view metagene.xml @ 5:423ad61697c4

Bugfix 1: [triplet] Lengths (frameCounting) if given should be a range (not zero). readingFrame function fails with subscript out of bounds. Bugfix 2: [triplet] Check if transcript name in SAM matches the name in FASTA. Produce an error message if it's not. This fixes the problem where an empty plot is produced (no bars). [ribosome_profile] - A proper error message is now produced if an invalid transcript name is provided. Updated test data

<tool id="riboseqr_metagene" name="Metagene Analysis" version="0.4.0">
    <description>
        (Step 3) Metagene analysis using riboSeqR.
    </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>
    <command interpreter="python">riboseqr/metagene.py
        --rdata_load "$rdata_load"
        --selected_lengths "$selected_lengths"
        --selected_frames "$selected_frames"
        --hit_mean "$hit_mean"
        --unique_hit_mean "$unique_hit_mean"
        --ratio_check "$ratio_check"
        --plot_lengths "$plot_lengths"
        --min5p "$min5p"
        --max5p "$max5p"
        --min3p "$min3p"
        --max3p "$max3p"
        --cap "$cap"
        --plot_title "$plot_title"
        --rdata_save "$rdata_save"
        --html_file "$html_file"
        --output_path "$html_file.files_path"
    </command>
    <inputs>
        <param name="rdata_load" type="data" format="rda"
               label="Select Triplet periodicity (R data file)"
               multiple="false" optional="false"
               help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;filterHits parameters (footprint reads to be used in the analysis)&lt;/font&gt;&lt;/h4&gt;">
            <validator type="expression"
                       message="Please check if the correct RDA file is selected">value.name == "Triplet periodicity (R data file)"</validator>
        </param>

        <param name="selected_lengths" type="text" value="27"
               label="Length of ribosome footprint
                      reads to be used in filtering (lengths)"
               help="ex: 27,28. Multiple values must be comma-separated.
                     Please consult Periodicity-report.txt." optional="false">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="selected_frames" type="text" value=""
               label="Frames of the ribosome footprint reads to be used in filtering
                      (frames)"
               help="ex: 1,0. Should be of equal length to the lengths parameter above.
                     Multiple values must be comma-separated.
                     Please consult the periodicity report from previous step."
               optional="false">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="hit_mean" size="4" type="integer" value="10"
               label="Mean number of hits within a replicate group that
                      should be observed to pass filtering (hitMean)" optional="false">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="unique_hit_mean" size="4" type="integer" value="1"
               label="Mean number of unique sequences within a replicate group
                      that should be observed to pass filtering
                      (unqhitMean)" optional="false">
            <validator type="empty_field" message="Field requires a value"/>
        </param>

        <param name="ratio_check" type="boolean" checked="yes"
               label="Check the ratios of the expected phase to maximal phase
                      within the putative coding sequence
                      (ratioCheck)" falsevalue="FALSE"
               truevalue="TRUE"
               help="&lt;br&gt;&lt;h4&gt;&lt;font color=&quot;#666666&quot;&gt;plotCDS parameters&lt;/font&gt;&lt;/h4&gt;"/>

        <param name="plot_lengths" type="text"
               label="Length of footprints to be
                      plotted (lengths)"
               help="Multiple values should be comma-separated.
                     In that case, multiple plots will be produced" value="27"/>

        <param name="min5p" label="The distance upstream of the translation
                                   start to be plotted (min5p)" value="-20" type="integer"/>

        <param name="max5p" label="The distance downstream of the translation
                                   start to be plotted (max5p)" value="200" type="integer"/>

        <param name="min3p" label="The distance upstream of the translation
                                   end to be plotted (min3p)" value="-200" type="integer"/>

        <param name="max3p" label="The distance downtream of the translation
                                   end to be plotted (max3p)" value="20" type="integer"/>

        <param name="cap"
               label="If given, caps the height of plotted values (cap)"
               value="" type="integer" optional="true"/>

        <param name="plot_title"
               label="Title of the plot (main)" type="text" size="30"
               value=""/>
    </inputs>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
    <outputs>
        <data format="rda" name="rdata_save"
              label="Metagene analysis (R data file)"/>
        <data format="html" name="html_file"
              label="Metagene analysis (HTML report)"/>
    </outputs>
    <!--<tests>-->
    <!--<test>-->
    <!--<param name="rdata_load" value="Triplet periodicity (R data file)" ftype="rda"/>-->
    <!--<param name="hit_mean" value="50"/>-->
    <!--<param name="unique_hit_mean" value="10"/>-->
    <!--<param name="min5p" value="-20"/>-->
    <!--<param name="max5p" value="200"/>-->
    <!--<param name="min3p" value="-200"/>-->
    <!--<param name="max3p" value="20"/>-->
    <!--<param name="cap" value=""/>-->
    <!--<param name="plot_title" value=""/>-->
    <!--<output name="rdata_save" file="Metagene analysis (R data file)" ftype="rda"/>-->
    <!--<output name="html_file" file="Metagene_analysis_(HTML_report).html">-->
    <!--<extra_files type="file" name="Metagene-analysis-plot1.pdf" value="Metagene-analysis-plot1.pdf"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot1_1.png" value="Metagene-analysis-plot1_1.png"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot1_2.png" value="Metagene-analysis-plot1_2.png"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot1_3.png" value="Metagene-analysis-plot1_3.png"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot1_4.png" value="Metagene-analysis-plot1_4.png"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot2.pdf" value="Metagene-analysis-plot2.pdf"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot2_1.png" value="Metagene-analysis-plot2_1.png"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot2_2.png" value="Metagene-analysis-plot2_2.png"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot2_3.png" value="Metagene-analysis-plot2_3.png"/>-->
    <!--<extra_files type="file" name="Metagene-analysis-plot2_4.png" value="Metagene-analysis-plot2_4.png"/>-->
    <!--</output>-->
    <!--</test>-->
    <!--</tests>-->
    <help>
Metagene Analysis
-----------------
riboSeqR version: ``1.0.5``.

The input is the R data file from the previous step - Triplet periodicity.

How to use?
-----------
Inputs
......
#. Select *Triplet periodicity (R data file)* from the previous step.

#. Specify length of ribosome footprint reads to be used in filtering
   (lengths). Only these reads **will** be used in the analysis.

#. Specify frames to consider. This information can be obtained
   from the *Triplet periodicity (HTML report)*.

   .. class:: warningmark

       Please note that the frames specified should correspond to the
       lengths of the reads.

#. Under *plotCDS parameters*, input length of footprints to be considered for
   generating the plot.

#. Review/change other options if necessary and execute program.

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

#. Metagene analysis (HTML report)

   A HTML file with results and links to other output files - plots for
   specified lengths (PDF) and R script used for the session.

#. Metagene analysis (R data file)

   Used as input for the next step - *Plot Rribosome Profile*.

riboSeqR functions used
.......................
``filterHits``.

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>