annotate pretext_snapshot.xml @ 6:326098bc19cc draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pretext commit e387e8541eb3e9c5ce56440f955a3b6f2aa27d08

<tool id="pretext_snapshot" name="Pretext Snapshot"  version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
        <description>image generator for Pretext contact maps</description>
    <macros>
        <token name="@TOOL_VERSION@">0.0.4</token>
        <token name="@VERSION_SUFFIX@">0</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">pretextsnapshot</requirement>
        <requirement type="package" version="1.601">rename</requirement>
    </requirements>
    <version_command>PretextSnapshot --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
        PretextSnapshot -m $input
        -f $formats.outformat
        #if $formats.outformat == 'jpeg':
            --jpegQuality $formats.jpegQuality
        #end if
        -r $resolution
        -c $colormap
        --sequences '$sequences'
        --minTexels $mintexels
        #if $grid.showGrid == 'yes':
            --gridSize $grid.gridsize
            --gridColour $grid.gridcolor
        #else:
            --gridSize 0
        #end if
        '${sequencenames}'
        -o output
        --prefix pretext_snapshot
        #if $formats.outformat == 'jpeg':
            && find ./output/* | rename -s .jpeg .jpg
        #end if
    ]]></command>
    <inputs>
        <param name="input" type="data" argument="--map" format="pretext" label="Input Pretext map file"/>
        <conditional name="formats">
            <param name="outformat" argument="-f" type="select" label="Output image format" help="Format of output image">
                <option value="png" selected="true">PNG</option>
                <option value="bmp">BMP</option>
                <option value="jpeg">JPG</option>
            </param>
            <when value="png"/>
            <when value="bmp"/>
            <when value="jpeg">
                <param argument="--jpegQuality" type="integer" label="JPEG quality factor" value="80" min="0" max="100" help="An integer between 0 and 100, default 80. Larger values result in increased image quality and file size."/>
            </when>
        </conditional>
        <param name="resolution" argument="-r" type="integer" label="Output image resolution" min="1" value="1000" help="Image resolution, a positive integer, default 1080. For non-square images this will be the resolution of the longest dimension."/>
        <param name="colormap" argument='-c' type="integer" label="Color Map" value="5" min="0" max="30" help="Color map based on list available in the help section"/>
        <param argument="--sequences" type="text" label="Sequence specification string" value="=full, =all" help="Each entry, except for '=all', corresponds to one output image. More information available in the help section.">
            <sanitizer invalid_char="">
                <valid initial="string.ascii_letters,string.digits">
                    <add value="="/>
                    <add value="_"/>
                    <add value="&#32;"/>
                    <add value="&#44;"/>
                    <add value="&#91;"/>
                    <add value="&#93;"/>
                    <add value="&#123;"/>
                    <add value="&#125;"/>
                    <add value="&#35;"/>
                    <add value="&#60;"/>
                    <add value="&#62;"/>
                </valid>
            </sanitizer>
        </param>
        <param name="mintexels" argument="--minTexels" type="integer" min="1" label="Min Texels" value="64" help="Minimum map texels per image (along a single dimension), a positive integer, Output images over too small a range that violate this minimum will not be created."/>
        <conditional name="grid">
            <param name="showGrid" label="Show grid?" type="select">
                <option value="no">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="yes">
                <param name="gridsize" argument="--gridSize" type="integer" label="Grid size" value="1" min="1" help="Width in pixels of the sequence separation grid, a non-negative integer. Set to 0 to not overlay a grid."/>
                <param name="gridcolor" argument="--gridColour" type="text" label="Grid color" value="black" help="Colour of the sequence separation grid. Either, one of: 'black'(default), 'white', 'red', 'green', 'blue', 'yellow', 'cyan' or 'magenta'. Or, a sRGBA 32-bit hex code in RRGGBBAA format, e.g. 'ff00ff80' (magenta at half-occupancy)."/>
            </when>
            <when value="no"/>
        </conditional>
        <param name="sequencenames" argument="--printSequenceNames" type="boolean" label="Print Sequence names" truevalue="--printSequenceNames" falsevalue="" help="Print list of all individual suequeces names on the map, in order of appearance."/>
    </inputs>
    <outputs>
        <collection name="pretext_snap_out" type="list" label="${tool.name} on ${on_string}">
            <discover_datasets directory="output" pattern="__name_and_ext__" />  
        </collection>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="input" value="map.pretext"/>
            <conditional name="formats">
                <param name="outformat" value="jpeg"/>
                <param name="jpegquality" value="80"/>
            </conditional>
            <param name="resolution" value="900"/>
            <param name="colormap" value="1"/>
            <param name="sequences" value="=full, =all"/>
            <param name="mintexels" value="30"/>
            <conditional name="grid">
                <param name="showGrid" value="yes"/>
                <param name="gridsize" value="2"/>
                <param name="gridcolor" value="red"/>
            </conditional>
            <param name="sequencenames" value="--printSequenceNames"/>
            <output_collection name="pretext_snap_out" count="4">
                <element name="pretext_snapshotFullMap" ftype="jpg" file="fullmap1.jpg"/>
                <element name="pretext_snapshotref_0" ftype="jpg" file="snapshot1.jpg"/>
                <element name="pretext_snapshotref_1" ftype="jpg" file="snapshot2.jpg"/>
                <element name="pretext_snapshotref_2" ftype="jpg" file="snapshot3.jpg"/>
            </output_collection>
        </test>
        <test expect_num_outputs="1">
            <param name="input" value="map.pretext"/>
            <conditional name="formats">
                <param name="outformat" value="bmp"/>
            </conditional>
            <param name="resolution" value="700"/>
            <param name="colormap" value="5"/>
            <param name="sequences" value="=full"/>
            <param name="mintexels" value="60"/>
            <output_collection name="pretext_snap_out" count="1">
                <element name="pretext_snapshotFullMap" ftype="bmp" file="fullmap2.bmp"/>
            </output_collection>
        </test>
    </tests>
    <help><![CDATA[
        **Color map:**

        +---------------------------------------+-------------------------------+-------------------------------+
        |0.   Inferno                           |11.    Blue 4                  |22.    Orange 2                |
        +---------------------------------------+-------------------------------+-------------------------------+
        |1.   Black Body                        |12.    Blue-Orange Divergent   |23.    Orange-Green-Blue-Gray  |
        +---------------------------------------+-------------------------------+-------------------------------+
        |2.   Kindlmann                         |13.    Brown 1                 |24.    Purple 1                |
        +---------------------------------------+-------------------------------+-------------------------------+
        |3.   Extended Kindlmann                |14.    Brown 2                 |25.    Purple 2                |
        +---------------------------------------+-------------------------------+-------------------------------+
        |4.   Three Wave Yellow-Grey-Blue       |15.    Brown 3                 |26.    Red 1                   |
        +---------------------------------------+-------------------------------+-------------------------------+
        |5.   Three Wave Blue-Green-Yellow      |16.    Green 1                 |27.    Red 2                   |
        +---------------------------------------+-------------------------------+-------------------------------+
        |6.   Four Wave Grey-Red-Green          |17.    Green 2                 |28.    Red 3                   |
        +---------------------------------------+-------------------------------+-------------------------------+
        |7.   Five Wave Yellow-Brown-Blue       |18.    Green 3                 |29.    Yellow 1                |
        +---------------------------------------+-------------------------------+-------------------------------+
        |8.   Blue 1                            |19.    Green 4                 |30.    Yellow 2                |
        +---------------------------------------+-------------------------------+-------------------------------+
        |9.   Blue 2                            |20.    Mellow Rainbow          |                               |
        +---------------------------------------+-------------------------------+-------------------------------+
        |10.  Blue 3                            |21.    Orange 1                |                               |
        +---------------------------------------+-------------------------------+-------------------------------+


        **Sequence strings:**
        
        * --sequences "=full"

            * Creates a single image of the full contact map.

        * --sequences "=full, =all"

            * Creates an image of the full contact map, plus an image of each sequence.

        * --sequences "seq_0"

            * Creates a single image of the sequence named "seq_0"

        * --sequences "seq_0, seq_1 > seq_2"

            * Creates an image of seq_0, and an image from the start of seq_1 to the end of seq_2

        * --sequences "seq_0[1000000] > seq_3"

            * Creates an image starting 1Mbp into seq_0, ending at the end of seq_3

        * --sequences "{seq_0, seq_1}"

            * Create an single image of the off-diagonal region between seq_0 and seq_1, 
            * i.e. the inter-sequence map of seq_0 and seq_1.

        * --sequences "{seq_2[2000000] > seq_4[1000000] , seq_0[3000000] > seq_1[4000000]} , seq_0 > seq_10"

            * Creates two images. The first is the off-diagonal region between 2Mbp into seq_2 and 1Mbp into seq_4 along the x-dimension, and 3Mbp into seq_0 and 4Mbp into seq_1 along the y-dimension.
            * The second image is the diagonal region between the start of seq_0 and the end of seq_10.

    ]]></help>
    <citations>
        <citation type="bibtex">
            @misc{Harry_et_al,
            Author={Harry, E},
            title={Paired REad TEXTure Snapshot: Command line image generator for Pretext contact maps.},
            url = {https://github.com/wtsi-hpag/PretextSnapshot},}
        </citation>
    </citations>
</tool>