mir_parser: MirParser.xml annotate

annotate MirParser.xml @ 4:933475df0fd2 draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit fe40dec87779c1fcfbd03330e653aa886f4a2cda

author	drosofff
date	Wed, 21 Oct 2015 11:25:01 -0400
parents	bf31563d22a1
children	74394e39ad22

rev	line source
4 933475df0fd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit fe40dec87779c1fcfbd03330e653aa886f4a2cda drosofff parents: 3 diff changeset	1 <tool id="MirParser" name="Parse miRNAs" version="0.9.4">
2 c68bfbff72d5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	2 <description>from aligment files</description>
0 035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	3 <requirements>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	4 <requirement type="package" version="0.12.7">bowtie</requirement>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	5 <requirement type="package" version="0.7.7">pysam</requirement>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	6 <requirement type="package" version="1.9">numpy</requirement>
4 933475df0fd2 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit fe40dec87779c1fcfbd03330e653aa886f4a2cda drosofff parents: 3 diff changeset	7 <requirement type="package" version="3.1.2">R</requirement>
0 035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	8 <requirement type="package" version="2.14">biocbasics</requirement>
2 c68bfbff72d5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	9 <requirement type="package" version="1.2">samtools</requirement>
0 035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	10 </requirements>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	11 <command interpreter="python">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	12 MirParser.py
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	13 #if $refGenomeSource.genomeSource == "history":
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	14 $refGenomeSource.ownFile ## index source sys.arg[1]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	15 --do_not_extract_index ## sys.argv[2]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	16 #else:
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	17 #silent reference= filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	18 $reference ## sys.argv[1]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	19 --extract_index ## sys.argv[2]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	20 #end if
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	21 $output1 ## for pre-mirs ## sys.argv[3]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	22 $output2 ## for mature mirs ## sys.argv[4]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	23 $GFF3 ## sys.argv[5]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	24 #if $plotting.plottingOption == "yes":
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	25 $lattice_dataframe ## sys.argv[6]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	26 $plotCode ## sys.argv[7]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	27 $latticePDF ## sys.argv[8]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	28 #else:
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	29 "dummy_dataframe_path" ## sys.argv[6]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	30 "dummy_plotCode" ## sys.argv[7]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	31 "dummy_latticePDF" ## sys.argv[8]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	32 #end if
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	33 #for $i in $refGenomeSource.input_list
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	34 $i $i.ext "$i.name" ## sys.argv[9,10,11] modulo 3
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	35 #end for
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	36 #silent plottingoption = $plotting.plottingOption
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	37 </command>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	38 <inputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	39 <conditional name="refGenomeSource">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	40 <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	41 <option value="indexed">Use a built-in index</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	42 <option value="history">Use one from the history</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	43 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	44 <when value="indexed">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	45 <param label="Select multiple alignments to parse" multiple="true" name="input_list" type="data" format="tabular,sam,bam">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	46 <validator message="database not set for this bowtie output. Select the database(=genome used for matching) manually, or select a reference fasta from your history." metadata_column="0" metadata_name="dbkey" table_name="bowtie_indexes" type="dataset_metadata_in_data_table" />
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	47 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	48 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	49 <when value="history">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	50 <param label="Select multiple alignments to parse" multiple="true" name="input_list" type="data" format="tabular,sam,bam"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	51 <param format="fasta" label="Select the fasta reference" name="ownFile" type="data" />
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	52 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	53 </conditional>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	54 <param label="miRbase GFF3 guide" name="GFF3" type="data" format="gff,gff3"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	55 <conditional name="plotting">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	56 <param label="Additional miRNA coverage graphs" name="plottingOption" type="select">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	57 <option selected="True" value="no">no</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	58 <option value="yes">yes</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	59 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	60 <when value="yes">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	61 <param label="Display Coverage with absolute number of reads or relatively to the total number of read matching the gene or mir" name="display" type="select">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	62 <option selected="True" value="relative">Relative Coverage</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	63 <option value="absolute">Absolute Coverage</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	64 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	65 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	66 </conditional>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	67 </inputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	68 <outputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	69 <data format="tabular" label="Premirs Count Lists" name="output1" />
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	70 <data format="tabular" label="Mature Mirs Count Lists" name="output2" />
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	71 <data format="tabular" label="Lattice Dataframe" name="lattice_dataframe">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	72 <filter>plotting['plottingOption'] == "yes"</filter>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	73 </data>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	74 <data format="pdf" label="Mir coverage" name="latticePDF">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	75 <filter>plotting['plottingOption'] == "yes"</filter>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	76 </data>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	77 </outputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	78 <tests>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	79 <test>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	80 <param name="genomeSource" value="history"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	81 <param name="ownFile" value="Dmel_r5.49_short.fa" ftype="fasta"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	82 <param name="input_list" value="input.bam" ftype="bam"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	83 <param name="GFF3" value="dme.gff3" ftype="gff3"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	84 <param name="plottingOption" value="yes"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	85 <output name="output1" file="output1.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	86 <output name="output2" file="output2.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	87 <output name="lattice_dataframe" file="lattice_dataframe.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	88 <output name="latticePDF" file="latticePDF.pdf" ftype="pdf"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	89 </test>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	90 </tests>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	91 <configfiles>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	92 <configfile name="plotCode">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	93 #if $plotting.plottingOption == "yes":
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	94 graph_type = "${plotting.display}" ## "relative" or "absolute"
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	95 ## Setup R error handling to go to stderr
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	96 options( show.error.messages=F,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	97 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	98 library(lattice)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	99 coverage = read.delim("${lattice_dataframe}", header=T)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	100 Numb_of_biosamples = length(levels(coverage\$sample))
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	101 if (graph_type=="relative") {
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	102 graph = xyplot(countsNorm~offsetNorm \| mir, data=coverage, groups=polarity, col=c("red", "blue"), type="l", lwd=1,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	103 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), layout=c(Numb_of_biosamples,15), as.table=TRUE, main="miRNA coverage maps")
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	104 } else {
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	105 graph = xyplot(counts~offset \| mir, data=coverage, groups=polarity, col=c("red", "blue"), type="l", lwd=1,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	106 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), layout=c(Numb_of_biosamples,15), as.table=TRUE, main="miRNA coverage maps")
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	107 }
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	108 ## pdf output
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	109 pdf(file="${latticePDF}", paper="special", height=11.69, width=8.2677)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	110 plot(graph, newpage = T)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	111 dev.off()
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	112 #end if
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	113 </configfile>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	114 </configfiles>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	115 <help>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	116
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	117 What it does
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	118
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	119 This tool uses a species-specific GFF3 file from mirBase_ to guide the parsing of an alignment file produced with the sRbowtie tool.
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	120
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	121 .. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	122
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	123 ------
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	124
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	125 .. class:: warningmark
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	126
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	127 the Guide GFF3 file must be in the following format:
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	128
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	129 2L . miRNA_primary_transcript 243035 243141 . - . ID=MI0005821;Alias=MI0005821;Name=dme-mir-965
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	130
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	131 2L . miRNA 243055 243076 . - . ID=MIMAT0005480;Alias=MIMAT0005480;Name=dme-miR-965-3p;Derives_from=MI0005821
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	132
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	133 2L . miRNA 243096 243118 . - . ID=MIMAT0020861;Alias=MIMAT0020861;Name=dme-miR-965-5p;Derives_from=MI0005821
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	134
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	135 2L . miRNA_primary_transcript 857542 857632 . + . ID=MI0005813;Alias=MI0005813;Name=dme-mir-375
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	136
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	137 2L . miRNA 857596 857617 . + . ID=MIMAT0005472;Alias=MIMAT0005472;Name=dme-miR-375-3p;Derives_from=MI0005813
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	138
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	139 2L . miRNA 857556 857579 . + . ID=MIMAT0020853;Alias=MIMAT0020853;Name=dme-miR-375-5p;Derives_from=MI0005813
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	140
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	141 2L . miRNA_primary_transcript 1831685 1831799 . - . ID=MI0011290;Alias=MI0011290;Name=dme-mir-2280
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	142
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	143 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)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	144
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	145 ------
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	146
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	147 Input formats
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	148
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	149 1. One or sereral alignment files generated with sRbowtie tool and renamed according to the name of the biosample (avoid spaces in biosample labels)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	150
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	151 .. class:: warningmark
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	152
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	153 Alignment datasets generated with sRbowtie must be renamed according to a biosample name
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	154
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	155 2. A GFF3 file retrieved from mirBase_
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	156
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	157 ------
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	158
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	159 Outputs
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	160
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	161 Two count list files for counts of reads aligned to pre-mir or mature miRNA
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	162
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	163 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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035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	165 </help>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	166 </tool>

Mercurial > repos > drosofff > mir_parser

annotate MirParser.xml @ 4:933475df0fd2 draft