--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pretext_snapshot.xml	Mon Apr 05 17:27:18 2021 +0000
@@ -0,0 +1,190 @@
+<tool id="pretext_snapshot" name="Pretext Snapshot"  version="@WRAPPER_VERSION@+@VERSION_SUFFIX@" profile="20.01">
+    <macros>
+        <token name="@WRAPPER_VERSION@">0.0.3</token>
+        <token name="@VERSION_SUFFIX@">galaxy0</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@WRAPPER_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"/>
+                <option value="bmp"/>
+                <option value="jpeg"/>
+            </param>
+            <when value="png"/>
+            <when value="bmp"/>
+            <when value="jpeg">
+                <param name="jpegQuality" argument="--jpegQuality" type="integer" label="JPEG quality factor" value="80" min="0" max="100" help="An integer between 1 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 name="sequences" 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="boolean" truevalue="yes" falsevalue="no"/>
+            <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>
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