view obitab.xml.orig @ 4:d0f6ac976373 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/obitools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

<<<<<<< HEAD
<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>
=======
<tool id="obi_tab" name="obitab" version="@TOOL_VERSION@">
    <description>converts sequence file to a tabular file that can be open by a spreadsheet program or R</description>
    <expand macro="bio_tools"/>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>

    <command>

        <![CDATA[
        obitab
        #if $additional_file
            --omit-attribute='$additional_file'
        #end if
        ${output_seq_option}
        ${no_definition_option}
        ${options_inputtype}
        ${options_seqtype}

        '$input' > '$output'
        ]]>

    </command>

    <inputs>
        <param name="input" type="data" format="fastq,fasta,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" />
        <param name="options_inputtype" type="select" label="Specify the input datatype">
            <expand macro="inputtype"/>
        </param>
        <param name="options_seqtype" type="select" label="Specify the sequence datatype" >
            <option value="--nuc" selected="true">nucleic</option>
            <option value="--prot">protein</option>
        </param>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="output.tabular with ${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="output_obisort.fastq" />
            <param name="output_seq_option" value="False"/>
            <param name="no_definition_option" value="True"/>
            <param name="options_inputtype" value="fasta"/>
            <param name="options_seqtype" value="--prot"/>
            <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>
>>>>>>> 7abad681f (add tools up until P)