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Added eXpress sam format support + 5 parameters (-B, -O, --calc-covar, -m, -s) with their associated tests
This commit is contained in:
Remi Marenco
@@ -362,7 +362,7 @@
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<tool file="ngs_rna/cufflinks_wrapper.xml" />
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<tool file="ngs_rna/cuffcompare_wrapper.xml" />
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<tool file="ngs_rna/express_wrapper.xml" />
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<tool file="ngs_rna/cuffmerge_wrapper.xml" />
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<tool file="ngs_rna/cuffmerge_wrapper.xml" />
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<tool file="ngs_rna/cuffdiff_wrapper.xml" />
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<!-- Trinity is very memory-intensive and should only be enabled/run
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on instances with sufficient resources.
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@@ -3,27 +3,97 @@
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<requirements>
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<requirement type="binary">eXpress</requirement>
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</requirements>
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<command>express --no-update-check $multiFasta $bamFile</command>
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<command>
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express --no-update-check
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## Additional parameters.
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#if $additional_params.use_additional == "yes":
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-B $additional_params.additional_batch
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-O $additional_params.additional_online
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#if str( $additional_params.calc_covar ) == 'yes':
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--calc-covar
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#end if
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-m $additional_params.mean_fragment_length
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-s $additional_params.fragment_length_deviation
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#end if
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## Input files
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$multiFasta
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$bamOrSamFile
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</command>
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<inputs>
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<param format="fasta" name="multiFasta" type="data" label="A set of target references (annotation) in multi-FASTA format" help="The multi-FASTA file can also be a fasta file" />
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<param format="bam" name="bamFile" type="data" label="Alignments in the BAM format" help="The set of aligned reads" />
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<param format="fasta" name="multiFasta" type="data" label="A set of target references (annotation) in multi-FASTA format" help="The multi-FASTA file can also be a fasta file." />
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<param format="sam,bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." />
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<conditional name="additional_params">
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<param name="use_additional" type="select" label="Use Additional Parameters?">
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<when value="no">
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</when>
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<when value="yes">
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<param name="additional_batch" type="integer" label="Additional batch EM rounds" value="0" help="0 is default. Can improve accuracy at the cost of time."/>
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<param name="additional_online" type="integer" label="Additional online EM rounds" value="0" help="0 is default. Can improve accuracy at the cost of time."/>
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<param name="calc_covar" type="select" label="Calculate the covariance between targets and outputs?" help="This calculation requires slightly more time and memory.">
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<option value="no">No</option>
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<option value="yes">Yes</option>
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</param>
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<param name="mean_fragment_length" type="integer" label="Specifies the mean fragment length" value="200" help="200 is default. While the empirical distribution is estimated from paired-end reads on-the-fly, this value paramaterizes the prior distribution."/>
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<param name="fragment_length_deviation" type="integer" label="Specified the fragment length standard deviation" value="60" help="60 is default. While the empirical distribution is estimated from paired-end reads on-the-fly, this value paramaterizes the prior distribution."/>
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="txt" name="params" from_work_dir="params.xprs"/>
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<data format="txt" name="results" from_work_dir="results.xprs"/>
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<data format="txt" name="varcov" from_work_dir="varcov.xprs">
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<filter>additional_params[ 'calc_covar' ] == "yes"</filter>
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</data>
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</outputs>
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<tests>
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<!-- Test for the most simple case : Running eXpress with a .bam file and a .fasta file -->
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<test>
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<!-- TopHat commands:
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eXpress hits.bam Trinity.fasta
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eXpress Trinity.fasta hits.bam
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-->
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<param name="bamFile" ftype="bam" value="eXpress_hits.bam"/>
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<param name="bamOrSamFile" ftype="bam" value="eXpress_hits.bam"/>
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<param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/>
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<param name="use_additional" value="no"/>
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<output name="params" file="eXpress_params.xprs" lines_diff="300"/>
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<output name="results" file="eXpress_results.xprs" lines_diff="10"/>
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</test>
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<!-- Test for an other simple case : Running eXpress with a .sam file and a .fasta file -->
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<test>
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<!-- TopHat commands:
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eXpress Trinity.fasta hits.sam
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-->
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<param name="bamOrSamFile" ftype="sam" value="eXpress_hits.sam"/>
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<param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/>
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<param name="use_additional" value="no"/>
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<output name="params" file="eXpress_params_sam.xprs" lines_diff="300"/>
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<output name="results" file="eXpress_results_sam.xprs" lines_diff="10"/>
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</test>
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<!-- Test for a complex case : All the parameters has been activated and modified -->
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<test>
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<!-- TopHat commands: eXpress -B 1 -O 1 ++calc-covar -m 300 -s 85 Trinity.fasta hits.sam -->
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<param name="bamOrSamFile" ftype="sam" value="eXpress_hits_all_params.bam"/>
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<param name="multiFasta" ftype="fasta" value="eXpress_Trinity_all_params.fasta"/>
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<output name="params" file="eXpress_params.xprs" />
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<output name="results" file="eXpress_results.xprs"/>
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<param name="use_additional" value="yes"/>
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<param name="additional_batch" value="1"/>
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<param name="additional_online" value="1" />
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<param name="calc_covar" value="yes"/>
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<param name="mean_fragment_length" value="300"/>
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<param name="fragment_length_deviation" value="85"/>
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<output name="params" file="eXpress_params_all_params.xprs" lines_diff="300"/>
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<output name="results" file="eXpress_results_all_params.xprs" lines_diff="10"/>
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<output name="varcov" file="eXpress_varcov_all_params.xprs"/>
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</test>
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</tests>
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<help>
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@@ -40,7 +110,7 @@ eXpress is a streaming tool for quantifying the abundances of a set of target se
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eXpress requires two input files:
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- A multi-FASTA file containing the transcript sequences.
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- Read alignments to the multi-FASTA file in BAM format.
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- Read alignments to the multi-FASTA file in BAM or SAM format.
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------
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@@ -48,6 +118,8 @@ eXpress requires two input files:
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- The output for eXpress is saved in a file called results.xprs in an easy-to-parse tab-delimited format.
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- Also, params.xprs contains the values of the other parameters (besides abundances and counts) estimated by eXpress.
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- Also, params.xprs contains the values of the other parameters (besides abundances and counts) estimated by eXpress.
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- If you choose to use to calculate the covariance between targets and outputs, an other output would be : varcov.xprs.
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</help>
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</tool>
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