Mercurial > repos > drosofff > mir_parser

annotate MirParser.xml @ 5:74394e39ad22 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
author drosofff
date Sun, 11 Jun 2017 05:56:29 -0400
parents 933475df0fd2
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
1 <tool id="MirParser" name="Parse miRNAs" version="0.9.6">
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>
5
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
4 <requirement type="package" version="1.1.2">bowtie</requirement>
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
5 <requirement type="package" version="1.11.2=py27_0">numpy</requirement>
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
6 <requirement type="package" version="0.11.2.1=py27_0">pysam</requirement>
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
7 <requirement type="package" version="0.20_33=r3.3.1_0">r-lattice</requirement>
0
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
8 </requirements>
5
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
9 <command><![CDATA[
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
10 python '$__tool_directory__'/MirParser.py
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
11 #if $refGenomeSource.genomeSource == "history":
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
12 '$refGenomeSource.ownFile' ## index source sys.arg[1]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
13 --do_not_extract_index ## sys.argv[2]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
14 #else:
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
15 #silent reference = filter( lambda x: str( x[0] ) == str( $input_list.dbkey ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
16 '$reference' ## sys.argv[1]
0
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
17 --extract_index ## sys.argv[2]
5
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
18 #end if
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
19 '$output1' ## for pre-mirs ## sys.argv[3]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
20 '$output2' ## for mature mirs ## sys.argv[4]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
21 '$GFF3' ## sys.argv[5]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
22 #if $plotting.plottingOption == "yes":
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
23 '$lattice_dataframe' ## sys.argv[6]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
24 '$plotCode' ## sys.argv[7]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
25 '$latticePDF' ## sys.argv[8]
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
26 #else:
0
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
27 "dummy_dataframe_path" ## sys.argv[6]
5
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
28 "dummy_plotCode" ## sys.argv[7]
0
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
29 "dummy_latticePDF" ## sys.argv[8]
5
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
30 #end if
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
31 #for $i in $refGenomeSource.input_list
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
32 '$i' '$i.ext' "$i.name" ## sys.argv[9,10,11] modulo 3
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
33 #end for
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
34 #silent plottingoption = $plotting.plottingOption
74394e39ad22 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/MirParser commit 76b92fc0dd106f009b1df4221347fd892cfdd31f
drosofff
parents: 4
diff changeset
35 ]]></command>
0
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
36 <inputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
37 <conditional name="refGenomeSource">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
38 <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
39 <option value="indexed">Use a built-in index</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
40 <option value="history">Use one from the history</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
41 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
42 <when value="indexed">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
43 <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
44 <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
45 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
46 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
47 <when value="history">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
48 <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
49 <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
50 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
51 </conditional>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
52 <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
53 <conditional name="plotting">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
54 <param label="Additional miRNA coverage graphs" name="plottingOption" type="select">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
55 <option selected="True" value="no">no</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
56 <option value="yes">yes</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
57 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
58 <when value="yes">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
59 <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
60 <option selected="True" value="relative">Relative Coverage</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
61 <option value="absolute">Absolute Coverage</option>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
62 </param>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
63 </when>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
64 </conditional>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
65 </inputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
66 <outputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
67 <data format="tabular" label="Premirs Count Lists" name="output1" />
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
68 <data format="tabular" label="Mature Mirs Count Lists" name="output2" />
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
69 <data format="tabular" label="Lattice Dataframe" name="lattice_dataframe">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
70 <filter>plotting['plottingOption'] == "yes"</filter>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
71 </data>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
72 <data format="pdf" label="Mir coverage" name="latticePDF">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
73 <filter>plotting['plottingOption'] == "yes"</filter>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
74 </data>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
75 </outputs>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
76 <tests>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
77 <test>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
78 <param name="genomeSource" value="history"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
79 <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
80 <param name="input_list" value="input.bam" ftype="bam"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
81 <param name="GFF3" value="dme.gff3" ftype="gff3"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
82 <param name="plottingOption" value="yes"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
83 <output name="output1" file="output1.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
84 <output name="output2" file="output2.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
85 <output name="lattice_dataframe" file="lattice_dataframe.tab" ftype="tabular"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
86 <output name="latticePDF" file="latticePDF.pdf" ftype="pdf"/>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
87 </test>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
88 </tests>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
89 <configfiles>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
90 <configfile name="plotCode">
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
91 #if $plotting.plottingOption == "yes":
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
92 graph_type = "${plotting.display}" ## "relative" or "absolute"
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
93 ## Setup R error handling to go to stderr
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
94 options( show.error.messages=F,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
95 error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
96 library(lattice)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
97 coverage = read.delim("${lattice_dataframe}", header=T)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
98 Numb_of_biosamples = length(levels(coverage\$sample))
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
99 if (graph_type=="relative") {
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
100 graph = xyplot(countsNorm~offsetNorm | mir, data=coverage, groups=polarity, col=c("red", "blue"), type="l", lwd=1,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
101 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), layout=c(Numb_of_biosamples,15), as.table=TRUE, main="miRNA coverage maps")
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
102 } else {
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
103 graph = xyplot(counts~offset | mir, data=coverage, groups=polarity, col=c("red", "blue"), type="l", lwd=1,
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
104 scales=list(x=list(cex=.5), y=list(cex=.5)), par.strip.text=list(cex=.5), strip=strip.custom(which.given=1, bg="lightblue"), layout=c(Numb_of_biosamples,15), as.table=TRUE, main="miRNA coverage maps")
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
105 }
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
106 ## pdf output
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
107 pdf(file="${latticePDF}", paper="special", height=11.69, width=8.2677)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
108 plot(graph, newpage = T)
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
109 dev.off()
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
110 #end if
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
111 </configfile>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
112 </configfiles>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
113 <help>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
114
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
115 **What it does**
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 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
118
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
119 .. _mirBase: ftp://mirbase.org/pub/mirbase/CURRENT/genomes/
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 ------
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 .. class:: warningmark
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 the Guide GFF3 file must be in the following format:
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 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
128
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
129 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
130
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
131 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
132
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
133 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
134
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
135 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
136
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
137 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
138
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
139 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
140
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
141 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
142
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 **Input formats**
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 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
148
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
149 .. class:: warningmark
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 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
152
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
153 2. A GFF3 file retrieved from mirBase_
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 ------
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 **Outputs**
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 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
160
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
161 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
162
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
163 </help>
035df35a257e planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
164 </tool>