Mercurial > repos > biotechcoder > riboseqr_wrapper
diff triplet.xml @ 0:e01de823e919 draft default tip
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| author | biotechcoder |
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| date | Fri, 01 May 2015 05:41:51 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/triplet.xml Fri May 01 05:41:51 2015 -0400 @@ -0,0 +1,151 @@ +<tool id="riboseqr_triplet_periodicity" name="Triplet Periodicity" + version="0.4.0"> + <description> + (Step 2) Plot triplet periodicity for different read lengths. + </description> + <requirements> + <requirement type="R-module">riboSeqR</requirement> + </requirements> + <command interpreter="python">riboseqr/triplet.py + --rdata_load "$rdata_load" + --fasta_file "$fasta_file" + --start_codons "$start_codons" + --stop_codons "$stop_codons" + --include_lengths "$include_lengths" + --analyze_plot_lengths "$analyze_plot_lengths" + --text_legend "$text_legend" + --rdata_save "$rdata_save" + --html_file "$html_file" + --output_path "$html_file.files_path" + </command> + <inputs> + <param name="rdata_load" type="data" format="rda" + label="Select prepared riboSeqR input (R data file)" + multiple="false" optional="false" + help="<br><h4><font color="#666666">findCDS + parameters</font></h4>"> + <validator type="expression" + message="Please check if the correct RDA file is selected">value.name == "Prepare riboSeqR input (R data file)"</validator> + </param> + + <param format="fasta" name="fasta_file" type="data" + label="Select FASTA file of the reference transcriptome" + help="This Fasta file is used to find start (ATG) and + stop codons(TAG, TAA, TGA) in frame with one another. If no files + are listed, you will need to upload a FASTA file of the reference + transcriptome."> + <validator type="empty_field" message="Field requires a value"/> + </param> + + <param name="start_codons" type="text" size="15" value="ATG" + label="Start codon(s) to use" + help="Default is ATG. Multiple values must be comma-separated."> + <validator type="empty_field" message="Field requires a value"/> + </param> + + <param name="stop_codons" type="text" size="15" value="TAG, TAA, TGA" + label="Stop codon(s) to use" + help="Default is TAG, TAA, TGA. Multiple values must be comma-separated. + <h4><font color="#666666">frameCounting + parameters</font></h4>"> + <validator type="empty_field" message="Field requires a value"/> + </param> + + <param name="include_lengths" type="text" + label="Lengths of ribosome footprints + to be included" + help="Here, you can specify the lengths of ribosome footprints to + be included in the riboData object. <br>For example 25:30. + Range, semi-colon separated. <h4><font color="#666666">readingFrame + parameters</font></h4>" value="25:30"/> + + <param name="analyze_plot_lengths" type="text" + label="Lengths of reads to be analysed for frame-shift, or to be plotted" + help="[Optional] If omitted, all lengths will be plotted. + <br>For example 26:30. Range, semi-colon separated. + <h4><font color="#666666">plotFS + parameters</font></h4>" value="26:30"/> + + <param name="text_legend" type="text" size="30" + value='Frame 0, Frame 1, Frame 2' + label="Text for legend used in the + plot" help="Comma-separated values."/> + </inputs> + <outputs> + <data format="rda" name="rdata_save" + label="Triplet periodicity (R data file)"/> + <data format="html" name="html_file" + label="Triplet periodicity (HTML report)"/> + </outputs> + <tests> + <test> + <param name="rdata_load" value="Prepare riboSeqR input (R data file)" ftype="rda"/> + <param name="fasta_file" value="zebrafish.fasta.bz2" /> + <param name="include_lengths" value="25:30" /> + <param name="analyze_plot_lengths" value="26:30" /> + <output name="html_file" file="Triplet_periodicity_(HTML_report).html"> + <extra_files type="file" name="Periodicity-plot.png" value="Periodicity-plot.png" ftype="png"/> + <extra_files type="file" name="Periodicity-plot.pdf" value="Periodicity-plot.pdf" ftype="pdf"/> + </output> + </test> + </tests> + <help> +About +----- +This tool can be used to plot triplet periodicity for different read lengths. +The inputs for this program are + +#. Prepare riboSeqR input (R data file) from the previous step. +#. FASTA format file of the reference transcriptome. + +riboSeqR version: **1.0.4**. + +How to use? +----------- +Inputs +...... +Select prepared R data file from the previous step. + +Select FASTA format file of the reference transcriptome, review/change other +options if necessary and execute program. + +Outputs +....... +The following files will be generated on completion: + +#. Triplet periodicity (HTML report) + + A HTML file with results and links to other output files - triplet + periodicity plot (PDF) and R script used for the session. + +#. Triplet periodicity (R data file) + + Used as input for the next step - *Metagene analysis*. + +riboSeqR functions used +....................... +findCDS, frameCounting, readingFrame and plotFS. + +For detailed description of the functions and the options used, please consult +the riboSeqR documentation. + +Links +..... +* `Bioconductor package information on riboSeqR`__ +* riboSeqR - `Reference manual`_ +* riboSeqR - `Introduction and workflow example`_ + +.. _riboSeqR: http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html + +__ riboSeqR_ + +.. _manual: http://bioconductor.org/packages/3.0/bioc/manuals/riboSeqR/man/riboSeqR.pdf + +.. _`Reference manual`: manual_ + +.. _documentation: http://bioconductor.org/packages/3.0/bioc/vignettes/riboSeqR/inst/doc/riboSeqR.pdf + +.. _`Introduction and workflow example`: documentation_ + + </help> +</tool>