                --fldSD $fldSD
+            #end if
+            #if $maxReadOcc:
+                --maxReadOcc $maxReadOcc
+            #end if
+            #if $geneMap:
+                --geneMap ./geneMap.${geneMap.ext}
+            #end if
+            $strictIntersect
+            $noEffectiveLengthCorrection
+            $useVBOpt
+            $discardOrphans
+            $unsmoothedFLD
+            --maxFragLen ${maxFragLen}
+            --txpAggregationKey '${txpAggregationKey}'
+            $ignoreLibCompat
+            $enforceLibCompat
+            $allowDovetail
+            #if str($numBiasSamples):
+                --numBiasSamples $numBiasSamples
+            #end if
+            #if str($numFragSamples):
+                --numFragSamples $numFragSamples
+            #end if
+            #if str($numGibbsSamples):
+                --numGibbsSamples $numGibbsSamples
+            #end if
+            #if str($numBootstraps):
+                --numBootstraps $numBootstraps
+            #end if
+]]>
+    </command>
+    <inputs>
+        <conditional name="refTranscriptSource">
+            <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+                <option value="indexed">Use a built-in index</option>
+                <option value="history" selected="True">Use one from the history</option>
+            </param>
+            <when value="indexed">
+                <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
+                    <options from_data_table="sailfish_indexes">
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
+                    </options>
+                </param>
+            </when>  <!-- build-in -->
+            <when value="history">
+                <param name="ownFile" type="data" format="fasta"  label="Select the reference transcriptome" help="in FASTA format" />
+                <param argument="kmerSize" type="integer" value="21" max="32" label="The size of the k-mer on which the index is built"
+                    help="There is a tradeoff here between the distinctiveness of the k-mers and their robustness to errors.
+                        The shorter the k-mers, the more robust they will be to errors in the reads, but the longer the k-mers,
+                        the more distinct they will be.  We generally recommend using a k-mer size of at least 20."/>
+            </when>  <!-- history -->
+        </conditional>  <!-- refTranscriptSource -->
+
+        <conditional name="single_or_paired">
+            <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
+                <option value="single">Single-end</option>
+                <option value="paired">Paired-end</option>
+            </param>
+            <when value="single">
+                <param name="input_singles" type="data" format="fastq,fasta,fastq.gz" label="FASTQ/FASTA file" help="FASTQ file." />
+                <expand macro="strandedness" />
+            </when>
+            <when value="paired">
+                <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 1" help="FASTQ file." />
+                <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz" label="Mate pair 2" help="FASTQ file." />
+                <param name="orientation" type="select" label="Relative orientation of reads within a pair">
+                    <option value="M">Mates are oriented in the same direction (M = matching)</option>
+                    <option value="O">Mates are oriented away from each other (O = outward)</option>
+                    <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
+                </param>
+                <expand macro="strandedness" />
+            </when>
+        </conditional>
+
+        <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True" label="File containing a mapping of transcripts to genes"
+            help="Calculates the aggregated gene-level abundance estimations. This file should be eiher a GTF file or tab-delimited format
+            where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
+
+        <param argument="--biasCorrect" type="boolean" truevalue="--biasCorrect" falsevalue="" checked="False"
+            label="Perform sequence-specific bias correction" help=""/>
+
+        <param argument="--gcBiasCorrect" type="boolean" truevalue="--gcBiasCorrect" falsevalue="" checked="False"
+            label="Perform fragment GC bias correction" help=""/>
+
+        <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
+            label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
+
+        <param argument="--gcSizeSamp" type="integer" value="1" optional="True"
+            label="The value by which to down-sample transcripts when representing the GC content"
+            help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/>
+
+        <param argument="--gcSpeedSamp" type="integer" value="1" optional="True"
+            label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias."
+            help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
+
+        <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
+            label="Strict Intersect." help="When this flag is set, if the intersection of the
+            quasi-mappings for the left and right is empty, then all mappings for the left and all mappings
+            for the right read are reported as orphaned quasi-mappings."/>
+
+        <param argument="--fldMean" type="integer" value="200" optional="True" label="Calculate effective lengths"
+            help="If single end reads are being used for quantification, or there are an insufficient number of uniquely
+            mapping reads when performing paired-end quantification
+            to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>
+
+        <param argument="--fldSD" type="integer" value="80" optional="True" label="Standard deviation"
+            help="The standard deviation used in the fragment length distribution for single-end quantification or
+            when an empirical distribution cannot be learned."/>
+
+        <param argument="--maxReadOcc" type="integer" value="200" optional="True" label="Maximal read mapping occurence"
+            help="Reads mapping to more than this many places won't be considered."/>
+
+        <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
+            label="Disable effective length correction" help="Disables effective length correction when computing the probability
+            that a fragment was generated from a transcript.
+            If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>
+
+        <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
+            label="Use Variational Bayesian EM algorithm for optimization" help="Use Variational Bayesian EM algorithm rather
+            than the traditional EM angorithm for optimization"/>
+
+        <param argument="--discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
+            label="Discard orphaned reads as valid hits when performing lightweight-alignment"
+            help="This option will discard orphaned fragments. This only has an effect on paired-end input, but enabling this option will discard, rather than count, any reads where only one of the paired fragments maps to a transcript."/>
+
+        <param argument="--unsmoothedFLD" type="boolean" truevalue="--unsmoothedFLD" falsevalue="" checked="False"
+            label="Use the un-smoothed approach to effective length correction" help="This traditional approach works by convolving the FLD with the
+            characteristic function over each transcript."/>
+
+        <param argument="--maxFragLen" type="integer" value="1000" optional="True"
+            label="The maximum length of a fragment to consider when building the empirical fragment length distribution"
+            help=""/>
+
+        <param argument="--txpAggregationKey" value="gene_id" type="text" label="The key for aggregating transcripts during gene-level estimates">
+            <help>
+              <![CDATA[
+              When generating the gene-level estimates, use the provided key for aggregating transcripts. The default is the "gene_id" field,
+              but other fields (e.g. "gene_name") might be useful depending on the specifics of the annotation being used. Note: this option only
+              affects aggregation when using a GTF annotation; not an annotation in "simple" format.]]>
+            </help>
+        </param>
+        <param argument="--ignoreLibCompat" type="boolean" truevalue="--ignoreLibCompat" falsevalue="" checked="False"
+                label="Disables strand-aware processing completely.">
+            <help>
+                <![CDATA[
+                All hits are considered "Valid".]]>
+            </help>
+        </param>
+        <param argument="--enforceLibCompat" type="boolean" truevalue="--enforceLibCompat" falsevalue="" checked="False"
+                label="Enforces strict library compatibility.">
+            <help>
+                <![CDATA[
+                Fragments that map in a manner other than what is specified by the expected library type will be discarded,
+                even if there are no mappings that agree with the expected library type.]]>
+            </help>
+        </param>
+        <param argument="--allowDovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False"
+                label="Allow paired-end reads from the same fragment to dovetail.">
+            <help>
+                <![CDATA[
+                Allow paired-end reads from the same fragment to "dovetail", such that the ends of the mapped reads can extend past each other.]]>
+            </help>
+        </param>
+        <param argument="--numBiasSamples" type="integer" value="1000000" optional="True"
+          label="Number of fragment mappings to use when learning the sequene-specific bias model"
+          help=""/>
+        <param argument="--numFragSamples" type="integer" value="10000" optional="True"
+          label="Number of fragments from unique alignments to sample when building the fragment length distribution"
+          help=""/>
+        <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
+          label="Number of Gibbs sampling rounds to perform."
+          help=""/>
+        <param argument="--numBootstraps" type="integer" value="0" optional="True"
+          label="Number of bootstrap samples to generate."
+          help="This is mutually exclusive with Gibbs"/>
+    </inputs>
+
+
+    <outputs>
+        <data name="output_quant" format="tabular" from_work_dir="results/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
+        <data name="output_gene_quant" format="tabular" from_work_dir="results/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
+            <filter>geneMap</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq" />
+            <param name="input_mate2" value="reads_2.fastq" />
+            <param name="biasCorrect" value="False" />
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
+        </test>
+        <test> <!-- gzipped version of above -->
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="input_mate2" value="reads_2.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="biasCorrect" value="False" />
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <output file="sailfish_quant_result1.tab" ftype="tabular" name="output_quant" />
+        </test>
+        <test>
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq" />
+            <param name="input_mate2" value="reads_2.fastq" />
+            <param name="biasCorrect" value="True" />
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />
+        </test>
+        <test>
+            <param name="single_or_paired_opts" value="paired" />
+            <param name="input_mate1" value="reads_1.fastq" />
+            <param name="input_mate2" value="reads_2.fastq" />
+            <param name="biasCorrect" value="True" />
+            <param name="TranscriptSource" value="history" />
+            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
+            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
+            <output file="sailfish_bias_result1.tab" ftype="tabular" name="output_quant" />
+            <output file="sailfish_genMap_result1.tab" ftype="tabular" name="output_gene_quant" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Sailfish is a tool for transcript quantification from RNA-seq data.  It
+requires a set of target transcripts (either from a reference or de-novo
+assembly) to quantify.  All you need to run Sailfish is a fasta file containing
+your reference transcripts and a (set of) fasta/fastq file(s) containing your
+reads.  Sailfish runs in two phases; indexing and quantification.  The indexing
+step is independent of the reads, and only need to be run one for a particular
+set of reference transcripts and choice of k (the k-mer size). The
+quantification step, obviously, is specific to the set of RNA-seq reads and is
+thus run more frequently.
+
+When the quantification output contains a number of columns:
+(1) Transcript ID,
+(2) Transcript Length,
+(3) Transcripts per Million (TPM) and
+(4) Estimated number of reads (an estimate of the number of reads drawn from this transcript given the transcript’s relative abundance and length).
+
+The first two columns are self-explanatory, the next four are measures of transcript abundance and the final is a commonly used input for differential expression tools.
+The Transcripts per Million quantification number is computed as described in [1], and is meant as an estimate of the number of transcripts, per million observed transcripts,
+originating from each isoform. Its benefit over the F/RPKM measure is that it is independent of the mean expressed transcript length
+(i.e. if the mean expressed transcript length varies between samples, for example, this alone can affect differential analysis based on the K/RPKM.).
+
+
+
+Fragment Library Types
+======================
+
+There are numerous library preparation protocols for RNA-seq that result in
+sequencing reads with different characteristics.  For example, reads can be
+single end (only one side of a fragment is recorded as a read) or paired-end
+(reads are generated from both ends of a fragment).  Further, the sequencing
+reads themselves may be unstraned or strand-specific.  Finally, paired-end
+protocols will have a specified relative orientation.  To characterize the
+various different typs of sequencing libraries, we've created a miniature
+"language" that allows for the succinct description of the many different types
+of possible fragment libraries.  For paired-end reads, the possible
+orientations, along with a graphical description of what they mean, are
+illustrated below:
+
+.. image:: ReadLibraryIllustration.png
+
+The library type string consists of three parts: the relative orientation of
+the reads, the strandedness of the library, and the directionality of the
+reads.
+
+The first part of the library string (relative orientation) is only provided if
+the library is paired-end. The possible options are:
+
+::
+
+    I = inward
+    O = outward
+    M = matching
+
+The second part of the read library string specifies whether the protocol is
+stranded or unstranded; the options are:
+
+::
+
+    S = stranded
+    U = unstranded
+
+If the protocol is unstranded, then we're done.  The final part of the library
+string specifies the strand from which the read originates in a strand-specific
+protocol — it is only provided if the library is stranded (i.e. if the
+library format string is of the form S).  The possible values are:
+
+::
+
+    F = read 1 (or single-end read) comes from the forward strand
+    R = read 1 (or single-end read) comes from the reverse strand
+
+So, for example, if you wanted to specify a fragment library of strand-specific
+paired-end reads, oriented toward each other, where read 1 comes from the
+forward strand and read 2 comes from the reverse strand, you would specify ``-l
+ISF`` on the command line.  This designates that the library being processed has
+the type "ISF" meaning, **I**\ nward (the relative orientation), **S**\ tranted
+(the protocol is strand-specific), **F**\ orward (read 1 comes from the forward
+strand).
+
+The single end library strings are a bit simpler than their pair-end counter
+parts, since there is no relative orientation of which to speak.  Thus, the
+only possible library format types for single-end reads are ``U`` (for
+unstranded), ``SF`` (for strand-specific reads coming from the forward strand)
+and ``SR`` (for strand-specific reads coming from the reverse strand).
+
+A few more examples of some library format strings and their interpretations are:
+
+::
+
+    IU (an unstranded paired-end library where the reads face each other)
+
+::
+
+    SF (a stranded single-end protocol where the reads come from the forward strand)
+
+::
+
+    OSR (a stranded paired-end protocol where the reads face away from each other,
+         read1 comes from reverse strand and read2 comes from the forward strand)
+
+.. note:: Correspondence to TopHat library types
+
+   The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
+   read aligner has a different convention for specifying the format of the library.
+   Below is a table that provides the corresponding sailfish/salmon library format
+   string for each of the potential TopHat library types:
+
+
+   +---------------------+-------------------------+
+   | TopHat              | Salmon (and Sailfish)   |
+   +=====================+============+============+
+   |                     | Paired-end | Single-end |
+   +---------------------+------------+------------+
+   |``-fr-unstranded``   |``-l IU``   |``-l U``    |
+   +---------------------+------------+------------+
+   |``-fr-firststrand``  |``-l ISR``  |``-l SR``   |
+   +---------------------+------------+------------+
+   |``-fr-secondstrand`` |``-l ISF``  |``-l SF``   |
+   +---------------------+------------+------------+
+
+   The remaining salmon library format strings are not directly expressible in terms
+   of the TopHat library types, and so there is no direct mapping for them.
+
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1038/nbt.2862</citation>
+    </citations>
+</tool>
diff -r c778eb2f721b -r 536873982e52 salmon.xml
--- a/salmon.xml	Tue Nov 15 11:23:48 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,486 +0,0 @@
-<tool id="salmon" name="Salmon" version="0.7.2">
-
-    <description>Transcript Quantification from RNA-seq data</description>
-
-    <macros>
-        <xml name="strandedness">
-            <param name="strandedness" type="select" label="Specify the strandedness of the reads">
-                <option value="U" selected="True">Not stranded (U)</option>
-                <option value="SF">read 1 (or single-end read) comes from the forward strand (SF)</option>
-                <option value="SR">read 1 (or single-end read) comes from the reverse strand (SR)</option>
-            </param>
-        </xml>
-    </macros>
-
-    <requirements>
-        <requirement type="package" version="0.7.2">salmon</requirement>
-    </requirements>
-
-    <stdio>
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <regex match="Error:" />
-        <regex match="Exception:" />
-        <regex match="Exception :" />
-    </stdio>
-    <version_command>salmon -version</version_command>
-    <command><![CDATA[
-        mkdir ./index
-        &&
-        mkdir ./output
-        &&
-        #if $refTranscriptSource.TranscriptSource == "history":
-            salmon index
-                --transcripts $refTranscriptSource.ownFile
-                --kmerLen $refTranscriptSource.kmerLen
-                --threads "\${GALAXY_SLOTS:-4}"
-                --index './index'
-                --type '$quasi_orphans.type'
-                $perfectHash
-                #if str($sasamp):
-                    --sasamp $sasamp
-                #end if
-            #set $index_path = './index'
-        #else:
-            #set $index_path = $refTranscriptSource.index.fields.path
-        #end if
-        &&
-        #if $single_or_paired.single_or_paired_opts == 'single':
-            #if $single_or_paired.input_singles.ext == 'fasta':
-                #set $ext = 'fasta'
-            #else:
-                #set $ext = 'fastq'
-            #end if
-            ln -s $single_or_paired.input_singles ./single.$ext &&
-        #else:
-            #if $single_or_paired.input_mate1.ext == 'fasta':
-                #set $ext = 'fasta'
-            #else:
-                #set $ext = 'fastq'
-            #end if
-            ln -s $single_or_paired.input_mate1 ./mate1.$ext &&
-            ln -s $single_or_paired.input_mate2 ./mate2.$ext &&
-        #end if
-        #if $geneMap:
-            ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
-        #end if
-        salmon quant
-            --index $index_path
-            #if $single_or_paired.single_or_paired_opts == 'single':
-                --libType ${single_or_paired.strandedness}
-                --unmatedReads ./single.$ext
-            #else:
-                --mates1 ./mate1.$ext
-                --mates2 ./mate2.$ext
-                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
-            #end if
-            --output ./output
-            #if str($quasi_orphans.type) == 'quasi':
-                --allowOrphans
-            #else:
-                $quasi_orphans.allowOrphans
-            #end if
-            $seqBias
-            $gcBias
-            --threads "\${GALAXY_SLOTS:-4}"
-            --incompatPrior $adv.incompatPrior
-            $adv.consistentHits
-            $adv.dumpEq
-            #if str($adv.gcSizeSamp):
-                --gcSizeSamp $adv.gcSizeSamp
-            #end if
-            #if str($adv.biasSpeedSamp):
-                --biasSpeedSamp $adv.biasSpeedSamp
-            #end if
-            $adv.strictIntersect
-            #if str($adv.fldMax):
-                --fldMax $adv.fldMax
-            #end if
-            #if str($adv.fldMean):
-                --fldMean $adv.fldMean
-            #end if
-            #if str($adv.fldSD):
-                --fldSD $adv.fldSD
-            #end if
-            #if $adv.forgettingFactor:
-                --forgettingFactor $adv.forgettingFactor
-            #end if
-            $adv.writeMappings
-            #if str($adv.maxOcc):
-                --maxOcc $adv.maxOcc
-            #end if
-            $adv.initUniform
-            $adv.noFragLengthDist
-            $adv.noBiasLengthThreshold
-            #if str($adv.maxReadOcc):
-                --maxReadOcc $adv.maxReadOcc
-            #end if
-            #if $geneMap:
-                --geneMap ./geneMap.${geneMap.ext}
-            #end if
-            $adv.noEffectiveLengthCorrection
-            $adv.useVBOpt
-            #if str($adv.numBiasSamples):
-                --numBiasSamples $adv.numBiasSamples
-            #end if
-            #if str($adv.numAuxModelSamples):
-                --numAuxModelSamples $adv.numAuxModelSamples
-            #end if
-            #if str($adv.numPreAuxModelSamples):
-                --numPreAuxModelSamples $adv.numPreAuxModelSamples
-            #end if
-            #if str($adv.numGibbsSamples):
-                --numGibbsSamples $adv.numGibbsSamples
-            #end if
-            #if str($adv.numBootstraps):
-                --numBootstraps $adv.numBootstraps
-            #end if
-            $adv.perTranscriptPrior
-            #if $adv.vbPrior:
-                --vbPrior $adv.vbPrior
-            #end if
-            $adv.writeUnmappedNames
-]]>
-    </command>
-
-    <inputs>
-        <conditional name="refTranscriptSource">
-            <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?" help="Built-ins were indexed using default options">
-                <option value="indexed">Use a built-in index</option>
-                <option value="history" selected="True">Use one from the history</option>
-            </param>
-            <when value="indexed">
-                <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
-                    <options from_data_table="salmon_indexes">
-                        <filter type="sort_by" column="2"/>
-                        <validator type="no_options" message="No indexes are available for the selected input dataset"/>
-                    </options>
-                </param>
-            </when>  <!-- build-in -->
-            <when value="history">
-              <param name="ownFile" type="data" format="fasta" label="Select the reference transcriptome" help="in FASTA format" />
-                <param argument="kmerLen" type="integer" value="31" label="The size should be odd number."/>
-            </when>  <!-- history -->
-        </conditional>
-        <conditional name="single_or_paired">
-            <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
-                <option value="single">Single-end</option>
-                <option value="paired">Paired-end</option>
-            </param>
-            <when value="single">
-                <param name="input_singles" type="data" format="fastq,fasta" label="FASTQ/FASTA file" help="FASTQ file." />
-                <expand macro="strandedness" />
-            </when>
-            <when value="paired">
-                <param name="input_mate1" type="data" format="fastq,fasta" label="Mate pair 1" help="FASTQ file." />
-                <param name="input_mate2" type="data" format="fastq,fasta" label="Mate pair 2" help="FASTQ file." />
-                <param name="orientation" type="select" label="Relative orientation of reads within a pair">
-                    <option value="M">Mates are oriented in the same direction (M = matching)</option>
-                    <option value="O">Mates are oriented away from each other (O = outward)</option>
-                    <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
-                </param>
-                <expand macro="strandedness" />
-            </when>
-        </conditional>
-        <conditional name="quasi_orphans">
-            <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
-                <option value="quasi" selected="True">quasi</option>
-                <option value="fmd">fmd</option>
-            </param>
-            <when value="quasi">
-            </when>  <!-- build-in -->
-            <when value="fmd">
-                <param argument="--allowOrphans" type="boolean" truevalue="--allowOrphans" falsevalue="" checked="True"
-                    label="Consider orphaned reads as valid hits when performing lightweight-alignment"
-                    help="This option will increase sensitivity (allow more reads to map and more transcripts to be detected), but may decrease specificity as orphaned alignments are more likely to be spurious."/>
-            </when>  <!-- history -->
-        </conditional>
-        <param argument="--perfectHash" type="boolean" truevalue="--perfectHash" falsevalue="" checked="False"
-            label="Perfect Hash"
-            help="Build the index using a perfect hash rather than a dense hash.  This will require  less memory (especially during quantification), but will take longer to construct "/>
-        <param argument="--sasamp" type="integer" value="1" optional="True" label="Suffix Array"
-            help="The interval at which the suffix array should be sampled. Smaller values are faster, but produce a larger index. The default should be OK, unless your transcriptome is huge. This value should be a power of 2."/>
-        <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
-            label="Perform sequence-specific bias correction"
-            help=""/>
-        <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
-            label="Perform fragment GC bias correction"
-            help=""/>
-        <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="True"
-            label="File containing a mapping of transcripts to genes.  If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab." />
-        <section name="adv" title="Additional Options">
-            <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
-                label="Write Mappings"
-                help=" Setting this option then the quasi-mapping results will be written out in SAM-cpmpatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead." />
-            <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"
-                label="Incompatible Prior"
-                help="This option sets the prior probability that an alignment that disagrees with the specified library type (--libType) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do" />
-            <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
-                label="Dump the equivalence class counts that were computed during quasi-mapping." help=""/>
-            <param argument="--gcSizeSamp" type="integer" value="1" optional="True"
-                label="The value by which to down-sample transcripts when representing the GC content" help="Larger values will reduce memory usage, but may decrease the fidelity of bias modeling results."/>
-            <param argument="--biasSpeedSamp" type="integer" value="1" optional="True"
-                label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
-            <param argument="--strictIntersect" type="boolean" truevalue="--strictIntersect" falsevalue="" checked="False"
-                label="Modifies how orphans are assigned." help="When this flag is set, if the intersection of the quasi-mappings for the left and right is empty, then all mappings for the left and all mappings for the right read are reported as orphaned quasi-mappings."/>
-            <param argument="--minLen" type="integer" value="19" optional="True"
-                label=" (S)MEMs smaller than this size won't be considered." help="" />
-            <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="False"
-                label="Perform sensitive quantification"
-                help=" Setting this option enables the splitting of SMEMs that are larger than 1.5 times the minimum seed length (minLen/k above).  This may reveal high scoring chains of MEMs that are masked by long SMEMs.  However, this option makes lightweight-alignment a bit slower and is usually not necessary if the reference is of reasonable quality." />
-            <param argument="--consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
-                label="Force hits gathered during quasi-mapping to be consistent"
-                help="" />
-            <param argument="--extraSensitive" type="boolean" truevalue="--extraSensitive" falsevalue="" checked="False"
-                label="Perform extra sensitive quantification"
-                help="Setting this option enables an extra pass of 'seed' search. Enabling this option may improve sensitivity (the number of reads having sufficient coverage), but will typically slow down quantification by ~40%.  Consider enabling this option if you find the mapping rate to be significantly lower than expected."/>
-            <param argument="--coverage" type="float" value="0.69999999999999996" optional="True"
-                label="Required coverage of read by union of SMEMs to consider it a hit"
-                help="" />
-            <param argument="--fldMax" type="integer" value="1000" optional="True"
-                label="The maximum fragment length to consider when building the empirical distribution."
-                help=""/>
-            <param argument="--fldMean" type="integer" value="200" optional="True"
-                label="The mean used in the fragment length distribution prior"
-                help="If single end reads are being used for quantification, or there are an insufficient number of uniquely mapping reads when performing paired-end quantification to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>
-            <param argument="--fldSD" type="integer" value="80" optional="True"
-                label="Standard deviation"
-                help="The standard deviation used in the fragment length distribution prior."/>
-            <param argument="--forgettingFactor" type="float" value="0.65000000000000002" optional="True"
-                label="The forgetting factor used in the online learning schedule."
-                help=" A smaller value results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable.  Value should be in the interval (0.5, 1.0]." />
-            <param argument="--maxOcc" type="integer" value="200" optional="True"
-                label="(S)MEMs occuring more than this many times won't be considered"
-                help=""/>
-            <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
-                label="Initialization with uniform parameters"
-                help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
-            <param argument="--maxReadOcc" type="integer" value="100" optional="True"
-                label="Maximal read mapping occurence"
-                help="Reads mapping to more than this many places won't be considered."/>
-            <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
-                label="Disable effective length correction"
-                help="Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>
-            <param argument="--noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
-                label="Ignore fragment length distribution"
-                help="[experimental] : Don't consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location.  Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment's a priori probability." />
-            <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
-                label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
-                help="This can increase the precision of bias correction, but harm robustness. The difault correction applies a threshold." />
-            <param argument="--numBiasSamples" type="integer" value="2000000" optional="True"
-                label="Number of fragment mappings to use when learning the sequence-specific bias model."
-                help="" />
-            <param argument="--numAuxModelSamples" type="integer" value="5000000" optional="True"
-                label="The first numAuxModelSamples are used to train the auxiliary model parameters."
-                help="(e.g. fragment length distribution, bias, etc.). After ther first numAuxModelSamples observations the auxiliary model parameters will be assumed to have converged and will be fixed." />
-            <param argument="--numPreAuxModelSamples" type="integer" value="1000000" optional="True"
-                label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models."
-                help=" The purpose of ignoring the auxiliary models for the first numPreAuxModelSamples observations is to avoid applying these models before thier parameters have been learned sufficiently well." />
-            <param argument="--splitWidth" type="integer" value="0" optional="True"
-                label=" If (S)MEM occurs fewer than this many times, search for smaller, contained  MEMs"
-                help="The default value will not split (S)MEMs, a higher value will result in more MEMs being explore and, thus, will result in increased running time." />
-            <param argument="--splitSpanningSeeds" type="boolean" truevalue="--splitSpanningSeeds" falsevalue="" checked="False"
-                label="Attempt to split seeds that happen to fall on the boundary between two transcripts."
-                help="This can improve the fragment hit-rate, but is usually not necessary."/>
-            <param argument="--useVBOpt" type="boolean" truevalue="--useVBOpt" falsevalue="" checked="False"
-                label="Use the Variational Bayesian EM rather than the traditional EM algorithm for optimization in the batch passes."
-                help=""/>
-            <param argument="--numGibbsSamples" type="integer" value="0" optional="True"
-                label=" Number of Gibbs sampling rounds to perform."
-                help="" />
-            <param argument="--numBootstraps" type="integer" value="0" optional="True"
-                label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling."
-                help="" />
-            <param argument="--perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
-                label="The prior will be interpreted as a transcript-level prior."
-                help="either the default or the argument provided via --vbPrior" />
-            <param argument="--vbPrior" type="float" value="0.001" optional="True"
-                label="The prior that will be used in the VBEM algorithm."
-                help="This is interpreted as a per-nucleotide prior, unless the --perTranscriptPrior flag is also given, in which case this is used as a transcript-level prior." />
-            <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
-                label="Write the names of un-mapped reads to the file unmapped_names.txt."
-                help=""/>
-        </section>
-    </inputs>
-
-    <outputs>
-        <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />
-        <data name="output_gene_quant" format="tabular" from_work_dir="output/quant.genes.sf" label="${tool.name} on ${on_string} (Gene Quantification)">
-            <filter>geneMap</filter>
-        </data>
-    </outputs>
-
-    <tests>
-        <test>
-            <param name="single_or_paired_opts" value="paired" />
-            <param name="input_mate1" value="reads_1.fastq" />
-            <param name="input_mate2" value="reads_2.fastq" />
-            <param name="biasCorrect" value="False" />
-            <param name="TranscriptSource" value="history" />
-            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
-            <output name="output_quant">
-                <assert_contents>
-                    <has_text text="EffectiveLength" />
-                    <has_text text="TPM" />
-                    <has_text text="NM_001168316" />
-                    <has_text text="NM_174914" />
-                    <has_text text="NM_018953" />
-                    <has_text text="NR_003084" />
-                    <has_text text="NM_017410" />
-                    <has_text text="NM_153693" />
-                    <has_text text="NR_031764" />
-                    <has_n_columns n="5" />
-                </assert_contents>
-            </output>
-        </test>
-        <test>
-            <param name="single_or_paired_opts" value="paired" />
-            <param name="input_mate1" value="reads_1.fastq" />
-            <param name="input_mate2" value="reads_2.fastq" />
-            <param name="TranscriptSource" value="history" />
-            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
-            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
-            <output name="output_quant">
-                <assert_contents>
-                    <has_text text="EffectiveLength" />
-                    <has_text text="TPM" />
-                    <has_text text="NM_001168316" />
-                    <has_text text="NM_174914" />
-                    <has_text text="NM_018953" />
-                    <has_text text="NR_003084" />
-                    <has_text text="NM_017410" />
-                    <has_text text="NM_153693" />
-                    <has_text text="NR_031764" />
-                    <has_n_columns n="5" />
-                </assert_contents>
-            </output>
-            <output name="output_gene_quant">
-                <assert_contents>
-                    <has_text text="EffectiveLength" />
-                    <has_text text="TPM" />
-                    <has_text text="baz" />
-                    <has_text text="bar" />
-                    <has_text text="2283" />
-                    <has_text text="1640" />
-                    <has_n_columns n="5" />
-                </assert_contents>
-            </output>
-        </test>
-    </tests>
-
-    <help><![CDATA[
-**What it does**
-salmon is a tool for transcript quantification from RNA-seq data.  It
-requires a set of target transcripts (either from a reference or de-novo
-assembly) to quantify.  All you need to run Salmon is a fasta file containing
-your reference transcripts and a (set of) fasta/fastq file(s) containing your
-reads.  Salmon runs in two phases; indexing and quantification.  The indexing
-step is independent of the reads, and only need to be run one for a particular
-set of reference transcripts and choice of k (the k-mer size). The
-quantification step, obviously, is specific to the set of RNA-seq reads and is
-thus run more frequently.
-When the quantification output contains a number of columns:
-(1) Transcript ID,
-(2) Transcript Length,
-(3) Transcripts per Million (TPM) and
-(4) Estimated number of reads (an estimate of the number of reads drawn from this transcript given the transcript’s relative abundance and length).
-The first two columns are self-explanatory, the next four are measures of transcript abundance and the final is a commonly used input for differential expression tools.
-The Transcripts per Million quantification number is computed as described in [1], and is meant as an estimate of the number of transcripts, per million observed transcripts,
-originating from each isoform. Its benefit over the F/RPKM measure is that it is independent of the mean expressed transcript length
-(i.e. if the mean expressed transcript length varies between samples, for example, this alone can affect differential analysis based on the K/RPKM.).
-
-
-Fragment Library Types
-======================
-
-There are numerous library preparation protocols for RNA-seq that result in
-sequencing reads with different characteristics.  For example, reads can be
-single end (only one side of a fragment is recorded as a read) or paired-end
-(reads are generated from both ends of a fragment).  Further, the sequencing
-reads themselves may be unstraned or strand-specific.  Finally, paired-end
-protocols will have a specified relative orientation.  To characterize the
-various different typs of sequencing libraries, we've created a miniature
-"language" that allows for the succinct description of the many different types
-of possible fragment libraries.  For paired-end reads, the possible
-orientations, along with a graphical description of what they mean, are
-illustrated below:
-.. image:: ReadLibraryIllustration.png
-The library type string consists of three parts: the relative orientation of
-the reads, the strandedness of the library, and the directionality of the
-reads.
-The first part of the library string (relative orientation) is only provided if
-the library is paired-end. The possible options are:
-::
-
-    I = inward
-    O = outward
-    M = matching
-
-The second part of the read library string specifies whether the protocol is
-stranded or unstranded; the options are:
-::
-
-    S = stranded
-    U = unstranded
-
-If the protocol is unstranded, then we're done.  The final part of the library
-string specifies the strand from which the read originates in a strand-specific
-protocol — it is only provided if the library is stranded (i.e. if the
-library format string is of the form S).  The possible values are:
-::
-
-    F = read 1 (or single-end read) comes from the forward strand
-    R = read 1 (or single-end read) comes from the reverse strand
-
-So, for example, if you wanted to specify a fragment library of strand-specific
-paired-end reads, oriented toward each other, where read 1 comes from the
-forward strand and read 2 comes from the reverse strand, you would specify ``-l
-ISF`` on the command line.  This designates that the library being processed has
-the type "ISF" meaning, **I**\ nward (the relative orientation), **S**\ tranted
-(the protocol is strand-specific), **F**\ orward (read 1 comes from the forward
-strand).
-The single end library strings are a bit simpler than their pair-end counter
-parts, since there is no relative orientation of which to speak.  Thus, the
-only possible library format types for single-end reads are ``U`` (for
-unstranded), ``SF`` (for strand-specific reads coming from the forward strand)
-and ``SR`` (for strand-specific reads coming from the reverse strand).
-A few more examples of some library format strings and their interpretations are:
-::
-
-    IU (an unstranded paired-end library where the reads face each other)
-
-::
-
-    SF (a stranded single-end protocol where the reads come from the forward strand)
-
-::
-
-    OSR (a stranded paired-end protocol where the reads face away from each other,
-         read1 comes from reverse strand and read2 comes from the forward strand)
-
-.. note:: Correspondence to TopHat library types
-
-   The popular `TopHat <http://ccb.jhu.edu/software/tophat/index.shtml>`_ RNA-seq
-   read aligner has a different convention for specifying the format of the library.
-   Below is a table that provides the corresponding Salmon/salmon library format
-   string for each of the potential TopHat library types:
-
-   +---------------------+-------------------------+
-   | TopHat              | Salmon (and Sailfish)   |
-   +=====================+============+============+
-   |                     | Paired-end | Single-end |
-   +---------------------+------------+------------+
-   |``-fr-unstranded``   |``-l IU``   |``-l U``    |
-   +---------------------+------------+------------+
-   |``-fr-firststrand``  |``-l ISR``  |``-l SR``   |
-   +---------------------+------------+------------+
-   |``-fr-secondstrand`` |``-l ISF``  |``-l SF``   |
-   +---------------------+------------+------------+
-
-   The remaining salmon library format strings are not directly expressible in terms
-   of the TopHat library types, and so there is no direct mapping for them.
-]]> </help>
-    <citations>
-        <citation type="doi">10.1101/021592</citation>
-    </citations>
-</tool>
diff -r c778eb2f721b -r 536873982e52 test-data/gene_map.tab
--- a/test-data/gene_map.tab	Tue Nov 15 11:23:48 2016 -0500
+++ b/test-data/gene_map.tab	Thu Apr 13 08:19:45 2017 -0400
@@ -1,4 +1,3 @@
 NM_174914	foo
 NM_001168316	bar
 NR_003084	baz
-NR_031764 foo
diff -r c778eb2f721b -r 536873982e52 test-data/reads_1.fastq.gz
Binary file test-data/reads_1.fastq.gz has changed
diff -r c778eb2f721b -r 536873982e52 test-data/reads_2.fastq.gz
Binary file test-data/reads_2.fastq.gz has changed
diff -r c778eb2f721b -r 536873982e52 test-data/sailfish_bias_result1.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sailfish_bias_result1.tab	Thu Apr 13 08:19:45 2017 -0400
@@ -0,0 +1,16 @@
+Name	Length	EffectiveLength	TPM	NumReads
+NM_001168316	2283	1528.95	12702.4	158.926
+NM_174914	2385	1599.63	114719	1501.66
+NR_031764	1853	1214.33	10407.1	103.415
+NM_004503	1681	1085.83	37300.1	331.428
+NM_006897	1541	984.724	82401.9	664
+NM_014212	2037	1316.12	5106.81	55
+NM_014620	2300	1541.27	46908.6	591.628
+NM_017409	1959	1273.24	4510.99	47
+NM_017410	2396	1562.29	3285.28	42
+NM_018953	1612	1019.15	27338	227.994
+NM_022658	2288	1634.87	364846	4881
+NM_153633	1666	1082.85	40694.7	360.597
+NM_153693	2072	1374.67	6520.1	73.3448
+NM_173860	849	483.271	243258	962
+NR_003084	1640	1052.77	1.09566	0.00943897
diff -r c778eb2f721b -r 536873982e52 test-data/sailfish_genMap_result1.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sailfish_genMap_result1.tab	Thu Apr 13 08:19:45 2017 -0400
@@ -0,0 +1,5 @@
+Name	Length	EffectiveLength	TPM	NumReads
+baz	1640	1052.77	1.09566	0.00943897
+NR_031764	1853	1214.33	10407.1	103.415
+foo	348.949	235.269	976889	9737.65
+bar	2283	1528.95	12702.4	158.926
diff -r c778eb2f721b -r 536873982e52 test-data/sailfish_quant_result1.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/sailfish_quant_result1.tab	Thu Apr 13 08:19:45 2017 -0400
@@ -0,0 +1,16 @@
+Name	Length	EffectiveLength	TPM	NumReads
+NM_001168316	2283	2082.61	12552.5	161.366
+NM_174914	2385	2184.61	111020	1497.1
+NR_031764	1853	1652.61	10345.6	105.535
+NM_004503	1681	1480.61	36162.7	330.503
+NM_006897	1541	1340.61	80240.2	664
+NM_014212	2037	1836.61	4851.45	55
+NM_014620	2300	2099.61	45082	584.273
+NM_017409	1959	1758.61	4329.67	47
+NM_017410	2396	2195.61	3098.99	42
+NM_018953	1612	1411.61	26165.8	227.994
+NM_022658	2288	2087.61	378779	4881
+NM_153633	1666	1465.61	40626.6	367.539
+NM_153693	2072	1871.61	6464.46	74.683
+NM_173860	849	648.611	240280	962
+NR_003084	1640	1439.61	1.04309	0.00926914
diff -r c778eb2f721b -r 536873982e52 test-data/salmon_genMap_result1.tab
--- a/test-data/salmon_genMap_result1.tab	Tue Nov 15 11:23:48 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-Name	Length	EffectiveLength	TPM	NumReads
-baz	1640	1052.77	1.09566	0.00943897
-NR_031764	1853	1214.33	10407.1	103.415
-foo	348.949	235.269	976889	9737.65
-bar	2283	1528.95	12702.4	158.926
diff -r c778eb2f721b -r 536873982e52 test-data/salmon_quant_result1.tab
--- a/test-data/salmon_quant_result1.tab	Tue Nov 15 11:23:48 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,16 +0,0 @@
-Name	Length	EffectiveLength	TPM	NumReads
-NM_001168316	2283	2106.09	12428	158.641
-NM_174914	2385	2208.09	112348	1503.55
-NR_031764	1853	1676.09	10021.5	101.805
-NM_004503	1681	1504.09	36259.8	330.551
-NM_006897	1541	1364.09	80313.1	664
-NM_014212	2037	1860.09	4878.54	55
-NM_014620	2300	2123.09	45879.2	590.368
-NM_017409	1959	1782.09	4351.4	47
-NM_017410	2396	2219.09	3122.74	42
-NM_018953	1612	1435.09	26213	228
-NM_022658	2288	2111.09	381473	4881
-NM_153633	1666	1489.09	40073.1	361.67
-NM_153693	2072	1895.09	6478.45	74.4115
-NM_173860	849	672.091	236161	962
-NR_003084	1640	1463.09	0.00490872	4.3529e-05
diff -r c778eb2f721b -r 536873982e52 tool-data/sailfish_indexes.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/sailfish_indexes.loc.sample	Thu Apr 13 08:19:45 2017 -0400
@@ -0,0 +1,14 @@
+# This is a sample file distributed with Galaxy that is used to define a
+# list of sailfish indices, using three columns tab separated:
+#
+# sailfish_index_id{tab}Sailfish Index desciption{tab}/data/sailfish_indexes/sailfish_index_id/
+#
+# An index can be created with the following command:
+#
+# sailfish index
+#     --transcripts your_transcripts.fasta
+#     --kmerSize 21
+#     --out /data/sailfish_indexes/sailfish_index_id/
+#     --threads 4
+#
+
diff -r c778eb2f721b -r 536873982e52 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Thu Apr 13 08:19:45 2017 -0400
@@ -0,0 +1,6 @@
+<tables>
+    <table name="sailfish_indexes" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="tool-data/sailfish_indexes.loc" />
+    </table>
+</tables>