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flaimapper-gtf-from-fasta.xml |
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| diff -r efd29213e8e5 -r 8faba9df2791 flaimapper-gtf-from-fasta.xml --- a/flaimapper-gtf-from-fasta.xml Fri Jul 31 05:30:48 2015 -0400 +++ b/flaimapper-gtf-from-fasta.xml Fri Jul 31 05:30:55 2015 -0400 |
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| @@ -1,43 +1,41 @@ <?xml version="1.0" encoding="UTF-8"?> -<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w1"> - <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description> - <requirements> - <requirement type="package" version="1.2.1">flaimapper</requirement> - </requirements> - - <stdio> - <regex - match="[fai_load] build FASTA index." - source="stderr" - level="log" - description="The FASTA file is being indexed." /> - </stdio> - - <version_command>flaimapper --version</version_command> - - <command> - gtf-from-fasta - -o $output - $fasta - </command> - - <inputs> - <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="" /> - </inputs> - - <outputs> - <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" /> - </outputs> - - <tests> - <test> - <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" /> - - <output name="output" file="test3/reference.gtf" /> - </test> - </tests> - - <help> +<tool id="flaimapper-gtf-from-fasta" name="FlaiMapper: extract GTF from FASTA" version="1.2.1.w2"> + <description>Extract GTF file from FASTA file (as FlaiMapper reference).</description> + <requirements> + <requirement type="package" version="1.2.1">flaimapper</requirement> + </requirements> + + <stdio> + <regex + match="[fai_load] build FASTA index." + source="stderr" + level="log" + description="The FASTA file is being indexed." /> + </stdio> + + <version_command>flaimapper --version</version_command> + + <command><![CDATA[ + gtf-from-fasta -o $output $fasta + ]]></command> + + <inputs> + <param name="fasta" type="data" format="fasta" label="Fasta sequence corresponding to reference genome" help="This is the FASTA file that fits the used reference genome (e.g. hg19 or a ncRNA database)." /> + </inputs> + + <outputs> + <data format="gtf" name="output" label="${tool.name} on ${fasta.name}" /> + </outputs> + + <tests> + <test> + <param name="fasta" value="test3/ncrnadb09.fa" ftype="fasta" /> + + <output name="output" file="test3/reference.gtf" /> + </test> + </tests> + + <help><![CDATA[ FlaiMapper wrapper for Galaxy ============================= @@ -100,14 +98,14 @@ * Repository-Maintainer: Youri Hoogstrate * Repository-Developers: Youri Hoogstrate -* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools +* Repository-Development: https://github.com/ErasmusMC-Bioinformatics/galaxy-tools The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands). - </help> - - <citations> - <citation type="doi">10.1093/bioinformatics/btu696</citation> - </citations> + ]]></help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btu696</citation> + </citations> </tool> |