Mercurial > repos > ximgchess > hexrd
comparison macros.xml @ 6:164e881c40e2 draft
"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c726809ab8080a1196c537fba343d0ba78333636"
author | ximgchess |
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date | Thu, 14 Oct 2021 18:03:22 +0000 |
parents | 36f0e168e5ef |
children | baba452d0613 |
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5:36f0e168e5ef | 6:164e881c40e2 |
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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"> |