Mercurial > repos > artbio > mircounts
changeset 1:cadc0f2c6b29 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit b403f95dd2e57e51932fa275bdaed5312ffc1ff1
| author | artbio |
|---|---|
| date | Tue, 25 Jul 2017 09:40:25 -0400 |
| parents | da29af78a960 |
| children | f59c643b00fc |
| files | mircounts.xml static/images/premirs_absolute.png static/images/premirs_relative.png |
| diffstat | 3 files changed, 27 insertions(+), 15 deletions(-) [+] |
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--- a/mircounts.xml Mon Jul 24 06:27:50 2017 -0400 +++ b/mircounts.xml Tue Jul 25 09:40:25 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="mircounts" name="miRcounts" version="0.9"> +<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> @@ -159,8 +159,12 @@ <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. + ++ 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/ @@ -170,27 +174,35 @@ **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 +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. -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. ------ +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 +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 +6. A PDF file with covererage plots + </help> <citations>