Mercurial > repos > ximgchess > hexrd
diff macros.xml @ 10:a35bda7ed678 draft default tip
"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 |
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--- a/macros.xml Wed Feb 02 16:40:24 2022 +0000 +++ b/macros.xml Thu Jul 07 01:53:44 2022 +0000 @@ -1,7 +1,7 @@ <macros> - <token name="@TOOL_VERSION@">0.8.18</token> + <token name="@TOOL_VERSION@">0.8.19</token> <token name="@VERSION_SUFFIX@">0</token> - <token name="@PROFILE@">21.09</token> + <token name="@PROFILE@">22.01</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement> @@ -60,6 +60,9 @@ </token> <xml name="common_config" token_multiple_inputs="true" > + <param name="analysis_name" type="text" value="analysis" label="analysis name"> + <validator type="empty_field" /> + </param> <param name="inputs" type="data" format="hexrd.images.npz" multiple="true" label="Image series frame-cache"/> <conditional name="detector"> <param name="panel_assignment" type="select" label="Assign detector panel to images"> @@ -73,7 +76,7 @@ </param> </when> </conditional> - <param name="instrument" type="data" format="yaml" label="instrument"/> + <param name="instrument" type="data" format="hexrd.yml" label="instrument"/> <param name="material" type="data" format="hexrd.materials.h5" label="material"/> <param name="active_material" type="select" label="active material name"> <options> @@ -101,7 +104,9 @@ </token> <token name="@FIT_GRAIN_LINKS@"><![CDATA[@CMD_LINKS@ ln -s '$ome_map' $ln_name($ome_map,'npz') && -ln -s '$accepted_orientations' $ln_name($accepted_orientations,'dat') && +## hexrd looks for file named: accepted_orientations_{analysis_id}_{active_material}.dat +#set $accepted_orientations_name = 'accepted_orientations_analysis_' + str($active_material) + '.dat' +ln -s '$accepted_orientations' '$accepted_orientations_name' && ##mkdir -p analysis && ##cp '$grains_estimate' analysis/$ln_name($grains_estimate,'out') && ]]> @@ -301,7 +306,7 @@ <xml name="fit_grains_config"> <expand macro="common_config" token_multiple_inputs="true"/> <param name="ome_map" type="data" format="hexrd.eta_ome.npz" label="analysis eta-ome_maps.npz from find_orientations"/> - <param name="accepted_orientations" type="data" format="tabular" label="accepted_orientations from find_orientations"/> + <param name="accepted_orientations" type="data" format="hexrd.accepted_orientations" label="accepted_orientations from find_orientations"/> <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/> <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/> <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/> @@ -313,7 +318,7 @@ <param name="omega" type="float" value="" min="0" label="omega"/> </repeat> <param name="refit" type="text" value="1" label="refit" help="float values separated by commas"> - <validator type="regex" message="">^[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?(,[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)*$</validator> + <validator type="regex" message="">^[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?(,[+-]?(\d+(\.\d*)?|\.\d+)([eE][+-]?\d+)?)+$</validator> </param> <conditional name="max_tth"> <param name="tth_max_value" type="select" label="Set tth_max"> @@ -345,7 +350,8 @@ #set $tth = [] #set $eta = [] #set $omega = [] -#set $refit = '[' + str($tolerance.refit) + ']' +## #set $refit_tol = str($tolerance.refit) +## #set $refit = '[' + $refit_tol + ']' #for $tol in $tolerance.tolerance_lists #silent $tth.append(float($tol.tth)) #silent $eta.append(float($tol.eta)) @@ -356,7 +362,7 @@ eta: $eta omega: $omega - refit: $refit + refit: [${tolerance.refit}] #if $tolerance.max_tth.tth_max_value == 'entered': tth_max: $tolerance.max_tth.tth_max # true, false, or a non-negative value, defaults to true #else