comparison obiuniq.xml @ 3:ec215ed98831 draft

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

2:c0f7b58b4ce4

<tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
<command>

    <![CDATA[

    obiuniq
    #if str( $options_attribute) == "merge"
        -m '$options_uniq'
    #else
        -c '$options_uniq'
    #end if
    ${mid}
    ${prefix}
    '$input' > '$output'

    ]]>

</command>

<inputs>
    <param name="input" type="data" format="fasta,fastq" label="Input sequences file" />
    <param name="options_uniq" type="select" label="Attribute to merge" >
        <expand macro="attributes"/>
    </param>
    <param name="options_attribute" type="select" label="Use specific option" >
        <option value="merge" selected="true">merge</option>
        <option value="category_attribute">category_attribute</option>
    </param>
    <param name="mid" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Add a merged attribute containing the list of sequence record ids merged within this group" />
	<param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching" />
</inputs>
<outputs>
    <data format="fasta" name="output" label="output.fasta with ${tool.name} on ${on_string}" />
</outputs>

<tests>
   <test>
       <param name="input" value="output_ngsfilter_error_3.fastq" />
       <param name="options_uniq" value="sample" />
       <param name="options_attribute" value="merge" />
       <param name="mid" value="False" />
       <param name="prefix" value="False" />
       <output name="output" file="output_obiuniq.fasta" ftype="fasta"/>
   </test>
   <test>
       <param name="input" value="output_ngsfilter_error_3.fastq" />
       <param name="options_uniq" value="family" />
       <param name="options_attribute" value="category_attribute" />
       <param name="mid" value="True" />
       <param name="prefix" value="True" />
       <output name="output" file="output_obiuniq_family.fasta" ftype="fasta"/>
   </test>

</tests>
<help><![CDATA[

.. class:: infomark

**What it does**

The obiuniq command is in some way analog to the standard Unix uniq -c command.

Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records.

A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.

The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed.

A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option.

As the identifier, the set of attributes (key=value) and the definition of the sequence records that are grouped together may be different, two options (-m and -i) allow refining how these parts of the records are reported.

\*  By default, only attributes with identical values within a group of sequence records are kept.

\*  A count attribute is set to the total number of sequence records for each group.

\*  For each attribute specified by the -m option, a new attribute whose key is prefixed by merged_ is created. These new attributes contain the number of times each value occurs within the group of sequence records.


@OBITOOLS_LINK@



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

3:ec215ed98831

<tool id="obi_uniq" name="obiuniq" version="@TOOL_VERSION@" profile="@PROFILE@">
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <command><![CDATA[
    @GUNZIP_INPUT@

    obiuniq
    --without-progress-bar
    #if str( $options_attribute) == "merge"
        -m '$options_uniq'
    #else
        -c '$options_uniq'
    #end if
    ${mid}
    ${prefix}
    @INPUT_FORMAT@
    input
    @GZIP_OUTPUT@
    > '$output'
    @GENERATE_GALAXY_JSON@
    ]]></command>
    <inputs>
        <param name="input" type="data" format="@INPUT_FORMATS@" label="Input sequences file" />
        <param name="options_uniq" type="select" label="Attribute to merge" >
            <expand macro="attributes"/>
        </param>
        <param name="options_attribute" type="select" label="Use specific option" >
            <option value="merge" selected="true">merge</option>
            <option value="category_attribute">category_attribute</option>
        </param>
        <param name="mid" type="boolean" checked="false" truevalue="-i" falsevalue="" label="Add a merged attribute containing the list of sequence record ids merged within this group" />
    	<param name="prefix" type="boolean" checked="false" truevalue="-p" falsevalue="" label="Dereplicate through a prefix matching" />
        <expand macro="input_format_options_macro"/>
    </inputs>
    <outputs>
        <data format="auto" name="output"/>
    </outputs>
    <tests>
       <test>
           <param name="input" value="output_ngsfilter_error_3.fastq" ftype="fastqsanger"/>
           <param name="options_uniq" value="sample" />
           <param name="options_attribute" value="merge" />
           <param name="mid" value="False" />
           <param name="prefix" value="False" />
           <output name="output" file="output_obiuniq.fasta" ftype="fasta"/>
       </test>
       <test>
           <param name="input" value="output_ngsfilter_error_3.fastq.gz" ftype="fastqsanger.gz"/>
           <param name="options_uniq" value="family" />
           <param name="options_attribute" value="category_attribute" />
           <param name="mid" value="True" />
           <param name="prefix" value="True" />
           <output name="output" file="output_obiuniq_family.fasta.gz" ftype="fasta.gz" decompress="true"/>
       </test>
    </tests>
    <help><![CDATA[
    .. class:: infomark

    **What it does**

    The obiuniq command is in some way analog to the standard Unix uniq -c command.

    Instead of working text line by text line as the standard Unix tool, the processing is done on sequence records.

    A sequence record is a complex object composed of an identifier, a set of attributes (key=value), a definition, and the sequence itself.

    The obiuniq command groups together sequence records. Then, for each group, a sequence record is printed.

    A group is defined by the sequence and optionally by the values of a set of attributes specified with the -c option.

    As the identifier, the set of attributes (key=value) and the definition of the sequence records that are grouped together may be different, two options (-m and -i) allow refining how these parts of the records are reported.

    \*  By default, only attributes with identical values within a group of sequence records are kept.

    \*  A count attribute is set to the total number of sequence records for each group.

    \*  For each attribute specified by the -m option, a new attribute whose key is prefixed by merged_ is created. These new attributes contain the number of times each value occurs within the group of sequence records.


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