annotate prepare.xml @ 0:c34c364ce75d

First commit

<tool id="riboseqr_prepare_input" name="Prepare riboSeqR input" version="0.4.0">
    <description>
        (Step 1) Prepare alignment file (SAM format, Ribo-Seq or RNA-Seq alignments)
        for riboSeqR analysis.
    </description>
    <requirements>
        <requirement type="package" version="3.1.2">R</requirement>
        <requirement type="package" version="6.2">readline</requirement>
        <requirement type="package" version="2.3.10">rpy2</requirement>
        <requirement type="package" version="0.4.0">riboseqr_wrapper_deps</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
    <command interpreter="python">riboseqr/prepare.py
        #set $files_ribo = []
        #set $files_rna = []
        #set $replicates = []

        #for $i, $s in enumerate($rnaseq.datasets)
        #silent $replicates.append($s.replicate_name.value)
        #silent $files_ribo.append($s.ribo_files.file_name)
        #try:
        #silent $s.rna_files
        #except:
        #pass
        #else:
        #silent $files_rna.append($s.rna_files.file_name)
        #end try
        #end for

        #set $ribofiles = ", ".join($files_ribo)
        #set $rnafiles = ", ".join($files_rna)
        #set $replicate_names = ", ".join($replicates)

        --ribo_files "$ribofiles"
        --rna_files "$rnafiles"
        --replicate_names "$replicate_names"
        --seqnames "$seqnames"
        --rdata_save "$rdata_save"
        --sam_format
        --html_file "$html_file"
        --output_path "$html_file.files_path"
    </command>
    <inputs>
        <conditional name="rnaseq">
            <param name="have-rnaseq" type="boolean" truevalue="checked"
                   falsevalue="unchecked" label="Have RNA-Seq data?"/>
            <when value="checked">
                <repeat name="datasets" title="Ribo and RNA-Seq alignment"
                        default="1">
                    <param type="text" name="replicate_name" size="20"
                           label="Provide a common name for each replicate group"
                           value=""/>
                    <param format="sam" name="ribo_files" type="data"
                           label="Ribo-Seq alignment file (SAM)"
                           multiple="false"/>
                    <param format="sam" name="rna_files" type="data"
                           label="RNA-Seq alignment file (SAM)"
                           multiple="false"/>
                </repeat>
            </when>
            <when value="unchecked">
                <repeat name="datasets" title="Ribo-Seq alignment" default="1">
                    <param type="text" name="replicate_name" size="20"
                           label="Provide a common name for each replicate group"
                           value=""/>
                    <param format="sam" name="ribo_files" type="data"
                           label="Ribo-Seq alignment file (SAM)"
                           multiple="false">
                    </param>
                </repeat>
            </when>
        </conditional>
        <param name="seqnames" type="text" area="True" label="Transcript (seqname)
                                                              names to be read" size="3x60"
               help="[Optional] - only the mapped footprints for these transcripts will be
                     used in further riboSeqR analysis. Multiple transcript names should
                     be separated by commas. There should be no quotes around transcript names.">
            <sanitizer>
                <valid>
                    <add value="|"/>
                </valid>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data format="RData" name="rdata_save"
              label="Prepare riboSeqR input (R data file)"/>
        <data format="html" name="html_file"
              label="Prepare riboSeqR input (HTML report)"/>
    </outputs>
    <!--<tests>-->
    <!--<test>-->
    <!--<param name="ribo_files" value="12hRPF.sam" />-->
    <!--<output name="html_file" file="Prepare_riboSeqR_input_(HTML_report).html">-->
    <!--<extra_files type="file" name="RiboSeq file 1" value="RiboSeq file 1"/>-->
    <!--</output>-->
    <!--</test>-->
    <!--</tests>-->
    <help>
Prepare riboSeqR Input
----------------------
riboSeqR version: ``1.0.5``.

This tool can be used to prepare input data for riboSeqR from SAM
format alignments of Ribo or RNA-Seq data to a reference transcriptome. You can
do this alignment manually using bowtie or the
"Transcriptome Mapping" -> "Align to transcriptome using Bowtie"
tool on `RiboGalaxy &lt;http://ribogalaxy.ucc.ie&gt;`_.

The required input format for riboSeqR is mentioned in the
*"Getting Data"* section of the documentation.

How to use?
-----------
Inputs
......
Select SAM format Ribo-Seq alignment files in the input section.

If you have RNA-Seq data, these can be included if the *"Have RNA-Seq data"*
option is checked.

Outputs
.......
The following files will be generated on completion:

#. Prepare riboSeqR input (HTML report) - A HTML file with links to all other
output files.

* Generated riboSeqR format input files of RiboSeq and RNASeq data(if provided).
These files are plain text and lines have the following information -
strand, transcript name, alignment position, sequence.

Please note the alignments are made *0-indexed*.

* R script used in this session.

#. Prepare riboSeqR input (R data file) - used as input for the next step -
*Triplet Periodicity*.

How are the SAM alignments processed?
.....................................
#. Lines starting with ``@`` are ignored.
#. Lines having a ``FLAG=0`` are considered as successful alignments. These are
considered for the next step.
#. Alignment start is located on ``column 4``. These are decremented by
1 as SAM alignments are 1-indexed.
#. riboSeqR input file is written with the strand (``+``), transcript name,
alignment start and the aligned sequence.

riboSeqR functions used
.......................
``readRibodata``.

For detailed description of the functions and the options used, please consult
the riboSeqR documentation.

Links
.....
`riboSeqR &lt;http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html&gt;`_

    </help>
    <citations>
        <citation type="bibtex">
            @Manual{,
            title = {riboSeqR: Analysis of sequencing data from ribosome
            profiling experiments.},
            author = {Thomas J. Hardcastle},
            year = {2014},
            note = {R package version 1.0.5},
            }
        </citation>
    </citations>
</tool>