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comparison flaimapper.xml @ 3:efd29213e8e5 draft

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author yhoogstrate
date Fri, 31 Jul 2015 05:30:48 -0400
parents 96d135d3c57f
children c143e7e1fdbf
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2:affc5ec4f65a 3:efd29213e8e5
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.w1"> 2 <tool id="flaimapper" name="FlaiMapper" version="1.2.1.w2">
3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> 3 <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.2.1">flaimapper</requirement> 5 <requirement type="package" version="1.2.1">flaimapper</requirement>
6 </requirements> 6 </requirements>
7 7
8 <stdio> 8 <stdio>
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" /> 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" /> 10 <regex match="[fai_load] build FASTA index." source="stderr" level="log" />
11 </stdio> 11 </stdio>
12 12
13 <version_command>flaimapper --version</version_command> 13 <version_command>flaimapper --version</version_command>
14 14
15 <command> 15 <command><![CDATA[
16 flaimapper 16 flaimapper
17 -v 17 -v
18 -f $output_format 18 -f $output_format
19 -o $output 19 -o $output
20 -m $mask 20 -m $mask
21 -r $fasta 21 -r $fasta
22 22
23 #for $alignment in $alignments 23 #for $alignment in $alignments
24 $alignment 24 $alignment
25 #end for 25 #end for
26 </command> 26 ]]></command>
27 27
28 <inputs> 28 <inputs>
29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" /> 29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />
30 30
31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" /> 31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
32 32
33 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> 33 <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" />
34 34
35 <param name="output_format" type="select" label="Output format"> 35 <param name="output_format" type="select" label="Output format">
36 <option value="1">Tabular (1 fragment per column)</option> 36 <option value="1">Tabular (1 fragment per column)</option>
37 <option value="2">Tabular (1 precursor per column)</option> 37 <option value="2">Tabular (1 precursor per column)</option>
38 <option value="3">GenBank</option> 38 <option value="3">GenBank</option>
39 <!-- option value="gtf">GTF/GFF</option --> 39 <!-- option value="gtf">GTF/GFF</option -->
40 </param> 40 </param>
41 </inputs> 41 </inputs>
42 42
43 <outputs> 43 <outputs>
44 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" /> 44 <data format="tabular" name="output" label="${tool.name} on ${', '.join([ str(a.hid)+': '+a.name for a in $alignments ])}" />
45 </outputs> 45 </outputs>
46 46
47 <tests> 47 <tests>
48 <test><!-- Testing "ncRNAdb09 alignment"-type analysis --> 48 <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
49 <param name="alignments" value="test1/snord81.bam" ftype="bam" /> 49 <param name="alignments" value="test1/snord81.bam" ftype="bam" />
50 <param name="mask" value="test1/ncrnadb09.v2.gtf" ftype="gtf" /> 50 <param name="mask" value="test1/ncrnadb09.v2.gtf" ftype="gtf" />
51 <param name="fasta" value="test1/ncrnadb09.fa" ftype="fasta" /> 51 <param name="fasta" value="test1/ncrnadb09.fa" ftype="fasta" />
52 <param name="output_format" value="1" /> 52 <param name="output_format" value="1" />
53 53
54 <output name="output" file="test1/snord81.flaimapper.txt" /> 54 <output name="output" file="test1/snord81.flaimapper.txt" />
55 </test> 55 </test>
56 <test><!-- Testing "Full genome alignment"-type analysis --> 56 <test><!-- Testing "Full genome alignment"-type analysis -->
57 <param name="alignments" value="test2/test_genomic_alignment.bam" ftype="bam" /> 57 <param name="alignments" value="test2/test_genomic_alignment.bam" ftype="bam" />
58 <param name="mask" value="test2/test_genomic_genes.gtf" ftype="gtf" /> 58 <param name="mask" value="test2/test_genomic_genes.gtf" ftype="gtf" />
59 <param name="fasta" value="test2/test_genomic_all_chromosomes.fa" ftype="fasta" /> 59 <param name="fasta" value="test2/test_genomic_all_chromosomes.fa" ftype="fasta" />
60 <param name="output_format" value="1" /> 60 <param name="output_format" value="1" />
61 61
62 <output name="output" file="test2/test_genomic_flaimapper_output.txt" /> 62 <output name="output" file="test2/test_genomic_flaimapper_output.txt" />
63 </test> 63 </test>
64 </tests> 64 </tests>
65 65
66 <help> 66 <help><![CDATA[
67 FlaiMapper wrapper for Galaxy 67 FlaiMapper wrapper for Galaxy
68 ============================= 68 =============================
69 69
70 https://github.com/yhoogstrate/flaimapper 70 https://github.com/yhoogstrate/flaimapper
71 http://www.ncbi.nlm.nih.gov/pubmed/25338717 71 http://www.ncbi.nlm.nih.gov/pubmed/25338717
154 ----------- 154 -----------
155 155
156 * Repository-Maintainer: Youri Hoogstrate 156 * Repository-Maintainer: Youri Hoogstrate
157 * Repository-Developers: Youri Hoogstrate 157 * Repository-Developers: Youri Hoogstrate
158 158
159 * Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools 159 * Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools
160 160
161 The tool wrapper has been written by Youri Hoogstrate from the Erasmus 161 The tool wrapper has been written by Youri Hoogstrate from the Erasmus
162 Medical Center (Rotterdam, Netherlands). 162 Medical Center (Rotterdam, Netherlands).
163 163 ]]></help>
164 </help> 164
165 165 <citations>
166 <citations> 166 <citation type="doi">10.1093/bioinformatics/btu696</citation>
167 <citation type="doi">10.1093/bioinformatics/btu696</citation> 167 </citations>
168 </citations>
169 </tool> 168 </tool>