comparison salmon.xml @ 8:6b0ba6de1424 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 36a1b1d98fc042a232b227f3b012e24739922b56

7:e7e885f718fb

                <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>
        </xml>
        <token name="@VERSION@">0.9.1</token>
    </macros>

    <requirements>
        <requirement type="package" version="1.0.6">bzip2</requirement>
        <requirement type="package" version="@VERSION@">salmon</requirement>

                --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
        &&

                    --unmatedReads <(bzcat < ./single.$ext)
                #else:
                    --unmatedReads ./single.$ext
                #end if
            #else:
                #if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
                    #if $compressed == 'BZ2':
                        --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)
                        --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2)
                    #else: 

                    #else:
                        --mates1 ./mate1.$ext
                        --mates2 ./mate2.$ext
                    #end if
                #end if
                --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
            $adv.reduceGCMemory

                --fldSD $adv.fldSD
            #end if
            #if $adv.forgettingFactor:
                --forgettingFactor $adv.forgettingFactor
            #end if
            #if str($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

            #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
            $adv.writeUnmappedNames
            #if str($adv.writeMappings):
                $adv.writeMappings > ${output_sam}
            #end if
]]>
    </command>

            </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" 
            help="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="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." />
            <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"

                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"

            <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."

                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="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)" />

                </collection>    
            </param> 
            <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" />

8:6b0ba6de1424

                <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>
        </xml>
        <token name="@VERSION@">0.11.2</token>
    </macros>

    <requirements>
        <requirement type="package" version="1.0.6">bzip2</requirement>
        <requirement type="package" version="@VERSION@">salmon</requirement>

                --kmerLen $refTranscriptSource.kmerLen
                --threads "\${GALAXY_SLOTS:-4}"
                --index './index'
                --type '$quasi_orphans.type'
                $perfectHash
            #set $index_path = './index'
        #else:
            #set $index_path = $refTranscriptSource.index.fields.path
        #end if
        &&

                    --unmatedReads <(bzcat < ./single.$ext)
                #else:
                    --unmatedReads ./single.$ext
                #end if
            #else:
                --libType "${single_or_paired.orientation}${single_or_paired.strandedness}"
                #if $single_or_paired.single_or_paired_opts == 'paired_interleaved':
                    #if $compressed == 'BZ2':
                        --mates1 <(bzcat < ./mate1.$ext | seqtk seq -1)
                        --mates2 <(bzcat < ./mate1.$ext | seqtk seq -2)
                    #else: 

                    #else:
                        --mates1 ./mate1.$ext
                        --mates2 ./mate2.$ext
                    #end if
                #end if
            #end if
            --output ./output
            #if str($quasi_orphans.type) == 'quasi':
                --allowOrphans
                $quasi_orphans.validateMappings
                --ma $quasi_orphans.matchScore
                --mp $quasi_orphans.mismatchPenalty
                --go $quasi_orphans.gapOpenPenalty
                --ge $quasi_orphans.gapExtensionPenalty
                --minScoreFraction $quasi_orphans.minScoreFraction
            #end if
            $seqBias
            $gcBias
            $noErrorModel
            --threads "\${GALAXY_SLOTS:-4}"
            --incompatPrior $adv.incompatPrior
            $adv.consistentHits
            $adv.dumpEq
            $adv.reduceGCMemory

                --fldSD $adv.fldSD
            #end if
            #if $adv.forgettingFactor:
                --forgettingFactor $adv.forgettingFactor
            #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
            $adv.useEM
            #if str($adv.numBiasSamples):
                --numBiasSamples $adv.numBiasSamples
            #end if
            #if str($adv.numAuxModelSamples):
                --numAuxModelSamples $adv.numAuxModelSamples

            #if str($adv.numGibbsSamples):
                --numGibbsSamples $adv.numGibbsSamples
            #end if
            #if str($adv.numBootstraps):
                --numBootstraps $adv.numBootstraps
            #end if
            #if str($adv.consensusSlack):
                --consensusSlack $adv.consensusSlack
            #else:
                #if $quasi_orphans.validateMappings:
                    --consensusSlack 1
                #else:
                    --consensusSlack 0
                #end if
            #end if
            $adv.perTranscriptPrior
            #if $adv.vbPrior:
                --vbPrior $adv.vbPrior
            #end if
            $adv.writeUnmappedNames
            --sigDigits $adv.sigDigits
            #if str($adv.writeMappings):
                $adv.writeMappings > ${output_sam}
            #end if
]]>
    </command>

            </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>
            </param>
            <when value="quasi">
                <param argument="--validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
                label="Validate mappings"
                help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
                <param name="matchScore" argument="--ma" type="integer" value="2"
                label="Match Score"
                help="The value given to a match between read and reference nucleotides in an alignment."/>
                <param name="mismatchPenalty" argument="--mp" type="integer" value="4"
                label="Mismatch Penalty"
                help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/>
                <param name="gapOpenPenalty" argument="--go" type="integer" value="5"
                label="Gap Open Penalty"
                help="The value given to a gap opening in an alignment."/>
                <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3"
                label="Gap Extension Penalty"
                help="The value given to a gap extension in an alignment."/>
                <param argument="--minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
                label="Min Score Fraction"
                help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
            </when>  <!-- build-in -->
        </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="--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" 
            help="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." />
        <param argument="--noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
            label="No Error Model"
            help="Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy."/>
        <section name="adv" title="Additional Options">
            <param argument="--writeMappings" type="boolean" truevalue="--writeMappings" falsevalue="" checked="False"
                label="Write Mappings"
                help="If this option is set to 'Yes', then the quasi-mapping results will be written out in SAM-compatible format. By default, output is directed to stdout." />
            <param argument="--incompatPrior" type="float" optional="True" value="9.9999999999999995e-21"

                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="--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"

            <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 default 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."

                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="--useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
                label="Use 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="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=""/>
            <param argument="--sigDigits" type="integer" value="3"
                label="Significant Digits"
                help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
            <param argument="--consensusSlack" type="integer" optional="True"
                label="Consensus Slack"
                help="The amount of slack allowed in the quasi-mapping consensus mechanism.  Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate.  The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
        </section>
    </inputs>

    <outputs>
        <data name="output_quant" format="tabular" from_work_dir="output/quant.sf" label="${tool.name} on ${on_string} (Quantification)" />

                </collection>    
            </param> 
            <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>
        <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" />
            <param name="validateMappings" value="True" />
            <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>
        <test>
            <param name="single_or_paired_opts" value="paired_collection" />
            <param name="input_1">
                <collection type="paired">
                    <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
                    <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
                </collection>    
            </param> 
            <param name="TranscriptSource" value="history" />
            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
            <param name="validateMappings" value="True" />
            <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>
        <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" />
            <param name="useEM" value="True" />
            <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>
        <test>
            <param name="single_or_paired_opts" value="paired_collection" />
            <param name="input_1">
                <collection type="paired">
                    <element name="forward" value="reads_1.fastq" ftype="fastqsanger" />
                    <element name="reverse" value="reads_2.fastq" ftype="fastqsanger" />
                </collection>    
            </param> 
            <param name="TranscriptSource" value="history" />
            <param name="ownFile" value="transcripts.fasta" ftype="fasta" />
            <param name="geneMap" value="gene_map.tab" ftype="tabular" />
            <param name="useEM" value="True" />
            <output name="output_quant">
                <assert_contents>
                    <has_text text="EffectiveLength" />
                    <has_text text="TPM" />
                    <has_text text="NM_001168316" />