Mercurial > repos > bgruening > cp_relate_objects
view starting_modules_nameandtypes.xml @ 6:48102a685037 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools commit 57a0433defa3cbc37ab34fbb0ebcfaeb680db8d5
author | bgruening |
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date | Sun, 05 Nov 2023 09:27:30 +0000 |
parents | 3a3033222f61 |
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<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="containregexp">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>