difftrans.xml

<tool id="difftrans" name="Differential Translation Analysis" version="0.1.0">
    <description>
        (Step 4) Get Ribo and RNA-Seq counts with riboSeqR. Perform differential
        translation analysis with baySeq.
    </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/difftrans.py
        --rdata_load "$rdata_load"
        --slice_lengths "$slice_lengths"
        --frames "$frames"
        --group1 "$group1"
        --group2 "$group2"
        --num_counts "$num_counts"
        --normalize "$normalize"
        --html_file "$html_file"
        --output_path "$html_file.files_path"
    </command>
    <inputs>
        <param name="rdata_load" format="RData" type="data"
               label="Select Metagene analysis (R data file)"
               multiple="false">
            <validator type="expression"
                       message="Please check if the correct RDA file is selected">value.name == "Metagene analysis (R data file)"</validator>
        </param>
        <param name="slice_lengths" type="text"
               label="&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;Ribo and RNA counts (riboSeqR)&lt;/font&gt;&lt;/h4&gt;Lengths of ribosome footprints to inform count data"
               value="27,28">
            <validator type="empty_field" message="Field requires a value"/>
        </param>
        <param name="frames" type="text" label="Frames corresponding to the lengths of ribosome footprints given above"
               value="0,2">
            <validator type="empty_field" message="Field requires a value"/>
        </param>
        <param type="text" name="group1"
               label="&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;baySeq Analysis&lt;/font&gt;&lt;/h4&gt;Group (model) structure to test on the data"
               help="ex. 1,1,1,1">
            <validator type="empty_field" message="Field requires a value"/>
        </param>
        <param type="text" name="group2" label="and" help="ex. WT,WT,M,M">
            <validator type="empty_field" message="Field requires a value"/>
        </param>
        <param type="integer" name="num_counts"
               label="How many results to return? (top candidates for differential translation)"
               value="10"/>

        <param name="normalize" type="boolean" checked="no"
               label="Normalize data?" falsevalue="FALSE" truevalue="TRUE"/>
    </inputs>
    <outputs>
        <data format="html" name="html_file"
              label="Differential Translation Analysis (HTML report)"/>
    </outputs>
    <!--<tests>-->
    <!--<test>-->
    <!--<param name="rdata_load" value="Metagene analysis (R data file)" ftype="RData" />-->
    <!--<param name="slice_lengths" value="27,28"/>-->
    <!--<param name="frames" value="0,2"/>-->
    <!--<param name="group1" value="1,1,1,1"/>-->
    <!--<param name="group2" value="WT,WT,M,M"/>-->
    <!--<param name="normalize" checked="yes"/>-->
    <!--<output name="html_file" file="Differential_Translation_Analysis_(HTML_report)">-->
    <!--<extra_files type="file" name="RNACounts.csv" value="RNACounts.csv" ftype="csv"/>-->
    <!--<extra_files type="file" name="RiboCounts.csv" value="RiboCounts.csv" ftype="csv"/>-->
    <!--<extra_files type="file" name="TopCounts.csv" value="TopCounts.csv" ftype="csv"/>-->
    <!--</output>-->
    <!--</test>-->
    <!--</tests>-->
    <help>
Differential Translation Analysis
---------------------------------
riboSeqR version: ``1.0.5``, baySeq version: ``2.0.50``.

This tool can be used for obtaining the Ribo and RNA-Seq counts and
finding the
top candidates for differential translation using baySeq. The input is
the
R data file from the Metagene analysis step.

How to use?
-----------
Inputs
......
Select *Metagene analysis (R data file)*, enter lengths of ribosome
footprints
and the frames. For baySeq analysis, enter the group model and the
number of
results to return. Please refer to the documentation for explanation of
the
options.

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

*Differential Translation Analysis (HTML report)*

A HTML file with results, links to other output files and the R script
used for
the session.

riboSeqR functions used
.......................
``sliceCounts``, ``rnaCounts``.

baySeq functions used
.....................
``getLibsizes``, ``getPriors``, ``getLikelihoods``, ``topCounts``.

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

Links
.....
* `riboSeqR &lt;http://bioconductor.org/packages/3.0/bioc/html/riboSeqR.html&gt;`_
* `baySeq &lt;http://bioconductor.org/packages/3.0/bioc/html/baySeq.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>
        <citation type="bibtex">
            @Manual{,
            title = {baySeq: Empirical Bayesian analysis of patterns of
            differential
            expression in count data},
            author = {Thomas J. Hardcastle},
            year = {2012},
            note = {R package version 2.0.50},
            }
        </citation>
        <citation type="doi">10.1186/1471-2105-11-422</citation>
    </citations>
</tool>