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comparison flaimapper.xml @ 1:96d135d3c57f draft

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planemo upload for repository https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools/raw/master/flaimapper commit 18c2fff1b59feb43640d744444d8fb6193def183-dirty
author yhoogstrate
date Wed, 03 Jun 2015 07:57:12 -0400
parents d6abffbc9ee7
children efd29213e8e5
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0:d6abffbc9ee7 1:96d135d3c57f
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>
8 7
9 <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" />
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
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