diff mircounts.xml @ 1:cadc0f2c6b29 draft

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

--- 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>