comparison fastx_collapser.xml @ 3:7ce1891db6f5 draft

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

2:421f0af4ee95

<tool id="cshl_fastx_collapser" version="1.0.0" name="Collapse">
    <description>sequences</description>
    <requirements>
        <requirement type="package" version="0.0.13">fastx_toolkit</requirement>
    </requirements>
    <command>
<![CDATA[
zcat -f < '$input' | fastx_collapser -v -o '$output'
#if $input.ext == "fastqsanger":
    -Q 33
#end if
]]>
    </command>

    <inputs>
        <param format="fasta,fastqsanger,fastqsolexa" name="input" type="data" label="Library to collapse" />
    </inputs>
    <outputs>
        <data format="fasta" name="output" metadata_source="input" />
    </outputs>
    <!-- The order of sequences in the test output differ between 32 bit and 64 bit machines.
    <tests>
        <test>
            <param name="input" value="fasta_collapser1.fasta" />
            <param name="output" file="fasta_collapser1.out" />
        </test>
    </tests>
    -->
    <help>
**What it does**

This tool collapses identical sequences in a FASTA file into a single sequence.

--------

    >2-4
    ATAT

means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.


------

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

 .. __: http://hannonlab.cshl.edu/fastx_toolkit/
    </help>
</tool>

3:7ce1891db6f5

<tool id="cshl_fastx_collapser" version="1.0.1" name="Collapse">
    <description>sequences</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <command detect_errors="exit_code"><![CDATA[
@CATS@ fastx_collapser -v
-o '$output'
@FQQUAL@
    ]]></command>

    <inputs>
        <expand macro="fastx_input" />
    </inputs>
    <outputs>
        <data name="output" format="fasta" metadata_source="input" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="fasta_collapser1.fasta" />
            <!-- The output is sorted differently depending on architecture,
                 so the sort attribute is needed here -->
            <output name="output" file="fasta_collapser1.out" sort="true" />
        </test>
    </tests>
    <help><![CDATA[
**What it does**

This tool collapses identical sequences in a FASTA file into a single sequence.

--------

    >2-4
    ATAT

means that the sequence "ATAT" is the second sequence in the file, and it appeared 4 times in the input FASTA file.

------

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

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