Mercurial > repos > yhoogstrate > flaimapper

annotate flaimapper.xml @ 8:4f22bd612754 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
author erasmus-medical-center
date Wed, 16 Aug 2017 11:07:51 -0400
parents 0ea90514e0a0
children 0addbdbc1344
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
1 <?xml version="1.0" encoding="UTF-8"?>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
2 <tool id="flaimapper" name="FlaiMapper" version="2.5.0-0">
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
3 <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
4 <requirements>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
5 <requirement type="package" version="2.5.0">flaimapper</requirement>
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
6 </requirements>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
7
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
8 <version_command><![CDATA[ flaimapper --version 2>&1 | head -n 1 ]]></version_command>
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
9
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
10 <command detect_errors="exit_code"><![CDATA[
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
11 flaimapper
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
12 -v
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
13 -f '${output_select.output_format}'
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
14 -o '${output}'
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
15
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
16 #if $output_select.output_format == '1':
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
17 #if $output_select.fasta:
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
18 -r '${output_select.fasta}'
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
19 #end if
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
20 #else
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
21 --offset5p ${output_select.offset5p}
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
22 --offset3p ${output_select.offset3p}
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
23 #end if
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
24
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
25 #if $parameters:
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
26 -p '${parameters}'
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
27 #end if
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
28
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
29 '${alignment}'
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
30 ]]></command>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
31
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
32 <inputs>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
33 <param name="alignment" type="data" format="bam" multiple="false"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
34 label="Alignment file"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
35 help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
36
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
37 <conditional name="output_select">
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
38 <param name="output_format" type="select" label="Output format" argument="-f">
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
39 <option value="1">Tabular</option>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
40 <option value="2">GTF</option>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
41 </param>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
42
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
43 <when value="1">
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
44 <param name="fasta" type="data" format="fasta" optional="true"
7
0ea90514e0a0 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c
erasmus-medical-center
parents: 6
diff changeset
45 label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database"
0ea90514e0a0 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c
erasmus-medical-center
parents: 6
diff changeset
46 help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
47 </when>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
48
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
49 <when value="2">
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
50 <param name="offset5p" type="integer" value="4"
7
0ea90514e0a0 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c
erasmus-medical-center
parents: 6
diff changeset
51 label="Add 5'-offset to exon-type entry in GTF output file"
0ea90514e0a0 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c
erasmus-medical-center
parents: 6
diff changeset
52 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset5p" />
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
53 <param name="offset3p" type="integer" value="4"
7
0ea90514e0a0 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c
erasmus-medical-center
parents: 6
diff changeset
54 label="Add 3'-offset to exon-type entry in GTF output file"
0ea90514e0a0 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit beb30713f9b8510c22f46d94cb58c92cf26c799c
erasmus-medical-center
parents: 6
diff changeset
55 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to add an offset to allow less stringent read counting." argument="--offset3p" />
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
56 </when>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
57 </conditional>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
58
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
59 <param name="parameters" type="data" format="txt,tabular" optional="true"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
60 label="(Optional) Custom parameters file" help="" argument="-p" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
61
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
62 </inputs>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
63
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
64 <outputs>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
65 <data format="tabular" name="output"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
66 label="${tool.name} on $on_string">
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
67 <change_format>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
68 <when input="output_select.output_format" value="1" format="tabular" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
69 <when input="output_select.output_format" value="2" format="gtf" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
70 </change_format>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
71 </data>
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
72 </outputs>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
73
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
74 <tests>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
75 <!-- tabular -->
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
76 <!-- Testing "ncRNAdb09 alignment"-type analysis -->
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
77 <test>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
78 <param name="alignment" value="snord81.bam" ftype="bam" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
79 <param name="fasta" value="snord81.fa" ftype="fasta" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
80 <param name="output_format" value="1" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
81
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
82 <output name="output" file="snord81.flaimapper.txt" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
83 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
84 <test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
85 <param name="alignment" value="snord81.bam" ftype="bam" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
86 <param name="output_format" value="1" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
87
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
88 <output name="output" file="snord81.flaimapper.no-seq.txt" />
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
89 </test>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
90 <!-- Testing "Full genome alignment"-type analysis -->
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
91 <test>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
92 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
93 <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
94 <param name="output_format" value="1" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
95
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
96 <output name="output" file="test_genomic_flaimapper_output.txt" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
97 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
98 <test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
99 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
100 <param name="output_format" value="1" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
101
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
102 <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
103 </test>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
104
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
105 <!-- GTF -->
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
106 <!-- Testing "ncRNAdb09 alignment"-type analysis -->
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
107 <test>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
108 <param name="alignment" value="snord81.bam" ftype="bam" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
109 <param name="output_format" value="2" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
110
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
111 <output name="output" file="snord81.flaimapper.gtf" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
112 </test>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
113 <!-- Testing "Full genome alignment"-type analysis -->
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
114 <test>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
115 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
116 <param name="output_format" value="2" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
117
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
118 <output name="output" file="test_genomic_flaimapper_output.gtf" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
119 </test>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
120
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
121 <!-- test custom parameters -->
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
122 <test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
123 <param name="alignment" value="snord81.bam" ftype="bam" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
124 <param name="output_format" value="2" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
125 <param name="offset5p" value="5" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
126 <param name="offset3p" value="5" />
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
127
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
128 <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
129 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
130 <test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
131 <param name="alignment" value="snord81.bam" ftype="bam" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
132 <param name="output_format" value="2" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
133 <param name="parameters" value="filter-parameters.duck.15.txt"/>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
134
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
135 <output name="output" file="snord81.flaimapper.duck-15.gtf" />
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
136 </test>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
137 </tests>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
138
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
139 <help><![CDATA[
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
140 FlaiMapper wrapper for Galaxy
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
141 =============================
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
142
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
143 Fragment Location Annotation Identification Mapper
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
144
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
145 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
146
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
147
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
148 Input
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
149 -----
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
150
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
151 Alignment
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
152 *********
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
153
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
154 This file has to contain aligned single end reads from a small RNA-Seq experiment, provided in the BAM format.
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
155
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
156 Prior to running FlaiMapper, it is common to align sequencing reads to either:
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
157
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
158 - mature ncRNA sequences
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
159 - all chromosomes
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
160
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
161 Example- and reference data
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
162 ***************************
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
163
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
164 The reference sequence should be provided in FASTA format.
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
165
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
166 You can access **ncRNAdb09** FASTA file at the following URL:
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
167 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
168
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
169 If you want to test FlaiMapper with example data you can obtain several
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
170 alignment files from the following directory tree:
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
171
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
172 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
173
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
174 More details are given in the manual at the following website:
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
175
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
176 https://github.com/yhoogstrate/flaimapper
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
177 ]]></help>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
178
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
179 <citations>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
180 <citation type="doi">10.1093/bioinformatics/btu696</citation>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
181 </citations>
8
4f22bd612754 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
erasmus-medical-center
parents: 7
diff changeset
182 </tool>