mir_parser: MirParser.xml annotate

annotate MirParser.xml @ 3:bf31563d22a1 draft

planemo upload for repository https://bitbucket.org/drosofff/gedtools/

author	drosofff
date	Mon, 17 Aug 2015 14:00:06 -0400
parents	c68bfbff72d5
children	933475df0fd2

rev	line source
3 bf31563d22a1 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 2 diff changeset	1 <tool id="MirParser" name="Parse miRNAs" version="0.9.3">
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>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	7 <requirement type="package" version="2.14">biocbasics</requirement>
2 c68bfbff72d5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: 0 diff changeset	8 <requirement type="package" version="1.2">samtools</requirement>
0 035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	9 </requirements>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	10 <command interpreter="python">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	11 MirParser.py
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	12 #if $refGenomeSource.genomeSource == "history":
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	13 $refGenomeSource.ownFile ## index source sys.arg[1]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	14 --do_not_extract_index ## sys.argv[2]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	15 #else:
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	16 #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	17 $reference ## sys.argv[1]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	18 --extract_index ## sys.argv[2]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	19 #end if
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	20 $output1 ## for pre-mirs ## sys.argv[3]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	21 $output2 ## for mature mirs ## sys.argv[4]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	22 $GFF3 ## sys.argv[5]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	23 #if $plotting.plottingOption == "yes":
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	24 $lattice_dataframe ## sys.argv[6]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	25 $plotCode ## sys.argv[7]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	26 $latticePDF ## sys.argv[8]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	27 #else:
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	28 "dummy_dataframe_path" ## sys.argv[6]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	29 "dummy_plotCode" ## sys.argv[7]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	30 "dummy_latticePDF" ## sys.argv[8]
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	31 #end if
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	32 #for $i in $refGenomeSource.input_list
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	33 $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	34 #end for
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	35 #silent plottingoption = $plotting.plottingOption
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	36 </command>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	37 <inputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	38 <conditional name="refGenomeSource">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	39 <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	40 <option value="indexed">Use a built-in index</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	41 <option value="history">Use one from the history</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	42 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	43 <when value="indexed">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	44 <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	45 <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	46 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	47 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	48 <when value="history">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	49 <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	50 <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	51 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	52 </conditional>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	53 <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	54 <conditional name="plotting">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	55 <param label="Additional miRNA coverage graphs" name="plottingOption" type="select">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	56 <option selected="True" value="no">no</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	57 <option value="yes">yes</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	58 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	59 <when value="yes">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	60 <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	61 <option selected="True" value="relative">Relative Coverage</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	62 <option value="absolute">Absolute Coverage</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	63 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	64 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	65 </conditional>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	66 </inputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	67 <outputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	68 <data format="tabular" label="Premirs Count Lists" name="output1" />
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	69 <data format="tabular" label="Mature Mirs Count Lists" name="output2" />
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	70 <data format="tabular" label="Lattice Dataframe" name="lattice_dataframe">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	71 <filter>plotting['plottingOption'] == "yes"</filter>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	72 </data>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	73 <data format="pdf" label="Mir coverage" name="latticePDF">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	74 <filter>plotting['plottingOption'] == "yes"</filter>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	75 </data>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	76 </outputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	77 <tests>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	78 <test>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	79 <param name="genomeSource" value="history"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	80 <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	81 <param name="input_list" value="input.bam" ftype="bam"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	82 <param name="GFF3" value="dme.gff3" ftype="gff3"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	83 <param name="plottingOption" value="yes"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	84 <output name="output1" file="output1.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	85 <output name="output2" file="output2.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	86 <output name="lattice_dataframe" file="lattice_dataframe.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	87 <output name="latticePDF" file="latticePDF.pdf" ftype="pdf"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	88 </test>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	89 </tests>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	90 <configfiles>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	91 <configfile name="plotCode">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	92 #if $plotting.plottingOption == "yes":
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	93 graph_type = "${plotting.display}" ## "relative" or "absolute"
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	94 ## Setup R error handling to go to stderr
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	95 options( show.error.messages=F,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	96 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	97 library(lattice)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	98 coverage = read.delim("${lattice_dataframe}", header=T)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	99 Numb_of_biosamples = length(levels(coverage\$sample))
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	100 if (graph_type=="relative") {
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	101 graph = xyplot(countsNorm~offsetNorm \| mir, data=coverage, groups=polarity, col=c("red", "blue"), type="l", lwd=1,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	102 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), layout=c(Numb_of_biosamples,15), as.table=TRUE, main="miRNA coverage maps")
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	103 } else {
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	104 graph = xyplot(counts~offset \| mir, data=coverage, groups=polarity, col=c("red", "blue"), type="l", lwd=1,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	105 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), layout=c(Numb_of_biosamples,15), as.table=TRUE, main="miRNA coverage maps")
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	106 }
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	107 ## pdf output
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	108 pdf(file="${latticePDF}", paper="special", height=11.69, width=8.2677)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	109 plot(graph, newpage = T)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	110 dev.off()
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	111 #end if
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	112 </configfile>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	113 </configfiles>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	114 <help>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	115
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	116 What it does
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	117
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	118 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	119
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	120 .. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	121
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 .. class:: warningmark
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	125
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	126 the Guide GFF3 file must be in the following format:
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	127
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	128 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	129
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	130 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	131
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	132 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	133
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	134 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	135
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	136 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	137
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	138 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	139
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	140 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	141
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	142 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	143
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 Input formats
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	147
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	148 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	149
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	150 .. class:: warningmark
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	151
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	152 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	153
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	154 2. A GFF3 file retrieved from mirBase_
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	155
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 Outputs
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	159
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	160 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	161
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	162 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.
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	163
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	164 </help>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	165 </tool>

Mercurial > repos > drosofff > mir_parser

annotate MirParser.xml @ 3:bf31563d22a1 draft