Mercurial > repos > artbio > mircounts
changeset 8:3f62272192f9 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 0eaefbad21786cabed6791a6d06e9a0de8af10b0
author | artbio |
---|---|
date | Mon, 23 Apr 2018 13:21:16 -0400 |
parents | 65befdc9925a |
children | 2a08a6eb471c |
files | mature_mir_gff_translation.py mircounts.xml |
diffstat | 2 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/mature_mir_gff_translation.py Sat Oct 14 18:53:02 2017 -0400 +++ b/mature_mir_gff_translation.py Mon Apr 23 13:21:16 2018 -0400 @@ -1,5 +1,4 @@ import argparse - from datetime import datetime
--- a/mircounts.xml Sat Oct 14 18:53:02 2017 -0400 +++ b/mircounts.xml Mon Apr 23 13:21:16 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="mircounts" name="miRcounts" version="1.1.1"> +<tool id="mircounts" name="miRcounts" version="1.2.0"> <description> Counts miRNA alignments from small RNA sequence data</description> <requirements> <requirement type="package" version="1.18">gnu-wget</requirement> @@ -75,7 +75,8 @@ </options> </param> <param name="mirbase_version" type="select" label="Choose miRbase version"> - <option selected="true" value="CURRENT">Current</option> +<!-- <option selected="true" value="22">22</option> # activate when gff parsing is fixed --> + <option value="21">21</option> <option value="20">20</option> <option value="19">19</option> </param> @@ -135,7 +136,7 @@ <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> <param name="v" value="0"/> <param name="genomeKey" value="dme"/> - <param name="mirbase_version" value="CURRENT"/> + <param name="mirbase_version" value="21"/> <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> <param name="plottingOption" value="no"/> <param name="output_premir_counts" value="True"/> @@ -153,7 +154,7 @@ <param name="clip_sequence" value="TCGTATGCCGTCTTCTGCTTG"/> <param name="v" value="0"/> <param name="genomeKey" value="dme"/> - <param name="mirbase_version" value="CURRENT"/> + <param name="mirbase_version" value="21"/> <param name="input" value="input.unclipped.fastqsanger" ftype="fastqsanger"/> <param name="plottingOption" value="yes"/> <param name="display" value="relative"/> @@ -170,7 +171,7 @@ <param name="cutoption" value="no" /> <param name="v" value="1"/> <param name="genomeKey" value="dme"/> - <param name="mirbase_version" value="CURRENT"/> + <param name="mirbase_version" value="21"/> <param name="clipped_input" value="input.clipped.fastqsanger" ftype="fastqsanger"/> <param name="plottingOption" value="yes"/> <param name="display" value="absolute"/> @@ -195,7 +196,7 @@ 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/ +.. _mirBase: ftp://mirbase.org/pub/mirbase/ ------