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comparison flaimapper.xml @ 28:19d1402611ef draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 0eac9a776e7bc33275b8ef5e76a4f17b7b5c1259-dirty
author yhoogstrate
date Wed, 03 Jun 2015 07:27:47 -0400
parents 19feb87f757d
children 3074e91f9f80
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27:19feb87f757d 28:19d1402611ef
1 <?xml version="1.0" encoding="UTF-8"?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="flaimapper" name="FlaiMapper" version="1.1.5.a"> 2 <tool id="flaimapper" name="FlaiMapper" version="1.2.1.w1">
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="0.8.2.1">pysam</requirement> 5 <requirement type="package" version="1.2.1">flaimapper</requirement>
6 <requirement type="package" version="1.1.5">flaimapper</requirement>
7 </requirements> 6 </requirements>
7
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" />
10 <regex match="[fai_load] build FASTA index." source="stderr" level="log" />
11 </stdio>
8 12
9 <version_command>flaimapper --version</version_command> 13 <version_command>flaimapper --version</version_command>
10 14
11 <command> 15 <command>
12 flaimapper 16 flaimapper
18 22
19 #for $alignment in $alignments 23 #for $alignment in $alignments
20 $alignment 24 $alignment
21 #end for 25 #end for
22 </command> 26 </command>
23
24 <stdio>
25 <regex match="[fai_load] build FASTA index." source="stderr" level="log" />
26 </stdio>
27 27
28 <inputs> 28 <inputs>
29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" /> 29 <param name="alignments" type="data" format="bam" label="Alignment file(s)" help="Aligned small RNA-Seq reads which may not be fragmented. In case you add multiple BAM files, FlaiMapper will simply concatenate the data and perform one single analysis on the entire set of alignments." multiple="true" />
30 30
31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" /> 31 <param name="mask" type="data" format="gtf,gff,gff3" label="small ncRNA Annotation (gtf)" help="" />
43 <outputs> 43 <outputs>
44 <data format="tabular" name="output" label="${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> 48 <test><!-- Testing "ncRNAdb09 alignment"-type analysis -->
49 <param name="alignments" value="snord81.bam" ftype="bam" /> 49 <param name="alignments" value="test1/snord81.bam" ftype="bam" />
50 <param name="mask" value="ncrnadb09.gtf" ftype="gtf" /> 50 <param name="mask" value="test1/ncrnadb09.v2.gtf" ftype="gtf" />
51 <param name="fasta" value="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="snord81.flaimapper.txt" /> 54 <output name="output" file="test1/snord81.flaimapper.txt" />
55 </test>
56 <test><!-- Testing "Full genome alignment"-type analysis -->
57 <param name="alignments" value="test2/test_genomic_alignment.bam" ftype="bam" />
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" />
60 <param name="output_format" value="1" />
61
62 <output name="output" file="test2/test_genomic_flaimapper_output.txt" />
55 </test> 63 </test>
56 </tests> 64 </tests>
57 65
58 <help> 66 <help>
59 FlaiMapper wrapper for Galaxy 67 FlaiMapper wrapper for Galaxy