comparison fastx_renamer.xml @ 2:d8a3d31554d7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/fastx_toolkit/fastx_renamer commit bbb2e6b6769b03602a8ab97001f88fbec52080a1

1:02f8a17a4ebd

<tool id="cshl_fastx_renamer" name="Rename sequences" version="0.0.11" >
    <description></description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
    <command>
<![CDATA[
zcat -f < '$input' | fastx_renamer -n $TYPE -o '$output' -v
#if $input.ext == "fastqsanger":
    -Q 33
#end if
]]>
    </command>

    <inputs>
        <param format="fastqsolexa,fasta,fastqsanger" name="input" type="data" label="FASTQ/A Library to rename" />

        <param name="TYPE" type="select" label="Rename sequence identifiers to">
            <option value="SEQ">Nucleotides sequence</option>
            <option value="COUNT">Numeric Counter</option>
        </param>
    </inputs>

    <outputs>
        <data format_source="input" name="output" metadata_source="input" />
    </outputs>
    <tests>
    </tests>
    <help>
**What it does**

This tool renames the sequence identifiers in a FASTQ/A file.

.. class:: infomark

------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    </help>
<!-- FASTQ-to-FASTA is part of the FASTX-toolkit, by A.Gordon ([e-mail]) -->
</tool>

2:d8a3d31554d7

<tool id="cshl_fastx_renamer" name="Rename sequences" version="@VERSION@+galaxy0" >
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
@CATS@ fastx_renamer
-n $TYPE
-o '$output'
-v
@FQQUAL@
    ]]></command>

    <inputs>
        <expand macro="fastx_input" />

        <param name="TYPE" type="select" label="Rename sequence identifiers to">
            <option value="SEQ">Nucleotides sequence</option>
            <option value="COUNT">Numeric Counter</option>
        </param>
    </inputs>

    <outputs>
        <data name="output" format_source="input" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="fastx_renamer-in1.fastq" />
            <param name="TYPE" value="SEQ" />
            <output name="output" file="fastx_renamer-out1.fastq" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool renames the sequence identifiers in a FASTQ/A file.

.. class:: infomark

------

This tool is based on `FASTX-toolkit`__ by Assaf Gordon.

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    ]]></help>
    <expand macro="citations" />
</tool>