Mercurial > repos > yhoogstrate > flaimapper
comparison flaimapper.xml @ 8:4f22bd612754 draft
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/flaimapper commit ad77d5da986c4cd976cd5de7abcdc91c6dd505ad
author | erasmus-medical-center |
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date | Wed, 16 Aug 2017 11:07:51 -0400 |
parents | 0ea90514e0a0 |
children | 0addbdbc1344 |
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7:0ea90514e0a0 | 8:4f22bd612754 |
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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>&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> |