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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
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5:79dcb1e0be6b 6:c143e7e1fdbf
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="flaimapper" name="FlaiMapper" version="1.2.1.w2"> 2 <tool id="flaimapper" name="FlaiMapper" version="2.3.4-0">
3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> 3 <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.2.1">flaimapper</requirement> 5 <requirement type="package" version="2.3.4">flaimapper</requirement>
6 </requirements> 6 </requirements>
7 7
8 <stdio> 8 <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command>
9 <regex match="in parse_gff.*?ValueError: invalid literal for int\(\) with base 10" source="stderr" level="fatal" description="The GTF file is corrupt: double check the columns of your GTF/GFF file.\n" />
10 <regex match="[fai_load] build FASTA index." source="stderr" level="log" />
11 </stdio>
12 9
13 <version_command>flaimapper --version</version_command> 10 <command detect_errors="exit_code"><![CDATA[
14
15 <command><![CDATA[
16 flaimapper 11 flaimapper
17 -v 12 -v
18 -f $output_format 13 -f '${output_select.output_format}'
19 -o $output 14 -o '${output}'
20 -m $mask 15
21 -r $fasta 16 #if $output_select.output_format == '1':
22 17 #if $output_select.fasta:
23 #for $alignment in $alignments 18 -r '${output_select.fasta}'
24 $alignment 19 #end if
25 #end for 20 #else
21 --offset5p ${output_select.offset5p}
22 --offset3p ${output_select.offset3p}
23 #end if
24
25 #if $parameters:
26 -p '${parameters}'
27 #end if
28
29 '${alignment}'
26 ]]></command> 30 ]]></command>
27 31
28 <inputs> 32 <inputs>
29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" /> 33 <param name="alignment" type="data" format="bam" multiple="false"
34 label="Alignment file"
35 help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" />
30 36
31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" /> 37 <conditional name="output_select">
38 <param name="output_format" type="select" label="Output format" argument="-f">
39 <option value="1">Tabular</option>
40 <option value="2">GTF</option>
41 </param>
32 42
33 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> 43 <when value="1">
44 <param name="fasta" type="data" format="fasta" optional="true"
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" />
46 </when>
47
48 <when value="2">
49 <param name="offset5p" type="integer" value="4"
50 label="5' offset added to the exon-type GTF entry"
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" />
52 <param name="offset3p" type="integer" value="4"
53 label="3' offset added to the exon-type GTF entry"
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" />
55 </when>
56 </conditional>
34 57
35 <param name="output_format" type="select" label="Output format"> 58 <param name="parameters" type="data" format="txt,tabular" optional="true"
36 <option value="1">Tabular (1 fragment per column)</option> 59 label="(Optional) Custom parameters file" help="" argument="-p" />
37 <option value="2">Tabular (1 precursor per column)</option> 60
38 <option value="3">GenBank</option>
39 <!-- option value="gtf">GTF/GFF</option -->
40 </param>
41 </inputs> 61 </inputs>
42 62
43 <outputs> 63 <outputs>
44 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> 64 <data format="tabular" name="output"
65 label="${tool.name} on $on_string">
66 <change_format>
67 <when input="output_select.output_format" value="1" format="tabular" />
68 <when input="output_select.output_format" value="2" format="gtf" />
69 </change_format>
70 </data>
45 </outputs> 71 </outputs>
46 72
47 <tests> 73 <tests>
74 <!-- tabular -->
48 <test><!-- Testing "ncRNAdb09 alignment"-type analysis --> 75 <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
49 <param name="alignments" value="test1/snord81.bam" ftype="bam" /> 76 <param name="alignment" value="snord81.bam" ftype="bam" />
50 <param name="mask" value="test1/ncrnadb09.v2.gtf" ftype="gtf" /> 77 <param name="fasta" value="snord81.fa" ftype="fasta" />
51 <param name="fasta" value="test1/ncrnadb09.fa" ftype="fasta" /> 78 <param name="output_format" value="1" />
52 <param name="output_format" value="1" />
53 79
54 <output name="output" file="test1/snord81.flaimapper.txt" /> 80 <output name="output" file="snord81.flaimapper.txt" />
81 </test>
82 <test>
83 <param name="alignment" value="snord81.bam" ftype="bam" />
84 <param name="output_format" value="1" />
85
86 <output name="output" file="snord81.flaimapper.no-seq.txt" />
55 </test> 87 </test>
56 <test><!-- Testing "Full genome alignment"-type analysis --> 88 <test><!-- Testing "Full genome alignment"-type analysis -->
57 <param name="alignments" value="test2/test_genomic_alignment.bam" ftype="bam" /> 89 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
58 <param name="mask" value="test2/test_genomic_genes.gtf" ftype="gtf" /> 90 <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" />
59 <param name="fasta" value="test2/test_genomic_all_chromosomes.fa" ftype="fasta" /> 91 <param name="output_format" value="1" />
60 <param name="output_format" value="1" />
61 92
62 <output name="output" file="test2/test_genomic_flaimapper_output.txt" /> 93 <output name="output" file="test_genomic_flaimapper_output.txt" />
94 </test>
95 <test>
96 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
97 <param name="output_format" value="1" />
98
99 <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" />
100 </test>
101
102 <!-- GTF -->
103 <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
104 <param name="alignment" value="snord81.bam" ftype="bam" />
105 <param name="output_format" value="2" />
106
107 <output name="output" file="snord81.flaimapper.gtf" />
108 </test>
109 <test><!-- Testing "Full genome alignment"-type analysis -->
110 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
111 <param name="output_format" value="2" />
112
113 <output name="output" file="test_genomic_flaimapper_output.gtf" />
114 </test>
115
116 <!-- test custom parameters -->
117 <test>
118 <param name="alignment" value="snord81.bam" ftype="bam" />
119 <param name="output_format" value="2" />
120 <param name="offset5p" value="5" />
121 <param name="offset3p" value="5" />
122
123 <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" />
124 </test>
125 <test>
126 <param name="alignment" value="snord81.bam" ftype="bam" />
127 <param name="output_format" value="2" />
128 <param name="parameters" value="filter-parameters.duck.15.txt"/>
129
130 <output name="output" file="snord81.flaimapper.duck-15.gtf" />
63 </test> 131 </test>
64 </tests> 132 </tests>
65 133
66 <help><![CDATA[ 134 <help><![CDATA[
67 FlaiMapper wrapper for Galaxy 135 FlaiMapper wrapper for Galaxy
68 ============================= 136 =============================
69
70 https://github.com/yhoogstrate/flaimapper
71 http://www.ncbi.nlm.nih.gov/pubmed/25338717
72 http://dx.doi.org/10.1093/bioinformatics/btu696
73 137
74 Fragment Location Annotation Identification Mapper 138 Fragment Location Annotation Identification Mapper
75 139
76 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data. 140 FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data.
77 141
78 142
79 Input 143 Input
80 ----- 144 -----
81 145
82 Alignments 146 Alignment
83 **********
84
85 Aligned reads from small RNA-Seq experiments have to be provided in the BAM format.
86 In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments.
87
88 Mask File
89 ********* 147 *********
90 148
91 There are two strategies to analyze using FlaiMapper: 149 This file has to contain aligned single end reads from a small RNA-Seq experiment, provided in the BAM format.
92 150
93 - Relative to mature ncRNA sequences 151 Prior to running FlaiMapper, it is common to align sequencing reads to either:
94 - Relative to chromosomes
95 152
96 Therefore FlaiMapper requires a list of ncRNA annotations relative to the used reference genome for the alignment files. These ncRNA locations within the sequences provided in the FASTA file (MASK) regions should be provided in the GFF/GTF format: 153 - mature ncRNA sequences
154 - all chromosomes
97 155
98 - http://genome.ucsc.edu/FAQ/FAQformat.html#format3 156 Example- and reference data
99 - http://www.ensembl.org/info/website/upload/gff.html 157 ***************************
100
101 If you are making use of a ncRNA database that has no GTF file available you can make use of the galaxy tool **flaimapper-gtf-from-fasta** to create one.
102
103
104 You can access **ncRNAdb09** GTF file at the following URL:
105 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.gtf *(mask file)*
106
107 Fasta sequence
108 **************
109 158
110 The reference sequence should be provided in FASTA format. 159 The reference sequence should be provided in FASTA format.
111 160
112 You can access **ncRNAdb09** FASTA file at the following URL: 161 You can access **ncRNAdb09** FASTA file at the following URL:
113 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)* 162 https://raw.githubusercontent.com/yhoogstrate/flaimapper/master/share/annotations/ncRNA_annotation/ncrnadb09.fa *(reference file)*
114 163
115 Example- and reference data
116 ***************************
117
118 To align reads to ncRNA you need aligner specific indexed version of the reference. We have made
119 the following available for ncRNAdb09:
120
121 - **Tophat1**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
122 - **Tophat2**: https://github.com/yhoogstrate/flaimapper/blob/master/share/annotations/ncRNA_annotation/ncrnadb09.bt2.tar.gz
123
124 If you want to test FlaiMapper with example data you can obtain several 164 If you want to test FlaiMapper with example data you can obtain several
125 alignment files from the following directory tree: 165 alignment files from the following directory tree:
126 166
127 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments 167 https://github.com/yhoogstrate/flaimapper/tree/master/share/small_RNA-seq_alignments
128 168
129 Installation 169 More details are given in the manual at the following website:
130 ------------
131 170
132 The wrapper makes use of easy_install to install a python egg. Please 171 https://github.com/yhoogstrate/flaimapper
133 ensure you have easy_install installed.
134
135 License
136 -------
137
138 **flaimapper** and **wrapper**:
139
140 GPL (>=3)
141
142 **pysam**:
143
144 The MIT License
145
146 Contact
147 -------
148
149 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
150 Medical Center (Rotterdam, Netherlands).
151
152
153 Development
154 -----------
155
156 * Repository-Maintainer: Youri Hoogstrate
157 * Repository-Developers: Youri Hoogstrate
158
159 * Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools
160
161 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
162 Medical Center (Rotterdam, Netherlands).
163 ]]></help> 172 ]]></help>
164 173
165 <citations> 174 <citations>
166 <citation type="doi">10.1093/bioinformatics/btu696</citation> 175 <citation type="doi">10.1093/bioinformatics/btu696</citation>
167 </citations> 176 </citations>