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comparison macros.xml @ 10:a35bda7ed678 draft default tip

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tree/master/tools/hexrd commit 082120888ad38a8e84b32834c698c374db6f0b0c-dirty"
author ximgchess
date Thu, 07 Jul 2022 01:53:44 +0000
parents e67ad9795525
children
comparison
equal deleted inserted replaced
9:e67ad9795525 10:a35bda7ed678
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.8.18</token> 2 <token name="@TOOL_VERSION@">0.8.19</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">21.09</token> 4 <token name="@PROFILE@">22.01</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement>
8 <yield/> 8 <yield/>
9 </requirements> 9 </requirements>
58 #return $img_name 58 #return $img_name
59 #end def 59 #end def
60 </token> 60 </token>
61 61
62 <xml name="common_config" token_multiple_inputs="true" > 62 <xml name="common_config" token_multiple_inputs="true" >
63 <param name="analysis_name" type="text" value="analysis" label="analysis name">
64 <validator type="empty_field" />
65 </param>
63 <param name="inputs" type="data" format="hexrd.images.npz" multiple="true" label="Image series frame-cache"/> 66 <param name="inputs" type="data" format="hexrd.images.npz" multiple="true" label="Image series frame-cache"/>
64 <conditional name="detector"> 67 <conditional name="detector">
65 <param name="panel_assignment" type="select" label="Assign detector panel to images"> 68 <param name="panel_assignment" type="select" label="Assign detector panel to images">
66 <option value="infer_from_name" selected="true">Infer the panel from the image name</option> 69 <option value="infer_from_name" selected="true">Infer the panel from the image name</option>
67 <option value="panel_table">Input a table with image panels assignments</option> 70 <option value="panel_table">Input a table with image panels assignments</option>
71 <param name="image_panel_table" type="data" format="tabular" label="Image panel assignment table"> 74 <param name="image_panel_table" type="data" format="tabular" label="Image panel assignment table">
72 <help>A 2-column table:image dataset name detector panel name</help> 75 <help>A 2-column table:image dataset name detector panel name</help>
73 </param> 76 </param>
74 </when> 77 </when>
75 </conditional> 78 </conditional>
76 <param name="instrument" type="data" format="yaml" label="instrument"/> 79 <param name="instrument" type="data" format="hexrd.yml" label="instrument"/>
77 <param name="material" type="data" format="hexrd.materials.h5" label="material"/> 80 <param name="material" type="data" format="hexrd.materials.h5" label="material"/>
78 <param name="active_material" type="select" label="active material name"> 81 <param name="active_material" type="select" label="active material name">
79 <options> 82 <options>
80 <filter type="data_meta" ref="material" key="materials"/> 83 <filter type="data_meta" ref="material" key="materials"/>
81 </options> 84 </options>
99 #end for 102 #end for
100 ]]> 103 ]]>
101 </token> 104 </token>
102 <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@ 105 <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@
103 ln -s '$ome_map' $ln_name($ome_map,'npz') && 106 ln -s '$ome_map' $ln_name($ome_map,'npz') &&
104 ln -s '$accepted_orientations' $ln_name($accepted_orientations,'dat') && 107 ## hexrd looks for file named: accepted_orientations_{analysis_id}_{active_material}.dat
108 #set $accepted_orientations_name = 'accepted_orientations_analysis_' + str($active_material) + '.dat'
109 ln -s '$accepted_orientations' '$accepted_orientations_name' &&
105 ##mkdir -p analysis && 110 ##mkdir -p analysis &&
106 ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') && 111 ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') &&
107 ]]> 112 ]]>
108 </token> 113 </token>
109 114
299 ]]></token> 304 ]]></token>
300 305
301 <xml name="fit_grains_config"> 306 <xml name="fit_grains_config">
302 <expand macro="common_config" token_multiple_inputs="true"/> 307 <expand macro="common_config" token_multiple_inputs="true"/>
303 <param name="ome_map" type="data" format="hexrd.eta_ome.npz" label="analysis eta-ome_maps.npz from find_orientations"/> 308 <param name="ome_map" type="data" format="hexrd.eta_ome.npz" label="analysis eta-ome_maps.npz from find_orientations"/>
304 <param name="accepted_orientations" type="data" format="tabular" label="accepted_orientations from find_orientations"/> 309 <param name="accepted_orientations" type="data" format="hexrd.accepted_orientations" label="accepted_orientations from find_orientations"/>
305 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/> 310 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/>
306 <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/> 311 <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/>
307 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/> 312 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/>
308 <param name="threshold" type="integer" value="25" min="1" label="threshold"/> 313 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
309 <section name="tolerance" title="Fit Grain Tolerance" expanded="true"> 314 <section name="tolerance" title="Fit Grain Tolerance" expanded="true">
311 <param name="tth" type="float" value="" min="0" label="tth"/> 316 <param name="tth" type="float" value="" min="0" label="tth"/>
312 <param name="eta" type="float" value="" min="0" label="eta"/> 317 <param name="eta" type="float" value="" min="0" label="eta"/>
313 <param name="omega" type="float" value="" min="0" label="omega"/> 318 <param name="omega" type="float" value="" min="0" label="omega"/>
314 </repeat> 319 </repeat>
315 <param name="refit" type="text" value="1" label="refit" help="float values separated by commas"> 320 <param name="refit" type="text" value="1" label="refit" help="float values separated by commas">
316 <validator type="regex" message="">^[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?(,[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)*$</validator> 321 <validator type="regex" message="">^[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?(,[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)+$</validator>
317 </param> 322 </param>
318 <conditional name="max_tth"> 323 <conditional name="max_tth">
319 <param name="tth_max_value" type="select" label="Set tth_max"> 324 <param name="tth_max_value" type="select" label="Set tth_max">
320 <option value="true" selected="true">true</option> 325 <option value="true" selected="true">true</option>
321 <option value="false">false</option> 326 <option value="false">false</option>
343 threshold: $threshold 348 threshold: $threshold
344 349
345 #set $tth = [] 350 #set $tth = []
346 #set $eta = [] 351 #set $eta = []
347 #set $omega = [] 352 #set $omega = []
348 #set $refit = '[' + str($tolerance.refit) + ']' 353 ## #set $refit_tol = str($tolerance.refit)
354 ## #set $refit = '[' + $refit_tol + ']'
349 #for $tol in $tolerance.tolerance_lists 355 #for $tol in $tolerance.tolerance_lists
350 #silent $tth.append(float($tol.tth)) 356 #silent $tth.append(float($tol.tth))
351 #silent $eta.append(float($tol.eta)) 357 #silent $eta.append(float($tol.eta))
352 #silent $omega.append(float($tol.omega)) 358 #silent $omega.append(float($tol.omega))
353 #end for 359 #end for
354 tolerance: 360 tolerance:
355 tth: $tth # tolerance lists must be identical length 361 tth: $tth # tolerance lists must be identical length
356 eta: $eta 362 eta: $eta
357 omega: $omega 363 omega: $omega
358 364
359 refit: $refit 365 refit: [${tolerance.refit}]
360 #if $tolerance.max_tth.tth_max_value == 'entered': 366 #if $tolerance.max_tth.tth_max_value == 'entered':
361 tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true 367 tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true
362 #else 368 #else
363 tth_max: $tolerance.max_tth.tth_max_value # true, false, or a non-negative value, defaults to true 369 tth_max: $tolerance.max_tth.tth_max_value # true, false, or a non-negative value, defaults to true
364 #end if 370 #end if