view change_fasta_header_using_tabular_file.xml @ 0:540425dc9746 draft default tip

planemo upload for repository https://github.com/portiahollyoak/Tools commit 132bb96bba8e7aed66a102ed93b7744f36d10d37-dirty

<tool id ="change_fasta_header_using_tabular_file" name="Change fasta header" version=" 0.1.0">
    <description>using a tabular file</description>
    <stdio>
        <exit_code range="1:" />
    </stdio>
    <command>python $__tool_directory__/change_fasta_header_using_tabular_file.py
        --tab_input "$input1"
        --fasta_input "$input2"
        "$output"
    </command>
    <inputs>
        <param format="tabular" name="input1" type="data" label="Tabular File"/>
        <param format="fasta" name="input2" type="data" label="Fasta file"/>
    </inputs>
    <outputs>
        <data format="fasta" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="tabular_file.tsv" ftype="tabular"/>
            <param name="input2" value="genbank_input.fasta" ftype="fasta"/>
            <output name="output" file="output.fasta"/>
        </test>
    </tests>
    <help> <![CDATA[

This tool takes 2 input files, a tabular file with text to replace in the first column,
and a replacement text in the 2nd column, as well as a fasta file.
Every occurence of values in the first column of the tabular file will be replaced with the
value in the 2nd column.

-----

*Example*

**Fasta header** ::

    >RT1C
    ATGCATGC

**Tabular file** ::

    RT1C    Rt1c

**Output file** ::

    >Rt1c
    ATGCATGC


    ]]> </help>
</tool>