view fasta_nucleotide_color_plot.xml @ 3:e4b5401adcec draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_nucleotide_color_plot commit ea2c53b2c83e61350bf471981d850fa061bf5512

<tool id="fasta_nucleotide_color_plot" name="Fasta nucleotide color plot" version="1.0.1">
    <description></description>
    <requirements>
        <requirement type="package" version="8.0.112">openjdk</requirement>
    </requirements>
    <macros>
        <import>macros.xml</import>
    </macros>
    <command detect_errors="exit_code"><![CDATA[
java -jar '$__tool_directory__/FourColorPlot.jar'
-f '$input'
-h $pixel_height
-w $pixel_width
#if str($a_select_color_cond.a_select_color) == "a_rgb":
    -A '$a_select_color_cond.a_rgb'
#else:
    -A $a_select_color_cond.color_a
#end if
#if str($t_select_color_cond.t_select_color) == "t_rgb":
    -T '$t_select_color_cond.t_rgb'
#else
    -T $t_select_color_cond.color_t
#end if
#if str($g_select_color_cond.g_select_color) == "g_rgb":
    -G '$g_select_color_cond.g_rgb'
#else
    -G $g_select_color_cond.color_g
#end if
#if str($c_select_color_cond.c_select_color) == "c_rgb":
    -C '$c_select_color_cond.c_rgb'
#else
    -C $c_select_color_cond.color_c
#end if
#if str($n_select_color_cond.n_select_color) == "n_rgb":
    -N '$n_select_color_cond.n_rgb'
#else
    -N $n_select_color_cond.color_n
#end if
-o '$output' 1>/dev/null
    ]]></command>
    <inputs>
        <param name="input" type="data" format="fasta" label="FASTA file" />
        <param name="pixel_height" type="integer" value="2" min="1" label="Pixel height per nucleotide" />
        <param name="pixel_width" type="integer" value="2" min="1" label="Pixel width per nucleotide" />
        <conditional name="a_select_color_cond">
            <param name="a_select_color" type="select" label="A nucleotide: specify RGB value or select color?">
                <option value="a_rgb" selected="True">specify RGB</option>
                <option value="a_color">select color</option>
            </param>
            <when value="a_color">
                <param name="color_a" type="select" label="Color">
                    <expand macro="color_selector" />
                </param>
            </when>
            <when value="a_rgb">
                <param name="a_rgb" type="text" value="254,25,24" label="RGB" />
            </when>
        </conditional>
        <conditional name="t_select_color_cond">
            <param name="t_select_color" type="select" label="T nucleotide: specify RGB value or select color?">
                <option value="t_rgb" selected="True">specify RGB</option>
                <option value="t_color">select color</option>
            </param>
            <when value="t_color">
                <param  name="color_t" type="select" label="Color">
                    <expand macro="color_selector" />
                </param>
            </when>
            <when value="t_rgb">
                <param name="t_rgb" type="text" value="50,204,60" label="RGB" />
            </when>
        </conditional>
        <conditional name="g_select_color_cond">
            <param name="g_select_color" type="select" label="G nucleotide: specify RGB value or select color?">
                <option value="g_rgb" selected="True">specify RGB</option>
                <option value="g_color">select color</option>
            </param>
            <when value="g_color">
                <param  name="color_g" type="select" label="Color">
                    <expand macro="color_selector" />
                </param>
            </when>
            <when value="g_rgb">
                <param name="g_rgb" type="text" value="252,252,80" label="RGB" />
            </when>
        </conditional>
        <conditional name="c_select_color_cond">
            <param name="c_select_color" type="select" label="C nucleotide: specify RGB value or select color?">
                <option value="c_rgb" selected="True">specify RGB</option>
                <option value="c_color">select color</option>
            </param>
            <when value="c_color">
                <param  name="color_c" type="select" label="Color">
                    <expand macro="color_selector" />
                </param>
            </when>
            <when value="c_rgb">
                <param name="c_rgb" type="text" value="43,49,246" label="RGB" />
            </when>
        </conditional>
        <conditional name="n_select_color_cond">
            <param name="n_select_color" type="select" label="N nucleotide: specify RGB value or select color?">
                <option value="n_rgb" selected="True">specify RGB</option>
                <option value="n_color">select color</option>
            </param>
            <when value="n_color">
                <param  name="color_n" type="select" label="Color">
                    <expand macro="color_selector" />
                </param>
            </when>
            <when value="n_rgb">
                <param name="n_rgb" type="text" value="128,128,128" label="RGB" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output" format="png" />
    </outputs>
    <tests>
        <test>
            <param name="input" value="input.fasta" ftype="fasta" />
            <output name="output" file="output1.png" ftype="png" compare="sim_size" />
        </test>
        <test>
            <param name="input" value="input.fasta" ftype="fasta" />
            <param name="color_a" value="255,0,0" />
            <param name="color_t" value="0,255,0" />
            <param name="color_g" value="0,0,255" />
            <param name="color_c" value="255,255,0" />
            <param name="color_n" value="128,0,128" />
            <output name="output" file="output2.png" ftype="png" compare="sim_size" />
        </test>
    </tests>
    <help>

**What it does**

Produces a graphical representation of FASTA data with each nucleotide represented by a selected color.

-----

**Options**

* **Pixel Height per Nucleotide** - height of each nucleotide in pixels
* **Pixel Width per Nucleotide** - width of each nucleotide in pixels
* **A Color** - color of A nucleotide
* **T Color** - color of T nucleotide
* **G Color** - color of G nucleotide
* **C Color** - color of C nucleotide
* **N Color** - color of N nucleotide

    </help>
    <expand macro="citations" />
</tool>