Mercurial > repos > ximgchess > hexrd

comparison macros.xml @ 2:f0db3e3b9d99 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit 447defcd2ae30127f163e6a3adec52926f4a6c9c"
author ximgchess
date Mon, 07 Dec 2020 22:32:14 +0000
parents a0be4e3aa66d
children 54513f5fc836
comparison
equal deleted inserted replaced
1:a0be4e3aa66d 2:f0db3e3b9d99
122 <xml name="find_orientations_config"> 122 <xml name="find_orientations_config">
123 <expand macro="common_config" token_multiple_inputs="true" /> 123 <expand macro="common_config" token_multiple_inputs="true" />
124 <section name="orientation_maps" title="Orientation Maps" expanded="true"> 124 <section name="orientation_maps" title="Orientation Maps" expanded="true">
125 <param name="threshold" type="integer" value="25" min="1" label="threshold"/> 125 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
126 <param name="bin_frames" type="integer" value="1" label="bin frames"/> 126 <param name="bin_frames" type="integer" value="1" label="bin frames"/>
127 <param name="active_hkls" type="text" value="" optional="true" label="active hkls"> 127 <!-- active_hkls should be able to be optional="true" -->
128 <validator type="regex" message="">^\d(,\d)*$</validator> 128 <param name="active_hkls" type="text" value="" label="active hkl planes">
129 <help>commas separated list of planes, e.g.: 0,1,2,3,4,5</help>
130 <validator type="regex" message="plane indeces separated by commas">^\d(,\d)*$</validator>
129 </param> 131 </param>
130 </section> 132 </section>
131 <param name="on_map_threshold" type="integer" value="1" min="1" label="on-map threshold used in the scoring"/> 133 <param name="on_map_threshold" type="integer" value="1" min="1" label="on-map threshold used in the scoring"/>
132 <section name="search_options" title="Search Options" expanded="true"> 134 <section name="search_options" title="Search Options" expanded="true">
133 <conditional name="search"> 135 <conditional name="search">
134 <param name="search_type" type="select" label="Specify Search"> 136 <param name="search_type" type="select" label="Specify Search">
135 <option value="seed_search" selected="true">use seed search</option> 137 <option value="seed_search" selected="true">use seed search</option>
136 <option value="use_quaternion_grid">use quaternion grid</option> 138 <option value="use_quaternion_grid">use quaternion grid</option>
137 </param> 139 </param>
138 <when value="seed_search"> 140 <when value="seed_search">
139 <param name="hkl_seeds" type="text" value="" optional="true" label="hkl seeds"> 141 <!-- hkl_seeds should be able to be optional="true" -->
142 <param name="hkl_seeds" type="text" value="" label="hkl seeds">
143 <help>commas separated list of planes, e.g.: 0,1,2 (subset of active hkl planes)</help>
140 <validator type="regex" message="">^\d(,\d)*$</validator> 144 <validator type="regex" message="">^\d(,\d)*$</validator>
141 </param> 145 </param>
142 <param name="fiber_step" type="float" value="0.5" min="0" max="10" label="fiber step"/> 146 <param name="fiber_step" type="float" value="0.5" min="0" max="10" label="fiber step"/>
143 <conditional name="params"> 147 <conditional name="params">
144 <param name="method" type="select" label="Method"> 148 <param name="method" type="select" label="Method">
309 # A file name must be specified. If it doesn't exist, one will be created 313 # A file name must be specified. If it doesn't exist, one will be created
310 file: $ln_name($ome_map,'npz') 314 file: $ln_name($ome_map,'npz')
311 315
312 fit_grains: 316 fit_grains:
313 do_fit: $do_fit # if false, extracts grains but doesn't fit. defaults to true 317 do_fit: $do_fit # if false, extracts grains but doesn't fit. defaults to true
314
315 # estimate: null 318 # estimate: null
316
317 npdiv: $npdiv # number of polar pixel grid subdivisions, defaults to 2 319 npdiv: $npdiv # number of polar pixel grid subdivisions, defaults to 2
318
319 threshold: $threshold 320 threshold: $threshold
320 321
321 #set $tth = [] 322 #set $tth = []
322 #set $eta = [] 323 #set $eta = []
323 #set $omega = [] 324 #set $omega = []
324 #set refit = '[' + str($tolerance.refit) + ']' 325 #set refit = '[' + str($tolerance.refit) + ']'
325 #for $tol in $tolerance.tolerance_lists 326 #for $tol in $tolerance.tolerance_lists
326 $tth.append(float($tol.tth)) 327 #silent $tth.append(float($tol.tth))
327 $eta.append(float($tol.eta)) 328 #silent $eta.append(float($tol.eta))
328 $omega.append(float($tol.omega)) 329 #silent $omega.append(float($tol.omega))
329 #end for 330 #end for
330 tolerance: 331 tolerance:
331 tth: $tth # tolerance lists must be identical length 332 tth: $tth # tolerance lists must be identical length
332 eta: $eta 333 eta: $eta
333 omega: $omega 334 omega: $omega
337 tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true 338 tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true
338 #else 339 #else
339 tth_max: $tolerance.max_tth.tth_max_value # true, false, or a non-negative value, defaults to true 340 tth_max: $tolerance.max_tth.tth_max_value # true, false, or a non-negative value, defaults to true
340 #end if 341 #end if
341 ]]></token> 342 ]]></token>
343 <token name="@HEXRD_HELP@"><![CDATA[
344 HEXRD_ provides analysis of x-ray diffraction data, especially high-energy x-ray diffraction. HEXRD is comprised of a library and API for writing scripts, a command line interface, and an interactive graphical user interface.
345
346 .. _HEXRD: https://github.com/HEXRD/hexrd
347 ]]></token>
348
349 <token name="@COMMON_INPUTS_HELP@"><![CDATA[
350
351 **INPUTS**
352
353 - imageseries - Detector image files converted to sparse matrix compressed numpy arrays.
354 - instrument - A yaml file that decribes the instrument
355 - materials.hexrd - A "pickled" hexrd Materials object that desscribes the sample material
356 ]]></token>
357 <token name="@FIT_GRAIN_INPUTS_HELP@"><![CDATA[@COMMON_INPUTS_HELP@
358 - analysis eta-ome_maps.npz from find_orientations
359 - accepted_orientations from find_orientations
360
361 ]]></token>
362
363 <token name="@COMMON_OUTPUTS_HELP@"><![CDATA[
364
365 **OUTPUTS**
366
367 - config yaml - parameter for hexrd
368 - log - the hexrd logging output
369 - grains.out
370 ]]></token>
371 <token name="@FIND_ORIENTATIONS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
372 - analysis eta-ome_maps.npz *(used as input for hexrd fit-grains)*
373 - analysis accepted_orientations_analysis.dat *(used as input for hexrd fit-grains)*
374 - analysis scored_orientations_analysis.npz
375 ]]></token>
376 <token name="@FIT_GRAINS_OUTPUTS_HELP@"><![CDATA[@COMMON_OUTPUTS_HELP@
377 - Collection of spots.out
378 ]]></token>
379
342 380
343 </macros> 381 </macros>