comparison mircounts.xml @ 1:cadc0f2c6b29 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1

0:da29af78a960

<tool id="mircounts" name="miRcounts" version="0.9">
    <description> Counts miRNA alignments from small RNA sequence data</description>
    <requirements>
        <requirement type="package" version="1.2">bowtie</requirement>
        <requirement type="package" version="1.4.1">samtools</requirement>
        <requirement type="package" version="0.11.2.1">pysam</requirement>

        </test>
    </tests>
    <help>

**What it does**
Clip adapter (optional), align small RNA read to miRNA mirBase_ reference using bowtie and compute pre-mir and mir counts using the pysam python package.
Optionally, pre-mir read coverages can be plotted using the R lattice package.
This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments.

.. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/

------


**Inputs**

1. a fastq file of reads that may or may not clipped from their adapter sequence. The tool includes a clipping option if needed.

2. select the appropriate organism from which reads originate

3. Choose whether you wish or not to plot the pre-mir coverages
Coverage can be expressed in absolute number of reads covering the real coordinates of the pre-mir sequences,
or, in fraction of reads relative to the maximum coverage (set to 1) covering the coordinates of pre-mirs
expressed as a fraction of the length of the pre-mirs.

------

**Outputs**

1. a BAM alignment of input reads
2. a gff3 file generated by the tool to compute mature mir counts
3  a table of pre-mir Counts
4  a table of mature mir Counts

Optional:
5. A table of pre-mir coverage
6. A pdf file with covererage plots

  </help>
  <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
      <citation type="doi">10.1186/gb-2009-10-3-r25</citation>

1:cadc0f2c6b29

<tool id="mircounts" name="miRcounts" version="0.9.1">
    <description> Counts miRNA alignments from small RNA sequence data</description>
    <requirements>
        <requirement type="package" version="1.2">bowtie</requirement>
        <requirement type="package" version="1.4.1">samtools</requirement>
        <requirement type="package" version="0.11.2.1">pysam</requirement>

        </test>
    </tests>
    <help>

**What it does**

+ Clips adapter (optional)
+ Aligns small RNA reads to miRNA mirBase_ reference using bowtie
+ Computes pre-mir and mir counts using the pysam python package
+ Plots pre-mir read coverages using R lattice package (optional)

This tool uses a species-specific GFF3 file generated from mirBase_ to guide the parsing of a bam file of small RNA alignments.

.. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/

------


**Inputs**

1. A fastq file of reads that may or may not be clipped from their adapter sequence. The tool includes a clipping option if needed.
2. Select the appropriate organism which reads originate from.
3. Choose whether you wish or not to plot the pre-mir coverages. The coverage can be expressed in absolute number of reads covering the real coordinates of the pre-mir sequences, or, as a fraction of the maximum coverage (set to 1) covering the coordinates of pre-mirs expressed as a fraction of the length of the pre-mirs.


------

Absolute :

+ .. image:: premirs_absolute.png

Relative :

+ .. image:: premirs_relative.png

-------

**Outputs**

1. A BAM alignment of input reads
2. A GFF3 file generated by the tool to compute mature mir counts
3. A table of pre-mir counts
4. A table of mature mir counts

Optional:

5. A table of pre-mir coverage
6. A PDF file with covererage plots


  </help>
  <citations>
      <citation type="doi">10.1093/bioinformatics/btp352</citation>
      <citation type="doi">10.1186/gb-2009-10-3-r25</citation>