| Previous changeset 1:239ce9f24386 (2019-12-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fargene commit d5aed24826ee23758798b458334b2f5e7c84eb0f |
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modified:
fargene.xml |
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| diff -r 239ce9f24386 -r b982a9ea939c fargene.xml --- a/fargene.xml Mon Dec 02 04:39:18 2019 -0500 +++ b/fargene.xml Fri Feb 09 21:30:09 2024 +0000 |
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| @@ -3,6 +3,9 @@ <macros> <import>macros.xml</import> </macros> + <xrefs> + <xref type="bio.tools">fargene</xref> + </xrefs> <expand macro="requirements" /> <version_command>fargene --version</version_command> <command detect_errors="exit_code"><![CDATA[ @@ -102,24 +105,17 @@ <option value="class_d_2">Class D beta-lactamases-2</option> <option value="qnr">QNR</option> </param> - <param name="score" argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as - a (almost) complete gene" /> - <param name="meta_score" argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as - a positive. Expressed as score per amino acid" /> - <param name="protein" argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" /> - <param name="min_orf_length" argument="--min-orf-length" type="integer" min="1" value="90" label="The minimal length for a retrieved predicted ORF (nt)" /> - <param name="retrieve_whole" argument="--retrieve-whole" type="boolean" truevalue="--retrieve-whole " falsevalue="" checked="False" label="Use this flag if the whole sequence where a hit is - detected should be retrieved" /> - <param name="no_orf_predict" argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" /> - <param name="no_quality_filtering" argument="--no-quality-filtering" type="boolean" truevalue="--no-quality-filtering" falsevalue="" checked="False" label="Use if no quality control should be performed on the - metagenomic data" /> - <param name="no_assembly" argument="--no-assembly" type="boolean" truevalue="--no-assembly" falsevalue="" checked="False" label="Use if you want to skip the assembly and retrieval of - contigs for metagenomic data" /> - <param name="orf_finder" argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF - prediction of genomes/contigs" /> - <param name="store_peptides" argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences. Useful if you plan to - redo the analysis using a different model and want to - skip the preprocessing steps" /> + <param argument="--score" type="float" value="0.0" label="The threshold score for a sequence to be classified as a (almost) complete gene" /> + <param argument="--meta-score" type="float" value="0.0" label="The threshold score for a fragment to be classified as a positive. Expressed as score per amino acid" /> + <param argument="--protein" type="boolean" truevalue="--protein" falsevalue="" checked="False" label="Rescue short unassmebled plasmids" /> + <param argument="--min-orf-length" type="integer" min="1" value="90" label="The minimal length for a retrieved predicted ORF (nt)" /> + <param argument="--retrieve-whole" type="boolean" truevalue="--retrieve-whole " falsevalue="" checked="False" label="Use this flag if the whole sequence where a hit is detected should be retrieved" /> + <param argument="--no-orf-predict" type="boolean" truevalue="--no-orf-predict" falsevalue="" checked="False" label="Do not perform ORF prediction" /> + <param argument="--no-quality-filtering" type="boolean" truevalue="--no-quality-filtering" falsevalue="" checked="False" label="Use if no quality control should be performed on the metagenomic data" /> + <param argument="--no-assembly" type="boolean" truevalue="--no-assembly" falsevalue="" checked="False" label="Use if you want to skip the assembly and retrieval of contigs for metagenomic data" /> + <param argument="--orf-finder" type="boolean" truevalue="--orf-finder" falsevalue="" checked="False" label="Use NCBI ORFfinder instead of prodigal for ORF prediction of genomes/contigs" /> + <param argument="--store-peptides" type="boolean" truevalue="--store-peptides" falsevalue="" checked="False" label="Store the translated sequences" + help="Useful if you plan to redo the analysis using a different model and want to skip the preprocessing steps" /> </inputs> <outputs> |