comparison obiconvert.xml @ 4:e328ced6cf0a draft default tip

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

3:374fd9feb032

<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@
        

        @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"/>

4:e328ced6cf0a

<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="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
        @GUNZIP_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 expect_num_outputs="1">
            <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"/>