Mercurial > repos > rnateam > piranha
changeset 0:f7f366ede872 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/piranha commit ba69207568a546d7c3b71a144f78095811e3e99a-dirty
author | rnateam |
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date | Fri, 24 Jul 2015 06:05:39 -0400 |
parents | |
children | |
files | piranha.xml test-data/testPrianha_zntb_unbinned.bam test-data/zntbr_unbinned_response.bed test-data/ztnbBinningTestModelOutput.expected.xml test-data/ztnbSimpleTest_output.expected.bed test-data/ztnbSimpleTest_response.bed test-data/ztnbrBinningTestModelOutput.expected.xml test-data/ztnbr_binning_cov1.bed test-data/ztnbr_binning_cov2.bed |
diffstat | 9 files changed, 74211 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/piranha.xml Fri Jul 24 06:05:39 2015 -0400 @@ -0,0 +1,162 @@ +<tool id="piranha" name="Piranha" version="0.1.0"> + <description>peak-caller for CLIP- and RIP-Seq data</description> + <requirements> + <requirement type="package" version="1.2.1">piranha</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + ln -s $input ./foo.$input.ext && + + Piranha + $sort + #if $p_threshold: + -p $p_threshold + #end if + $no_pval_correct + #if $background_thresh: + -a $background_thresh + #end if + #if $bin_size_reponse: + -b $bin_size_reponse + #end if + #if $bin_size_covars: + -i $bin_size_covars + #end if + #if $bin_size_both: + -z $bin_size_both + #end if + #if $merge_bins.merge=="yes": + -u $merge_bins.cluster_dist + #else: + -u $merge_bins.merge + #end if + $print_covars + $fit + #if $dist: + -d $dist + #end if + $fitMethod + #if $model: + -m $model + #end if + $stranded + $no_normalisation + $log_covars + ./foo.$input.ext + #for $covariate in $covariates: + $covariate.covariate_file + #end for + + -o ./piranha.out + ]]></command> + <inputs> + <param name="input" type="data" format="bed,bam" label="Choose input BED or BAM file"/> + <repeat name="covariates" title="Choose covariate"> + <param name="covariate_file" type="data" format="bed" label="Choose covariate BED file"/> + </repeat> + <param name="sort" type="boolean" label="Is your input file already sorted?" checked="False" falsevalue="-s" truevalue=""/> + <param name="p_threshold" type="float" min="0" max="1" value="1" label="Significance threshold for sites"/> + <param name="no_pval_correct" type="boolean" checked="False" falsevalue="" truevalue="-c" + label="Disable p-values correction for multiple hypothesis testing?" help="We correct by default using B & H."/> + <param name="background_thresh" type="float" optional="true" + label="Indicates that this proportion of the lowest scores should be considered the background"/> + <param name="bin_size_reponse" type="integer" optional="true" + label="Indicates that input is raw reads and should be binned into bins of this size"/> + <param name="bin_size_covars" type="integer" optional="true" + label="Indicates that the covariates are raw reads and should be binned into bins of this size"/> + <param name="bin_size_both" type="integer" optional="true" label="Synonymous with -b x -i x for any x"/> + <conditional name="merge_bins"> + <param name="merge" type="select" label="Merge significant bins within certain distance?"> + <option value="yes">Yes</option> + <option value="0" selected="true">No</option> + </param> + <when value="yes"> + <param name="cluster_dist" type="integer" value="1" label="Merge significant bins within this distance" + help="Default is 1 (merge adjacent)"/> + </when> + </conditional> + <param name="print_covars" type="boolean" checked="True" truevalue="" falsevalue="-r" label="Print covariate values in output" help="(-r)" /> + <param name="fit" type="boolean" checked="False" truevalue="-f" falsevalue="" label="Fit only" /> + <param name="dist" type="select" label="Select distribution type"> + <option value="">None</option> + <option value="Poisson">Poisson</option> + <option value="NegativeBinomial">NegativeBinomial</option> + <option value="ZeroTruncatedPoisson">ZeroTruncatedPoisson</option> + <option value="ZeroTruncatedNegativeBinomial">ZeroTruncatedNegativeBinomial</option> + <option value="PoissonRegression">PoissonRegression</option> + <option value="NegativeBinomialRegression">NegativeBinomialRegression</option> + <option value="ZeroTruncatedPoissonRegression">ZeroTruncatedPoissonRegression</option> + <option value="ZeroTruncatedNegativeBinomialRegression">ZeroTruncatedNegativeBinomialRegression</option> + </param> + <param name="fitMethod" type="boolean" checked="False" truevalue="-t" + falsevalue="" label="Use component fitting method" help="(-t)"/> + <param name="model" type="data" optional="True" format="xml" label="Select the model file"/> + + <param name="stranded" type="boolean" checked="True" truevalue="" + falsevalue="-x" label="Preserve strand information" + help="If not set all the peaks will be associated to the positive strand. (-x)"/> + <param name="no_normalisation" type="boolean" checked="yes" falsevalue="-n" + truevalue="" label="Normalise covariates?" help="(-n)"/> + <param name="log_covars" type="boolean" checked="False" truevalue="-l" + falsevalue="" label="Convert covariates to log scale?" help="(-l)"/> + </inputs> + <outputs> + <data format="tabular" name="output_bed" from_work_dir="piranha.out" + label="${tool.name} on ${on_string}: BED with p-values"> + <filter>fit is False</filter> + </data> + <data format="xml" name="output_xml" from_work_dir="piranha.out" + label="${tool.name} on ${on_string}: Model file"> + <filter>fit is True</filter> + </data> + </outputs> + <tests> + <test> + <param name="input" value="zntbr_unbinned_response.bed" ftype="bed"/> + <repeat name="covariates"> + <param name="covariate_file" value="ztnbr_binning_cov1.bed" ftype="bed"/> + </repeat> + <repeat name="covariates"> + <param name="covariate_file" value="ztnbr_binning_cov2.bed" ftype="bed"/> + </repeat> + <param name="fit" value="True"/> + <param name="bin_size_reponse" value="1"/> + <param name="background_thresh" value="1"/> + <output name="output_xml" file="ztnbrBinningTestModelOutput.expected.xml" ftype="xml"/> + </test> + <test> + <param name="input" value="testPrianha_zntb_unbinned.bam" ftype="bam"/> + <param name="fit" value="True"/> + <param name="bin_size_reponse" value="1"/> + <param name="background_thresh" value="1"/> + <output name="output_xml" file="ztnbBinningTestModelOutput.expected.xml" ftype="xml"/> + </test> + <test> + <param name="input" value="ztnbSimpleTest_response.bed" ftype="bed"/> + <param name="no_pval_correct" value="True"/> + <param name="p_threshold" value="1"/> + <param name="background_thresh" value="1"/> + <param name="-" value="ZeroTruncatedNegativeBinomial"/> + <output name="output_xml" file="ztnbSimpleTest_output.expected.bed" ftype="tabular"/> + </test> + </tests> + <help><![CDATA[ +**What it does** + +`Piranha <http://smithlabresearch.org/software/piranha/>`_ is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process. + + + ]]></help> + <citations> + <citation type="bibtex"> + @ARTICLE{bgruening_galaxytools, + Author = {Björn Grüning, Cameron Smith, Torsten Houwaart, Nicola Soranzo, Eric Rasche}, + keywords = {bioinformatics, ngs, galaxy, cheminformatics, rna}, + title = {{Galaxy Tools - A collection of bioinformatics and cheminformatics tools for the Galaxy environment}}, + url = {https://github.com/bgruening/galaxytools} + } + </citation> + </citations> +</tool>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ztnbBinningTestModelOutput.expected.xml Fri Jul 24 06:05:39 2015 -0400 @@ -0,0 +1,5 @@ +<ZTNB> + <mean> 156.449 </mean> + + <alpha> 1.31103 </alpha> +</ZTNB>
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ztnbrBinningTestModelOutput.expected.xml Fri Jul 24 06:05:39 2015 -0400 @@ -0,0 +1,5 @@ +<ZeroTruncatedNegativeBinomialRegression> +<coefficient> 0.2419 </coefficient> +<coefficient> 2.67587 </coefficient> +<alpha>3.82529</alpha> +</ZeroTruncatedNegativeBinomialRegression>
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