root/galaxy-central/tools/fastx_toolkit/fastx_collapser.xml

<tool id="cshl_fastx_collapser" name="Collapse">
        <description>sequences</description>
        <requirements><requirement type="package">fastx_toolkit</requirement></requirements>
        <command>zcat -f '$input' | fastx_collapser -v -o '$output' </command>

        <inputs>
                <param format="fastqsolexa,fasta" name="input" type="data" label="Library to collapse" />
        </inputs>

    <!-- 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" />
                        <output name="output" file="fasta_collapser1.out" />
                </test>
        </tests>
    -->
        <outputs>
                <data format="fasta" name="output" metadata_source="input" />
        </outputs>
  <help>

**What it does**

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

--------

**Example**

Example Input File (Sequence "ATAT" appears multiple times):: 

    >CSHL_2_FC0042AGLLOO_1_1_605_414
    TGCG
    >CSHL_2_FC0042AGLLOO_1_1_537_759
    ATAT
    >CSHL_2_FC0042AGLLOO_1_1_774_520
    TGGC
    >CSHL_2_FC0042AGLLOO_1_1_742_502
    ATAT
    >CSHL_2_FC0042AGLLOO_1_1_781_514
    TGAG
    >CSHL_2_FC0042AGLLOO_1_1_757_487
    TTCA
    >CSHL_2_FC0042AGLLOO_1_1_903_769
    ATAT
    >CSHL_2_FC0042AGLLOO_1_1_724_499
    ATAT

Example Output file::

    >1-1
    TGCG
    >2-4
    ATAT
    >3-1
    TGGC
    >4-1
    TGAG
    >5-1
    TTCA
    
.. class:: infomark

Original Sequence Names / Lane descriptions (e.g. "CSHL_2_FC0042AGLLOO_1_1_742_502") are discarded. 

The output sequence name is composed of two numbers: the first is the sequence's number, the second is the multiplicity value.

The following output::

    >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.

</help>
</tool>