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comparison macros.xml @ 6:164e881c40e2 draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
author ximgchess
date Thu, 14 Oct 2021 18:03:22 +0000
parents 36f0e168e5ef
children baba452d0613
comparison
equal deleted inserted replaced
5:36f0e168e5ef 6:164e881c40e2
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.8.4</token> 2 <token name="@TOOL_VERSION@">0.8.12</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <token name="@PROFILE@">21.09</token>
4 <xml name="requirements"> 5 <xml name="requirements">
5 <requirements> 6 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement>
7 <yield/> 8 <yield/>
8 </requirements> 9 </requirements>
57 #return $img_name 58 #return $img_name
58 #end def 59 #end def
59 </token> 60 </token>
60 61
61 <xml name="common_config" token_multiple_inputs="true" > 62 <xml name="common_config" token_multiple_inputs="true" >
62 <param name="inputs" type="data" format="hexrd.npz" multiple="true" label="Image series frame-cache"/> 63 <param name="inputs" type="data" format="hexrd.images.npz" multiple="true" label="Image series frame-cache"/>
63 <conditional name="detector"> 64 <conditional name="detector">
64 <param name="panel_assignment" type="select" label="Assign detector panel to images"> 65 <param name="panel_assignment" type="select" label="Assign detector panel to images">
65 <option value="infer_from_name" selected="true">Infer the panel from the image name</option> 66 <option value="infer_from_name" selected="true">Infer the panel from the image name</option>
66 <option value="panel_table">Input a table with image panels assignments</option> 67 <option value="panel_table">Input a table with image panels assignments</option>
67 </param> 68 </param>
72 </param> 73 </param>
73 </when> 74 </when>
74 </conditional> 75 </conditional>
75 <param name="instrument" type="data" format="hexrd.yml" label="instrument"/> 76 <param name="instrument" type="data" format="hexrd.yml" label="instrument"/>
76 <param name="material" type="data" format="hexrd.materials.h5" label="material"/> 77 <param name="material" type="data" format="hexrd.materials.h5" label="material"/>
78 <param name="active_material" type="select" label="active material name">
79 <options>
80 <filter type="data_meta" ref="material" key="materials"/>
81 </options>
82 </param>
83 <param name="dmin" type="float" value="1.0" min="0" max="10" optional="true" label="dmin angstroms" help="used to figure out the maximum sampling for g-vectors default 1.0"/>
84 <param name="tth_width" type="float" value="0.25" min="0" max="10" optional="true" label="tth tolerance in degrees" help="tth_width default 0.25 "/>
85 <param name="min_sfac_ratio" type="float" value="" min="0" max="1" optional="true" label="min percentage of max to exclude" help="min_sfac_ratio min percentage of max |F|^2 to exclude; default None"/>
86 <!--
77 <param name="active_material" type="text" value="" label="active material name"> 87 <param name="active_material" type="text" value="" label="active material name">
78 <validator type="empty_field" /> 88 <validator type="empty_field" />
79 </param> 89 </param>
90 -->
80 </xml> 91 </xml>
81 92
82 <token name="@CMD_LINKS@"><![CDATA[@CMD_IMPORTS@ 93 <token name="@CMD_LINKS@"><![CDATA[@CMD_IMPORTS@
83 mkdir -p imageseries && 94 mkdir -p imageseries &&
84 ln -s '$material' $ln_name($material,'h5') && 95 ln -s '$material' $ln_name($material,'h5') &&
97 </token> 108 </token>
98 109
99 <token name="@CONVERT2TAB@"><![CDATA[for i in `find analysis -name '[gs]*.out'`; do sed -i.bak "s/[ ][ ][ ]*/\$(printf '\t')/g" \${i}; done]]></token> 110 <token name="@CONVERT2TAB@"><![CDATA[for i in `find analysis -name '[gs]*.out'`; do sed -i.bak "s/[ ][ ][ ]*/\$(printf '\t')/g" \${i}; done]]></token>
100 111
101 <token name="@COMMON_YML@"><![CDATA[@CMD_IMPORTS@ 112 <token name="@COMMON_YML@"><![CDATA[@CMD_IMPORTS@
113 #slurp
114 #set instrument_file = $ln_name($instrument,'yml')
102 analysis_name: analysis 115 analysis_name: analysis
103 116
104 multiprocessing: -1 117 multiprocessing: -1
105 118
106 material: 119 material:
107 definitions: $ln_name($material,'h5') 120 definitions: $ln_name($material,'h5')
108 active: $active_material 121 active: $active_material
109 122 #if $dmin
110 instrument: $ln_name($instrument,'yml') 123 dmin: $dmin # defaults to 1.0 angstrom
124 #end if
125 #if $tth_width
126 tth_width: $tth_width # defaults to 0.25 degrees
127 #end if
128 #if $min_sfac_ratio
129 min_sfac_ratio: $min_sfac_ratio # min percentage of max |F|^2 to exclude; default None
130 #end if
111 131
112 image_series: 132 image_series:
113 format: frame-cache 133 format: frame-cache
114 data: 134 data:
115 #for $input in $inputs 135 #for $input in $inputs
116 - file: imageseries/$ln_name($input,'npz') 136 - file: imageseries/$ln_name($input,'npz')
117 args: {} 137 args: {}
118 panel: $get_panel($input) # must match detector key 138 panel: $get_panel($input) # must match detector key
119 #end for 139 #end for
140
141 instrument: $instrument_file
120 142
121 ]]></token> 143 ]]></token>
122 144
123 <xml name="find_orientations_config"> 145 <xml name="find_orientations_config">
124 <expand macro="common_config" token_multiple_inputs="true" /> 146 <expand macro="common_config" token_multiple_inputs="true" />
276 298
277 ]]></token> 299 ]]></token>
278 300
279 <xml name="fit_grains_config"> 301 <xml name="fit_grains_config">
280 <expand macro="common_config" token_multiple_inputs="true"/> 302 <expand macro="common_config" token_multiple_inputs="true"/>
281 <param name="ome_map" type="data" format="hexrd.npz" label="analysis eta-ome_maps.npz from find_orientations"/> 303 <param name="ome_map" type="data" format="hexrd.eta_ome.npz" label="analysis eta-ome_maps.npz from find_orientations"/>
282 <param name="accepted_orientations" type="data" format="tabular" label="accepted_orientations from find_orientations"/> 304 <param name="accepted_orientations" type="data" format="hexrd.accepted_orientations" label="accepted_orientations from find_orientations"/>
283 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/> 305 <param name="grains_estimate" type="data" format="tabular" label="grains.out from find_orientations"/>
284 <param name="do_fit" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fit grains" help="if false, extracts grains but doesn't fit"/> 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"/>
285 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/> 307 <param name="npdiv" type="integer" value="2" min="1" label="number of polar pixel grid subdivisions"/>
286 <param name="threshold" type="integer" value="25" min="1" label="threshold"/> 308 <param name="threshold" type="integer" value="25" min="1" label="threshold"/>
287 <section name="tolerance" title="Fit Grain Tolerance" expanded="true"> 309 <section name="tolerance" title="Fit Grain Tolerance" expanded="true">