annotate ribocount.xml @ 8:844eb8c36f32

Add help section in xml and update usage documentation

<tool id="ribocount" name="ribocount" version="0.1.0">
    <description>Get read counts for all transcripts in an alignment (BAM)
    </description>
    <requirements>
        <requirement type="package" version="0.8.3">pysam</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
    <command interpreter="python">riboplot/ribocount.py
    --ribo_file "${ribo_file}"
    --transcriptome_fasta "${transcriptome_fasta}"
    --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="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="ribocount (HTML report)"/>
    </outputs>
    <help>
**RiboCount**

Output read counts for all transcripts in an alignment.

----

**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. Read lengths to consider [optional] (Integer - 0 or greater)

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

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

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

----

**Output**

Read counts for all transcripts in the alignment (ZIP)

The output file ``ribocount_output.zip`` should first be uncompressed. This will generate
a folder called ``ribocount_output``. Open ``index.html`` in a web browser to view the results of ribocount.

Total reads for each transcript will be displayed in a table along with the name of the transcript and a link
to the CSV file containing the read counts in 3 frames for each position in the transcript.

.. image:: images/ribocount.png

    </help>
</tool>