view obitab.xml @ 3:5f7003111e32 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit 5d3c7a7b3f7d687bb03ef7993ddf1a6507d655bd"

<tool id="obi_tab" name="obitab" version="@TOOL_VERSION@" profile="@PROFILE@">
    <description>converts sequence file to a tabular file</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        @GUNZIP_INPUT@
        
        obitab
        --without-progress-bar
        #if $additional_file
            --omit-attribute='$additional_file'
        #end if
        ${output_seq_option}
        ${no_definition_option}
        @INPUT_FORMAT@
        input > '$output'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="@INPUT_FORMATS@,txt,tabular" label="Input sequences file" />
        <param name="output_seq_option" type="boolean" checked="false" truevalue="-o" falsevalue="" label="Do you want to add an extra column?" help="Use this option if you want to add an extra column at the end of the table for the sequence itself"/>
        <param name="no_definition_option" type="boolean" checked="false" truevalue="-d" falsevalue="" label="Do you want to remove column containing the sequence definition?" help="Use this option if you want to remove column containing the sequence definition in the output tab file"/>
        <param name="additional_file" type="data" optional="true" format="tabular" label="filter attributes from tabular file" />
        <expand macro="input_format_options_macro"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>
    <tests>
        <test>
            <param name="input" value="output_obisort.fastq" />
            <param name="output_seq_option" value="False"/>
            <param name="no_definition_option" value="True"/>
            <output name="output" file="output_obitab.txt" ftype="tabular"/>
        </test>
    </tests>
    <help><![CDATA[


.. class:: infomark

**What it does**

obitab command converts sequence file to a tabular file that can be open by a spreadsheet program or R

@OBITOOLS_LINK@

    ]]>
    </help>
    <expand macro="citation" />
</tool>