# HG changeset patch
# User artbio
# Date 1500374181 14400
# Node ID ed37e8c6e23260ad7c38e2f847a3270aaf5dfdf3
# Parent 10f0e4c00b13131b734d949003b1e258f28a939b
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 356a4309668ba4b07b85013753d34358464222e8
diff -r 10f0e4c00b13 -r ed37e8c6e232 mircounts.xml.back
--- a/mircounts.xml.back Tue Jul 18 06:30:40 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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- Counts miRNA alignments from small RNA sequence data
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- bowtie
- samtools
- pysam
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- /dev/null | samtools sort -O bam -o '$output'
- ##samtools view -bS output.sam -o output.bam &&
- ##samtools sort output.bam output.sorted &&
- ##samtools index output.sorted &&
- ## mv output.sorted.bam $output
- ## bowtie parse :
- ## Be careful:
- ## Bam: 0-based; SAM: 1-based; GFF: 1-based
- ## end refactoring
- ]]>
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-**What it does**
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-This tool uses a species-specific GFF3 file from mirBase_ to guide the parsing of an alignment file produced with the sRbowtie tool.
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-.. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/
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-------
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-.. class:: warningmark
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-the Guide GFF3 file must be in the following format:
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-2L . miRNA_primary_transcript 243035 243141 . - . ID=MI0005821;Alias=MI0005821;Name=dme-mir-965
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-2L . miRNA 243055 243076 . - . ID=MIMAT0005480;Alias=MIMAT0005480;Name=dme-miR-965-3p;Derives_from=MI0005821
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-2L . miRNA 243096 243118 . - . ID=MIMAT0020861;Alias=MIMAT0020861;Name=dme-miR-965-5p;Derives_from=MI0005821
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-2L . miRNA_primary_transcript 857542 857632 . + . ID=MI0005813;Alias=MI0005813;Name=dme-mir-375
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-2L . miRNA 857596 857617 . + . ID=MIMAT0005472;Alias=MIMAT0005472;Name=dme-miR-375-3p;Derives_from=MI0005813
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-2L . miRNA 857556 857579 . + . ID=MIMAT0020853;Alias=MIMAT0020853;Name=dme-miR-375-5p;Derives_from=MI0005813
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-2L . miRNA_primary_transcript 1831685 1831799 . - . ID=MI0011290;Alias=MI0011290;Name=dme-mir-2280
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-With name for mature miRNA (3rd column = miRNA) containing either the -3p or -5p string in the attribute Name (Name=dme-miR-965-3p, for instance)
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-------
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-**Input formats**
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-1. One or sereral alignment files generated with sRbowtie tool and **renamed** according to the name of the biosample (avoid spaces in biosample labels)
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-.. class:: warningmark
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-Alignment datasets generated with sRbowtie must be renamed according to a biosample name
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-2. A GFF3 file retrieved from mirBase_
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-**Outputs**
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-Two count list files for counts of reads aligned to pre-mir or mature miRNA
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-A pdf of pre-mir coverages. Red coverages indicate that the mir gene is in the genomic up strand, blue coverages indicate that the mir gene is in the genomic down strand.
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diff -r 10f0e4c00b13 -r ed37e8c6e232 tool-data/GFFs_v21.tar.gz
Binary file tool-data/GFFs_v21.tar.gz has changed
diff -r 10f0e4c00b13 -r ed37e8c6e232 tool-data/hairpin_v21.fa.gz
Binary file tool-data/hairpin_v21.fa.gz has changed
diff -r 10f0e4c00b13 -r ed37e8c6e232 tool_data_table_conf.xml.test
--- a/tool_data_table_conf.xml.test Tue Jul 18 06:30:40 2017 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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