annotate riboplot.xml @ 19:6e3b13906b54

Use packages from the test toolshed. Add bedtools dependency

<tool id="riboplot" name="riboplot" version="0.1.0">
    <description>Plot and output read counts for a single transcript in an alignment (BAM)
    </description>
    <requirements>
        <requirement type="package" version="1.2.1">matplotlib</requirement>
        <requirement type="package" version="0.8.3">pysam</requirement>
        <requirement type="package" version="2.18">bedtools</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
    <command interpreter="python">riboplot/riboplot.py
    --ribo_file "${ribo_file}"
    --transcriptome_fasta "${transcriptome_fasta}"
    --transcript_name "${transcript_name}"
    #if $rnacov.rnacov_select=="yes"
        --rna_file "${rna_file}"
    #end if
    --read_length "${read_length}"
    --read_offset "${read_offset}"
    --html_file "${html_file}"
    --output_path "${html_file.files_path}"
    ## --debug
    </command>
    <inputs>
        <param name="ribo_file" type="data" format="bam" label="Ribo-Seq alignment file in BAM format"/>
        <param name="transcriptome_fasta" type="data" format="fasta" label="FASTA format file of the transcriptome"/>
        <param name="transcript_name" type="text" label="Name of the transcript to plot (as in FASTA)" size="40">
            <validator type="expression" message="Please input a single transcript name">len(value.split(',')) == 1</validator>
            <validator type="empty_field" message="Field requires a value"/>
            <sanitizer>
                <valid>
                    <add value="|"/>
                </valid>
            </sanitizer>
        </param>
        <conditional name="rnacov">
            <param name="rnacov_select" type="select" label="Include RNA Coverage">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="rna_file" type="data" format="bam" label="RNA-Seq alignment file in BAM format"/>
            </when>
            <when value="no" />
        </conditional>
        <param name="read_length" type="integer" label="Read length to consider" value="28"/>
        <param name="read_offset" type="integer" label="Offset" value="0"/>
    </inputs>
    <outputs>
        <data format="html" name="html_file" label="riboplot (HTML report)"/>
    </outputs>
    <help>
**RiboPlot**

Plot and output Ribo-Seq read counts of a single transcript from an alignment file (sorted BAM).

----

**Parameters**

1. Ribo-Seq alignment file (Sorted BAM file)

   A Bowtie 1 output (BAM) from an alignment of Ribo-Seq data to the transcriptome. This BAM
   file should be sorted. This can be done using one of the following methods.

   1. RiboGalaxy -> Sort Data -> Sort BAM dataset.
   2. ``samtools sort input.bam inputsorted``

2. Transcriptome (FASTA)

   A FASTA format file with sequences of the transcripts.

3. Name of the transcript to plot (Text)

   The name of the transcript to plot **should** match the name in the transcriptome (FASTA)
   and the Ribo-Seq/RNA-Seq alignment (BAM).

4. RNA coverage [optional] (Sorted BAM file)

   If you have RNA-Seq data (sorted BAM), you can select the option to plot RNA coverage.

5. Read lengths to consider [Optional] (Integer - 0 or greater)

   If this option is provided, only Ribo-Seq data of the given length is considered.

6. Offset [optional] (Integer - 0 or greater)

   If this option is provided, this offset is added to the read alignment positions.

----

**Output**

1. Plots (PNG and SVG)

   Ribo-Seq read counts as a bar plot in 3 frames (color codes: 1: red, 2: green, 3: blue)

   RNA coverage as a gray background (if the RNA coverage option was selected).

   The open reading frame architecture appears below the plot with start (ATG) and stop codons ('TAA', 'TAG', 'TGA') in all 3 frames.

   The color codes are start (white) and stop (dark gray).

   .. image:: images/riboplot.png

2. RiboSeq read counts in 3 frames for each position in the transcript (CSV)

    </help>
</tool>