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comparison flaimapper.xml @ 8:4f22bd612754 draft

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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
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7:0ea90514e0a0 8:4f22bd612754
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="flaimapper" name="FlaiMapper" version="2.4.0-0"> 2 <tool id="flaimapper" name="FlaiMapper" version="2.5.0-0">
3 <description>detects small ncRNA derived fragments in small RNA-Seq data</description> 3 <description>detects small ncRNA derived fragments in small RNA-Seq data</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2.4.0">flaimapper</requirement> 5 <requirement type="package" version="2.5.0">flaimapper</requirement>
6 </requirements> 6 </requirements>
7 7
8 <version_command>flaimapper --version 2&gt;&amp;1 | head -n 1</version_command> 8 <version_command><![CDATA[ flaimapper --version 2>&1 | head -n 1 ]]></version_command>
9 9
10 <command detect_errors="exit_code"><![CDATA[ 10 <command detect_errors="exit_code"><![CDATA[
11 flaimapper 11 flaimapper
12 -v 12 -v
13 -f '${output_select.output_format}' 13 -f '${output_select.output_format}'
14 -o '${output}' 14 -o '${output}'
26 -p '${parameters}' 26 -p '${parameters}'
27 #end if 27 #end if
28 28
29 '${alignment}' 29 '${alignment}'
30 ]]></command> 30 ]]></command>
31 31
32 <inputs> 32 <inputs>
33 <param name="alignment" type="data" format="bam" multiple="false" 33 <param name="alignment" type="data" format="bam" multiple="false"
34 label="Alignment file" 34 label="Alignment file"
35 help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" /> 35 help="Aligned small RNA-Seq reads must be single end and should not be fragmented in the library preparation" />
36 36
37 <conditional name="output_select"> 37 <conditional name="output_select">
38 <param name="output_format" type="select" label="Output format" argument="-f"> 38 <param name="output_format" type="select" label="Output format" argument="-f">
39 <option value="1">Tabular</option> 39 <option value="1">Tabular</option>
40 <option value="2">GTF</option> 40 <option value="2">GTF</option>
41 </param> 41 </param>
42 42
43 <when value="1"> 43 <when value="1">
44 <param name="fasta" type="data" format="fasta" optional="true" 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" 45 label="(Optional) Genome reference in FASTA format that corresponds to the reference genome or RNA database"
46 help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" /> 46 help="By selecting this file, sequences will be provided in the corresponding column in the output file" argument="-r" />
47 </when> 47 </when>
48 48
49 <when value="2"> 49 <when value="2">
50 <param name="offset5p" type="integer" value="4" 50 <param name="offset5p" type="integer" value="4"
51 label="Add 5'-offset to exon-type entry in GTF output file" 51 label="Add 5'-offset to exon-type entry in GTF output file"
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" /> 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" />
53 <param name="offset3p" type="integer" value="4" 53 <param name="offset3p" type="integer" value="4"
54 label="Add 3'-offset to exon-type entry in GTF output file" 54 label="Add 3'-offset to exon-type entry in GTF output file"
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" /> 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" />
56 </when> 56 </when>
57 </conditional> 57 </conditional>
58 58
59 <param name="parameters" type="data" format="txt,tabular" optional="true" 59 <param name="parameters" type="data" format="txt,tabular" optional="true"
60 label="(Optional) Custom parameters file" help="" argument="-p" /> 60 label="(Optional) Custom parameters file" help="" argument="-p" />
61 61
62 </inputs> 62 </inputs>
63 63
64 <outputs> 64 <outputs>
65 <data format="tabular" name="output" 65 <data format="tabular" name="output"
66 label="${tool.name} on $on_string"> 66 label="${tool.name} on $on_string">
67 <change_format> 67 <change_format>
68 <when input="output_select.output_format" value="1" format="tabular" /> 68 <when input="output_select.output_format" value="1" format="tabular" />
69 <when input="output_select.output_format" value="2" format="gtf" /> 69 <when input="output_select.output_format" value="2" format="gtf" />
70 </change_format> 70 </change_format>
71 </data> 71 </data>
72 </outputs> 72 </outputs>
73 73
74 <tests> 74 <tests>
75 <!-- tabular --> 75 <!-- tabular -->
76 <test><!-- Testing "ncRNAdb09 alignment"-type analysis --> 76 <!-- Testing "ncRNAdb09 alignment"-type analysis -->
77 <test>
77 <param name="alignment" value="snord81.bam" ftype="bam" /> 78 <param name="alignment" value="snord81.bam" ftype="bam" />
78 <param name="fasta" value="snord81.fa" ftype="fasta" /> 79 <param name="fasta" value="snord81.fa" ftype="fasta" />
79 <param name="output_format" value="1" /> 80 <param name="output_format" value="1" />
80 81
81 <output name="output" file="snord81.flaimapper.txt" /> 82 <output name="output" file="snord81.flaimapper.txt" />
82 </test> 83 </test>
83 <test> 84 <test>
84 <param name="alignment" value="snord81.bam" ftype="bam" /> 85 <param name="alignment" value="snord81.bam" ftype="bam" />
85 <param name="output_format" value="1" /> 86 <param name="output_format" value="1" />
86 87
87 <output name="output" file="snord81.flaimapper.no-seq.txt" /> 88 <output name="output" file="snord81.flaimapper.no-seq.txt" />
88 </test> 89 </test>
89 <test><!-- Testing "Full genome alignment"-type analysis --> 90 <!-- Testing "Full genome alignment"-type analysis -->
91 <test>
90 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" /> 92 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
91 <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" /> 93 <param name="fasta" value="test_genomic_all_chromosomes.fa" ftype="fasta" />
92 <param name="output_format" value="1" /> 94 <param name="output_format" value="1" />
93 95
94 <output name="output" file="test_genomic_flaimapper_output.txt" /> 96 <output name="output" file="test_genomic_flaimapper_output.txt" />
95 </test> 97 </test>
96 <test> 98 <test>
97 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" /> 99 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
98 <param name="output_format" value="1" /> 100 <param name="output_format" value="1" />
99 101
100 <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" /> 102 <output name="output" file="test_genomic_flaimapper_output.no-seq.txt" />
101 </test> 103 </test>
102 104
103 <!-- GTF --> 105 <!-- GTF -->
104 <test><!-- Testing "ncRNAdb09 alignment"-type analysis --> 106 <!-- Testing "ncRNAdb09 alignment"-type analysis -->
107 <test>
105 <param name="alignment" value="snord81.bam" ftype="bam" /> 108 <param name="alignment" value="snord81.bam" ftype="bam" />
106 <param name="output_format" value="2" /> 109 <param name="output_format" value="2" />
107 110
108 <output name="output" file="snord81.flaimapper.gtf" /> 111 <output name="output" file="snord81.flaimapper.gtf" />
109 </test> 112 </test>
110 <test><!-- Testing "Full genome alignment"-type analysis --> 113 <!-- Testing "Full genome alignment"-type analysis -->
114 <test>
111 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" /> 115 <param name="alignment" value="test_genomic_alignment.bam" ftype="bam" />
112 <param name="output_format" value="2" /> 116 <param name="output_format" value="2" />
113 117
114 <output name="output" file="test_genomic_flaimapper_output.gtf" /> 118 <output name="output" file="test_genomic_flaimapper_output.gtf" />
115 </test> 119 </test>
116 120
117 <!-- test custom parameters --> 121 <!-- test custom parameters -->
118 <test> 122 <test>
119 <param name="alignment" value="snord81.bam" ftype="bam" /> 123 <param name="alignment" value="snord81.bam" ftype="bam" />
120 <param name="output_format" value="2" /> 124 <param name="output_format" value="2" />
121 <param name="offset5p" value="5" /> 125 <param name="offset5p" value="5" />
122 <param name="offset3p" value="5" /> 126 <param name="offset3p" value="5" />
123 127
124 <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" /> 128 <output name="output" file="snord81.flaimapper.offsets_5_5.gtf" />
125 </test> 129 </test>
126 <test> 130 <test>
127 <param name="alignment" value="snord81.bam" ftype="bam" /> 131 <param name="alignment" value="snord81.bam" ftype="bam" />
128 <param name="output_format" value="2" /> 132 <param name="output_format" value="2" />
129 <param name="parameters" value="filter-parameters.duck.15.txt"/> 133 <param name="parameters" value="filter-parameters.duck.15.txt"/>
130 134
131 <output name="output" file="snord81.flaimapper.duck-15.gtf" /> 135 <output name="output" file="snord81.flaimapper.duck-15.gtf" />
132 </test> 136 </test>
133 </tests> 137 </tests>
134 138
135 <help><![CDATA[ 139 <help><![CDATA[
136 FlaiMapper wrapper for Galaxy 140 FlaiMapper wrapper for Galaxy
137 ============================= 141 =============================
138 142
139 Fragment Location Annotation Identification Mapper 143 Fragment Location Annotation Identification Mapper
169 173
170 More details are given in the manual at the following website: 174 More details are given in the manual at the following website:
171 175
172 https://github.com/yhoogstrate/flaimapper 176 https://github.com/yhoogstrate/flaimapper
173 ]]></help> 177 ]]></help>
174 178
175 <citations> 179 <citations>
176 <citation type="doi">10.1093/bioinformatics/btu696</citation> 180 <citation type="doi">10.1093/bioinformatics/btu696</citation>
177 </citations> 181 </citations>
178 </tool> 182 </tool>