comparison mmquant.xml @ 1:87c5fa8651c1 draft

planemo upload commit fb76aa0a938a2498d3206e6039bc1d9906e6c2ce-dirty

0:60abb6540004

			-l "$overlap"
			"$gene_name"
			-c "$count"
			-m "$merge"
			-o "$output"
    ]]></command>
    <inputs>
        <param name="annotation" type="data" label="Annotation" format="gtf" />
		<repeat name="reads_info" title="Reads" min="1" default="1">
			<param name="reads"  type="data"   label="Reads"  multiple="false" format="sam,bam" />

		</repeat>
		<param name="overlap" type="float" value="-1" label="Overlap type" help="&lt;0: read is included, &lt;1: overlap, otherwise: # nt" />
        <param name="gene_name" type="boolean" label="Print gene name instead of IDs" truevalue="-g" falsevalue="" help="use gene name instead of gene ID in the output file" />
		<param name="count" type="integer" value="0" min="0" label="Count threshold" help="Do not display genes with less than N reads" />
		<param name="merge" type="float" value="0.0" min="0.0" max="1.0" label="Merge threshold" help="Merge gene aggregate count with parent aggregate if count is low" />
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>

.. _samtools: http://www.htslib.org/
.. _specification: https://samtools.github.io/hts-specs/SAMv1.pdf
.. _TopHat2: http://ccb.jhu.edu/software/tophat/index.shtml
.. _STAR: https://github.com/alexdobin/STAR/releases


**Output file**

The output is a tab-separated file, to be use in EdgeR or DESeq, for instance.  If the user provided *n* reads files, the output will contain *n+1* columns:

1:87c5fa8651c1

			-l "$overlap"
			"$gene_name"
			-c "$count"
			-m "$merge"
			-o "$output"
			-d "$n_overlap"
			-D "$pc_overlap"
    ]]></command>
    <inputs>
        <param name="annotation" type="data" label="Annotation" format="gtf" />
		<repeat name="reads_info" title="Reads" min="1" default="1">
			<param name="reads"  type="data"   label="Reads"  multiple="false" format="sam,bam" />

		</repeat>
		<param name="overlap" type="float" value="-1" label="Overlap type" help="&lt;0: read is included, &lt;1: overlap, otherwise: # nt" />
        <param name="gene_name" type="boolean" label="Print gene name instead of IDs" truevalue="-g" falsevalue="" help="use gene name instead of gene ID in the output file" />
		<param name="count" type="integer" value="0" min="0" label="Count threshold" help="Do not display genes with less than N reads" />
		<param name="merge" type="float" value="0.0" min="0.0" max="1.0" label="Merge threshold" help="Merge gene aggregate count with parent aggregate if count is low" />
		<param name="n_overlap" type="integer" value="30" min="1" label="Difference of overlapping" help="Number of overlapping bp between the best matches and the other matches" />
		<param name="pc_overlap" type="float" value="0.5" min="0.0" max="1.0" label="Ratio of overlapping" help="Ratio of overlapping bp between the best matches and the other matches" />
    </inputs>
    <outputs>
        <data name="output" format="txt" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>

.. _samtools: http://www.htslib.org/
.. _specification: https://samtools.github.io/hts-specs/SAMv1.pdf
.. _TopHat2: http://ccb.jhu.edu/software/tophat/index.shtml
.. _STAR: https://github.com/alexdobin/STAR/releases

**Read mapping to several genes**

We will suppose here that the ``-l 1`` strategy is used (i.e. a read is attributed to a gene as soon as at least 1 nucleotide overlap). The example can be extended to other strategies as well.

If a read (say, of size 100), maps unambiguously and overlaps with gene A and B, it will be counted as 1 for the new "gene" gene_A--gene_B. However, suppose that only 1 nucleotide overlaps with gene A, whereas 100 nucleotides overlap with gene B (yes, genes A and B overlap). You probably would like to attribute the read to gene B.

The options ``Difference of overlapping`` and ``Ratio of overlapping`` control this. We compute the number of overlapping nucleotides between a read and the overlapping genes. If a read overlaps "significantly" more with one gene than with all the other genes, they will attribute the read to the former gene only.

The option ``Difference of overlapping`` *n* computes the differences of overlapping nucleotides. Let us name *N_A* and *N_B* the number of overlapping nucleotides with genes A and B respectively. If *N_A >= N_B + n*, then the read will be attributed to gene A only.

The option ``Ratio of overlapping`` *m* compares the ratio of overlapping nucleotides. If *N_A / N_B >= m*, then the read will be attributed to gene A only.

If both option ``Difference of overlapping`` *n* and ``Ratio of overlapping`` *m* are used, then the read will be attributed to gene A only iff both *N_A >= N_B + n* and *N_A / N_B >= m*.


**Output file**

The output is a tab-separated file, to be use in EdgeR or DESeq, for instance.  If the user provided *n* reads files, the output will contain *n+1* columns: