Mercurial > repos > iuc > obi_convert
view obiconvert.xml @ 3:374fd9feb032 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"
author | iuc |
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date | Mon, 10 May 2021 19:36:34 +0000 |
parents | 6259965de501 |
children | e328ced6cf0a |
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<tool id="obi_convert" name="obiconvert" version="@TOOL_VERSION@" profile="@PROFILE@"> <description>converts sequence files to different output formats</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <command><![CDATA[ @GUNZIP_INPUT@ obiconvert #if $db -d '$db' #end if #if $tax -t '$tax' #end if @INPUT_FORMAT@ @OUT_FORMAT@ ${uppercase} ${ecopcrdb} #if str( $ecopcrdb) == "--ecopcrdb" --ecopcrdb-output=${ecopcrdb_output} #end if input @GZIP_OUTPUT@ > '${output}' @GENERATE_GALAXY_JSON@ ]]></command> <inputs> <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" help="database used for the in silico PCR. The database must be in the ecoPCR format (for example output of obiconvert)" /> <param name="db" type="data" optional="true" format="txt,tabular" label="ecoPCR taxonomy database" /> <param name="tax" type="data" optional="true" format="txt,tabular" label="NCBI taxonomy dump repository"/> <expand macro="input_format_options_macro"/> <expand macro="out_format_macro"/> <param name="ecopcrdb" type="boolean" truevalue="--ecopcrdb" falsevalue="" label="Do you want to create an ecoPCR database from sequence records results?" help="Use this option if you want to generate an ecoPCR database output file" /> <param name="uppercase" type="boolean" truevalue="--uppercase" falsevalue="" label="Do you want to print sequences in upper case?" /> </inputs> <outputs> <data format="txt" name="ecopcrdb_output" label="${tool.name} on ${on_string}: ecopcrdb"> <filter>ecopcrdb == True</filter> </data> <data format="auto" name="output"/> </outputs> <tests> <test> <param name="input" value="output_obisort.fasta" /> <param name="options_inputtype" value="--fasta"/> <param name="options_seqtype" value="--nuc"/> <param name="out_format" value="fasta"/> <param name="ecopcrdb" value="false"/> <param name="uppercase" value="true"/> <output name="output" file="output_obiconvert.fasta" ftype="fasta"/> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** obiconvert converts sequence files to different output formats. See the documentation for more details on the different formats. Input files can be in : fasta format extended OBITools fasta format Sanger fastq format Solexa fastq format ecoPCR format ecoPCR database format GenBank format EMBL format obiconvert converts those files to the : extended OBITools fasta format Sanger fastq format ecoPCR database format If no file name is specified, data is read from standard input. @OBITOOLS_LINK@ ]]> </help> <expand macro="citation" /> </tool>