Mercurial > repos > yhoogstrate > flaimapper

annotate flaimapper.xml @ 6:c143e7e1fdbf 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 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
author yhoogstrate
date Mon, 23 Jan 2017 03:13:40 -0500
parents efd29213e8e5
children 0ea90514e0a0
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"?>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
2 <tool id="flaimapper" name="FlaiMapper" version="2.3.4-0">
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>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
5 <requirement type="package" version="2.3.4">flaimapper</requirement>
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
6 </requirements>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
7
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
8 <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command>
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
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>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
31
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" />
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
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>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
42
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"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
45 label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database" help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
46 </when>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
47
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
48 <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
49 <param name="offset5p" type="integer" value="4"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
50 label="5' offset added to the exon-type GTF entry"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
51 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to use an offset." argument="--offset5p" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
52 <param name="offset3p" type="integer" value="4"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
53 label="3' offset added to the exon-type GTF entry"
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
54 help="Exon-type entries are often used to measure expression. Because of the small size of the fragments it may be desired to use an offset." argument="--offset3p" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
55 </when>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
56 </conditional>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
57
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
58 <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
59 label="(Optional) Custom parameters file" help="" argument="-p" />
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
60
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
61 </inputs>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
62
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
63 <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
64 <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
65 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
66 <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
67 <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
68 <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
69 </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
70 </data>
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
71 </outputs>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
72
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
73 <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
74 <!-- tabular -->
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
75 <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
76 <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
77 <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
78 <param name="output_format" value="1" />
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
79
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
80 <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
81 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
82 <test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
83 <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
84 <param name="output_format" 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
85
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
86 <output name="output" file="snord81.flaimapper.no-seq.txt" />
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
87 </test>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
88 <test><!-- Testing "Full genome alignment"-type analysis -->
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
89 <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
90 <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
91 <param name="output_format" 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
92
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
93 <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
94 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
95 <test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
96 <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
97 <param name="output_format" 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
98
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
99 <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
100 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
101
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
102 <!-- GTF -->
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><!-- Testing "ncRNAdb09 alignment"-type analysis -->
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
104 <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
105 <param name="output_format" value="2" />
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
106
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
107 <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
108 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
109 <test><!-- Testing "Full genome alignment"-type analysis -->
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
110 <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
111 <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
112
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
113 <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
114 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
115
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
116 <!-- 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
117 <test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
118 <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
119 <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
120 <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
121 <param name="offset3p" 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
122
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
123 <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
124 </test>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
125 <test>
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="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
127 <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
128 <param name="parameters" value="filter-parameters.duck.15.txt"/>
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
129
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
130 <output name="output" file="snord81.flaimapper.duck-15.gtf" />
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
131 </test>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
132 </tests>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
133
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
134 <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
135 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
136 =============================
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
137
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
138 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
139
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: 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
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 Input
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
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
146 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
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
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
149 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
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 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
152
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
153 - 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
154 - 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
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 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
157 ***************************
0
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
158
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
159 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
160
d6abffbc9ee7 planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0f4aa594becc89b07073f7fcccd889e38974e10c-dirty
yhoogstrate
parents:
diff changeset
161 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
162 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
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 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
165 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
166
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://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
168
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
169 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
170
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
171 https://github.com/yhoogstrate/flaimapper
3
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
172 ]]></help>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
173
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
174 <citations>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
175 <citation type="doi">10.1093/bioinformatics/btu696</citation>
efd29213e8e5 Uploaded
yhoogstrate
parents: 1
diff changeset
176 </citations>
6
c143e7e1fdbf planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit 0c5344c3f9c398cdcc18f6bb61681afe48f0c306
yhoogstrate
parents: 3
diff changeset
177 </tool>