Mercurial > repos > yhoogstrate > flaimapper
diff flaimapper.xml @ 1:96d135d3c57f draft
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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--- a/flaimapper.xml Thu May 21 07:26:46 2015 -0400 +++ b/flaimapper.xml Wed Jun 03 07:57:12 2015 -0400 @@ -1,12 +1,12 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="flaimapper" name="FlaiMapper" version="1.1.5.a"> +<tool id="flaimapper" name="FlaiMapper" version="1.2.1.w1"> <description>Detect small ncRNA derived fragments using Fragment Location Annotation Identification Mapper.</description> <requirements> - <requirement type="package" version="0.8.2.1">pysam</requirement> - <requirement type="package" version="1.1.5">flaimapper</requirement> + <requirement type="package" version="1.2.1">flaimapper</requirement> </requirements> <stdio> + <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" /> <regex match="[fai_load] build FASTA index." source="stderr" level="log" /> </stdio> @@ -45,13 +45,21 @@ </outputs> <tests> - <test> - <param name="alignments" value="snord81.bam" ftype="bam" /> - <param name="mask" value="ncrnadb09.gtf" ftype="gtf" /> - <param name="fasta" value="ncrnadb09.fa" ftype="fasta" /> - <param name="output_format" value="1" /> + <test><!-- Testing "ncRNAdb09 alignment"-type analysis --> + <param name="alignments" value="test1/snord81.bam" ftype="bam" /> + <param name="mask" value="test1/ncrnadb09.v2.gtf" ftype="gtf" /> + <param name="fasta" value="test1/ncrnadb09.fa" ftype="fasta" /> + <param name="output_format" value="1" /> - <output name="output" file="snord81.flaimapper.txt" /> + <output name="output" file="test1/snord81.flaimapper.txt" /> + </test> + <test><!-- Testing "Full genome alignment"-type analysis --> + <param name="alignments" value="test2/test_genomic_alignment.bam" ftype="bam" /> + <param name="mask" value="test2/test_genomic_genes.gtf" ftype="gtf" /> + <param name="fasta" value="test2/test_genomic_all_chromosomes.fa" ftype="fasta" /> + <param name="output_format" value="1" /> + + <output name="output" file="test2/test_genomic_flaimapper_output.txt" /> </test> </tests>