Mercurial > repos > bgruening > cp_gray_to_color
diff starting_modules_nameandtypes.xml @ 3:bbf1ef17c01b draft
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit c3917e27eb1c1deeb381aa0dc8161c07699562fb"
author | bgruening |
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date | Mon, 11 May 2020 07:56:38 -0400 |
parents | |
children | ad271f78a87a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/starting_modules_nameandtypes.xml Mon May 11 07:56:38 2020 -0400 @@ -0,0 +1,182 @@ +<macros> + <xml name="macro_image_type" token_thing="images"> + <param name="name_to_assign" type="text" value="DNA" label="Name to assign these @THING@" /> + </xml> + + <xml name="image_type_condition"> + <conditional name="con_set_intensity"> + <param name="set_intensity_range_from" type="select" label="Set intensity range from" help="This option determines how the image intensity should be rescaled from 0.0 - 1.0."> + <option value="Image metadata">Image metadata</option> + <option value="Image bit-depth">Image bit-depth</option> + <option value="Manual">Manual</option> + </param> + <when value="Manual"> + <param name="maximum_intensity" type="float" value="255.0" label="Maximum intensity" help="The pixel value is divided, as read from the image file, by this value to get the loaded image’s per-pixel intensity." /> + + </when> + <when value="Image metadata" /> + <when value="Image bit-depth" /> + </conditional> + </xml> + <xml name="name_type_rule_matching_file"> + <param name="operator" type="select"> + <option value="does">Does</option> + <option value="doesnot">Does not</option> + </param> + <param name="contain" type="select"> + <option value="contain">Contain</option> + <option value="Contain regular expression">Contain regular expression</option> + <option value="startwith">Start with</option> + <option value="endwith">End with</option> + <option value="Exactly match">Exactly match</option> + </param> + <param name="match_value" type="text"/> + </xml> + <xml name="name_type_rule_image"> + <param name="operator" type="select"> + <option value="does">Is</option> + <option value="doesnot">Is not</option> + </param> + <param name="match_type" type="select"> + <option value="iscolor">Color</option> + <option value="ismonochrome">Monochrome</option> + <option value="isstack">Stack</option> + <option value="isstackframe">Stack frame</option> + </param> + </xml> + <xml name="name_type_rule_metadata"> + <param name="operator" type="select"> + <option value="does">Does</option> + <option value="doesnot">Does not</option> + </param> + <param name="match_type" type="select"> + <option value="FileLocation">Have FileLocation matching</option> + <option value="Frame">Have Frame matching</option> + <option value="Screen">Have Screen matching</option> + <option value="Series">Have Series matching</option> + </param> + <param name="match_value" type="text"/> + </xml> + <xml name="name_type_rule_ext"> + <param name="operator" type="select"> + <option value="does">Is</option> + <option value="doesnot">Is not</option> + </param> + <param name="match_type" type="select"> + <option value="istif">tif, tiff, ome.tif or ome.tiff</option> + <option value="isjpeg">jpg, jpeg</option> + <option value="ispng">png</option> + <option value="isimage">the extension of an image file</option> + <option value="isflex">flex</option> + <option value="ismovie">mov, avi</option> + + </param> + </xml> + <xml name="image_matching_rules"> + <repeat name="r_match_rule" title="Another image"> + <param name="match_all_any" type="select" display="radio" label="Match the following rules"> + <option value="and">All</option> + <option value="or">Any</option> + </param> + <repeat name="r_match" title="rule"> + <conditional name="con_match"> + <param name="rule_type" type="select" label="Select rule criteria"> + <option value="file">File</option> + <option value="directory">Directory</option> + <option value="extension">Extension</option> + <option value="image">Image</option> + <option value="metadata">Metadata</option> + </param> + <when value="file"> + <expand macro="name_type_rule_matching_file"/> + </when> + <when value="directory"> + <expand macro="name_type_rule_matching_file"/> + </when> + <when value="extension"> + <expand macro="name_type_rule_ext" /> + </when> + <when value="image"> + <expand macro="name_type_rule_image" /> + </when> + <when value="metadata"> + <expand macro="name_type_rule_metadata" /> + </when> + </conditional> + </repeat> + <conditional name="con_select_image_type"> + <param name="select_image_type" type="select" label="Select the image type" help="You can specify how these images should be treated"> + <option value="Grayscale image">Grayscale image</option> + <option value="Color image">Color image</option> + <option value="Binary mask">Binary mask</option> + <option value="Illumination function">Illumination function</option> + <option value="Objects">Objects</option> + + </param> + <when value ="Grayscale image"> + <expand macro="macro_image_type" thing="images"/> + <expand macro="image_type_condition" /> + </when> + <when value="Color image"> + <expand macro="macro_image_type" thing="images"/> + <expand macro="image_type_condition" /> + </when> + <when value="Binary mask"> + <expand macro="macro_image_type" thing="images"/> + </when> + <when value="Illumination function"> + <expand macro="macro_image_type" thing="images"/> + </when> + <when value="Objects"> + <expand macro="macro_image_type" thing="objects"/> + </when> + </conditional> + </repeat> + </xml> + <xml name="starting_modules_nameandtypes"> + <section name="nameandtypes" title="NamesAndTypes" expanded="false"> + <conditional name="pixel_space"> + <param name="process_3d" type="select" label="Process 3D" help="If you want to treat the data as three-dimensional, select 'Yes' to load files as volumes. Otherwise, select 'No' to load files as separate, two-dimensional images."> + <option value="Yes">Yes, process 3D data</option> + <option value="No">No, do not process 3D data</option> + </param> + <when value="Yes"> + <param name="x_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the X dimension, relative to Y and Z" help="Normally, you will set one of these values to 1 and the others relative to that." /> + <param name="y_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Y dimension, relative to X and Z"/> + <param name="z_spacing" type="float" value="1.0" label="Enter the spacing between voxels in the Z dimension, relative to X and Y"/> + </when> + <when value="No"/> + </conditional> + <conditional name="con_assign_a_name_to"> + <param name="assign_a_name_to" type="select" label="Assign a name to" help="This setting allows you to specify a name for types of images or subsets of images so they can be treated separately by downstream tools."> + <option value="All images">Give every image the same name</option> + <option value="Images matching rules">Give images one of several names depending on the metadata</option> + </param> + <when value="All images"> + <expand macro="macro_image_type" thing="images" /> + <conditional name="con_select_image_type"> + <param name="select_image_type" type="select" label="Select the image type"> + <option value="Grayscale image">Grayscale image</option> + <option value="Color image">Color image</option> + <option value="Binary mask">Binary mask</option> + </param> + <when value ="Grayscale image"> + <expand macro="image_type_condition" /> + </when> + <when value="Color image"> + <expand macro="image_type_condition" /> + </when> + <when value="Binary mask" /> + </conditional> + </when> + <when value="Images matching rules"> + <expand macro="image_matching_rules"/> + <param name="matching_method" type="select" label="Image set matching method"> + <option value="Order">Order</option> + <option value="Metadata">Metadata</option> + </param> + </when> + </conditional> + </section> +</xml> +</macros>