Mercurial > repos > bzonnedda > conifer2
changeset 15:8354ca911187 draft
Uploaded
author | bzonnedda |
---|---|
date | Tue, 21 Feb 2017 06:04:21 -0500 |
parents | a899c18be1f6 |
children | 558f04d13648 |
files | c_plotcalls.xml |
diffstat | 1 files changed, 57 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/c_plotcalls.xml Tue Feb 21 06:04:21 2017 -0500 @@ -0,0 +1,57 @@ +<tool id="conifer_plotcalls" name="CoNIFER plot caller" version="1.0"> + <description>cnv caller</description> + <command interpreter="perl"> + conifer_wrapper.pl --input $input --regions $plot_option.regions --html_file $html_file --html_folder $html_file.files_path + #if str($plot_option.plot_option_select) == "single" + --sample "$plot_option.sample" + #else + --window $plot_option.window + --multiple + #end if + 2>&1 + </command> + <inputs> + <param format="hdf5" name="input" type="data" label="CoNIFER output analysis file (hdf5)"/> + <conditional name="plot_option"> + <param name="plot_option_select" type="select" label="Single or multiple regions?"> + <option value="single" selected="true">Single region</option> + <option value="multiple">Multiple regions</option> + </param> + <when value="single"> + <param name="regions" type="text" size="50" optional="false" label="Region" help="Region for the plot (i.e. chr1:1000-2000)"/> + <param name="sample" type="text" size="50" optional="true" value="" label="Sample" help="Sample names to be highlighted in the plot (optional)"/> + </when> + <when value="multiple"> + <param format="tabular" name="regions" type="data" label="CoNIFER output calls file (tabular)"/> + <param name="window" size="10" type="integer" value="50" label="Window"/> + </when> + </conditional> + </inputs> + <outputs> + <data format="html" name="html_file" label="${tool.name} on ${on_string}" /> + </outputs> +<help> +**What it does** + +Draw a HTML page with CNV plots. It accepts as input either a single region or a file with CoNIFER calls. + +**License and citation** + +This Galaxy tool is Copyright © 2013 `CRS4 Srl.`_ and is released under the `MIT license`_. + +.. _CRS4 Srl.: http://www.crs4.it/ +.. _MIT license: http://opensource.org/licenses/MIT + +If you use this tool in Galaxy, please cite |Cuccuru2014|_. + +.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted +.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135 + +This tool uses CoNIFER, which is licensed separately. Please cite: + +- |Krumm2012|_. + +.. |Krumm2012| replace:: (Krumm et al., 2012) Copy number variation detection and genotyping from exome sequence data. Genome research. +.. _Krumm2012: http://genome.cshlp.org/content/22/8/1525.full?sid=4a7a300a-b960-4544-8611-effc3315411c + </help> +</tool>