Mercurial > repos > devteam > express
diff express_wrapper.xml @ 0:7b0708761d05 draft default tip
Imported from capsule None
| author | devteam |
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| date | Mon, 27 Jan 2014 09:27:10 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/express_wrapper.xml Mon Jan 27 09:27:10 2014 -0500 @@ -0,0 +1,125 @@ +<tool id="express" name="eXpress" version="1.1.1"> + <description>Quantify the abundances of a set of target sequences from sampled subsequences</description> + <requirements> + <requirement type="package" version="1.1.1">eXpress</requirement> + </requirements> + <command> + express --no-update-check + ## Additional parameters. + #if $additional_params.use_additional == "yes": + -B $additional_params.additional_batch + -O $additional_params.additional_online + + #if str( $additional_params.calc_covar ) == 'yes': + --calc-covar + #end if + + -m $additional_params.mean_fragment_length + + -s $additional_params.fragment_length_deviation + #end if + + ## Input files + $multiFasta + $bamOrSamFile + </command> + <inputs> + <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." /> + <param format="sam,bam" name="bamOrSamFile" type="data" label="Alignments in the BAM or SAM format" help="The set of aligned reads." /> + <conditional name="additional_params"> + <param name="use_additional" type="select" label="Use Additional Parameters?"> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <when value="no"> + </when> + <when value="yes"> + <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."/> + <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."/> + <param name="calc_covar" type="select" label="Calculate the covariance between targets and outputs?" help="This calculation requires slightly more time and memory."> + <option value="no">No</option> + <option value="yes">Yes</option> + </param> + <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."/> + <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."/> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="params" from_work_dir="params.xprs"/> + <data format="txt" name="results" from_work_dir="results.xprs"/> + <data format="txt" name="varcov" from_work_dir="varcov.xprs"> + <filter>additional_params[ 'use_additional' ] == "yes" and additional_params[ 'calc_covar' ] == "yes"</filter> + </data> + </outputs> + + <tests> + <!-- Test for the most simple case : Running eXpress with a .bam file and a .fasta file --> + <test> + <!-- TopHat commands: + eXpress Trinity.fasta hits.bam + --> + <param name="bamOrSamFile" ftype="bam" value="eXpress_hits.bam"/> + <param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/> + <param name="use_additional" value="no"/> + + <output name="params" file="eXpress_params.xprs" lines_diff="300"/> + <output name="results" file="eXpress_results.xprs" lines_diff="10"/> + </test> + <!-- Test for an other simple case : Running eXpress with a .sam file and a .fasta file --> + <test> + <!-- TopHat commands: + eXpress Trinity.fasta hits.sam + --> + <param name="bamOrSamFile" ftype="sam" value="eXpress_hits.sam"/> + <param name="multiFasta" ftype="fasta" value="eXpress_Trinity.fasta"/> + <param name="use_additional" value="no"/> + + <output name="params" file="eXpress_params_sam.xprs" lines_diff="300"/> + <output name="results" file="eXpress_results_sam.xprs" lines_diff="10"/> + </test> + <!-- Test for a complex case : All the parameters has been activated and modified --> + <test> + <!-- TopHat commands: eXpress -B 1 -O 1 ++calc-covar -m 300 -s 85 Trinity.fasta hits.sam --> + <param name="bamOrSamFile" ftype="sam" value="eXpress_hits_all_params.bam"/> + <param name="multiFasta" ftype="fasta" value="eXpress_Trinity_all_params.fasta"/> + + <param name="use_additional" value="yes"/> + <param name="additional_batch" value="1"/> + <param name="additional_online" value="1" /> + <param name="calc_covar" value="yes"/> + <param name="mean_fragment_length" value="300"/> + <param name="fragment_length_deviation" value="85"/> + + <output name="params" file="eXpress_params_all_params.xprs" lines_diff="300"/> + <output name="results" file="eXpress_results_all_params.xprs" lines_diff="10"/> + <output name="varcov" file="eXpress_varcov_all_params.xprs"/> + </test> + </tests> + <help> +**eXpress Overview** + +eXpress is a streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences. Example applications include transcript-level RNA-Seq quantification, allele-specific/haplotype expression analysis (from RNA-Seq), transcription factor binding quantification in ChIP-Seq, and analysis of metagenomic data. + +.. _Ensembl: http://bio.math.berkeley.edu/eXpress/ + +----- + +**Input format** + +eXpress requires two input files: + +- A multi-FASTA file containing the transcript sequences. +- Read alignments to the multi-FASTA file in BAM or SAM format. + +------ + +**Outputs** + +- The output for eXpress is saved in a file called results.xprs in an easy-to-parse tab-delimited format. + +- Also, params.xprs contains the values of the other parameters (besides abundances and counts) estimated by eXpress. + +- If you choose to use to calculate the covariance between targets and outputs, an other output would be : varcov.xprs. + </help> +</tool>