comparison obitab.xml @ 4:4cf47c504672 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit dabf62d438facc62f3e606ff4419092fdcdfaa44

3:5f7003111e32

<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@
        

        ${no_definition_option}
        @INPUT_FORMAT@
        input > '$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>

4:4cf47c504672

<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="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        @GUNZIP_INPUT@
        

        ${no_definition_option}
        @INPUT_FORMAT@
        input > '$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 expect_num_outputs="1">
            <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>