Mercurial > repos > ximgchess > hexrd

changeset 7:baba452d0613 draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit c6c9ce811a27cdee735c2eeac9f6a29f95d9ae90"
author ximgchess
date Tue, 04 Jan 2022 22:07:42 +0000
parents 164e881c40e2
children 4bb02acaaabc
files datatypes_conf.xml hexrd_find_orientations.xml hexrd_fit_grains.xml macros.xml
diffstat 4 files changed, 13 insertions(+), 19 deletions(-) [+]
line wrap: on
line diff
--- a/datatypes_conf.xml	Thu Oct 14 18:03:22 2021 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-<?xml version="1.0"?>
-<datatypes>
-  <registration>
-    <datatype extension="hexrd.yml" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
-  </registration>
-</datatypes>
--- a/hexrd_find_orientations.xml	Thu Oct 14 18:03:22 2021 +0000
+++ b/hexrd_find_orientations.xml	Tue Jan 04 22:07:42 2022 +0000
@@ -25,20 +25,20 @@
         <expand macro="find_orientations_config"/> 
     </inputs>
     <outputs>
-        <data name="config" format="hexrd.yml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
+        <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
         <data name="log" format="txt" label="${tool.name} on ${on_string}: find-orientations_analysis_${active_material}.log"/>
         <data name="ome_maps" format="hexrd.eta_ome.npz" label="${tool.name} on ${on_string}: analysis_${active_material}_eta-ome_maps.npz"/>
-        <data name="score_orientations" format="hexrd.npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
-        <data name="accepted_orientations" format="hexrd.accepted_orientations" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
+        <data name="score_orientations" format="npz" label="${tool.name} on ${on_string}: scored_orientations_analysis_${active_material}.npz"/>
+        <data name="accepted_orientations" format="tabular" label="${tool.name} on ${on_string}: accepted_orientations_analysis_${active_material}.dat"/>
         <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
     </outputs>
     <tests>
         <test>
-            <param name="inputs" ftype="hexrd.npz" value="RUBY_0000-fc_GE.npz,RUBY_0001-fc_GE.npz,RUBY_0002-fc_GE.npz,RUBY_0003-fc_GE.npz,RUBY_0004-fc_GE.npz,RUBY_0005-fc_GE.npz"/>
+            <param name="inputs" ftype="hexrd.images.npz" value="RUBY_0000-fc_GE.npz,RUBY_0001-fc_GE.npz,RUBY_0002-fc_GE.npz,RUBY_0003-fc_GE.npz,RUBY_0004-fc_GE.npz,RUBY_0005-fc_GE.npz"/>
             <conditional name="detector">
                 <param name="panel_assignment" value="infer_from_name"/>
             </conditional>
-            <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
+            <param name="instrument" ftype="yaml" value="ge_detector.yml"/>
             <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
             <param name="active_material" value="ruby"/>
             <section name="orientation_maps">
--- a/hexrd_fit_grains.xml	Thu Oct 14 18:03:22 2021 +0000
+++ b/hexrd_fit_grains.xml	Tue Jan 04 22:07:42 2022 +0000
@@ -22,7 +22,7 @@
         <expand macro="fit_grains_config"/>
     </inputs>
     <outputs>
-        <data name="config" format="hexrd.yml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
+        <data name="config" format="yaml" label="${tool.name} on ${on_string}: ${active_material}_config.yml"/>
         <data name="log" format="txt" label="${tool.name} on ${on_string}:fit_grains_analysis_${active_material}.log"/>
         <data name="grains" format="tabular" label="${tool.name} on ${on_string}: grains.out" from_work_dir="analysis/grains.out" />
         <collection name="spots" type="list" label="${tool.name} on ${on_string}:spots">
@@ -31,14 +31,14 @@
     </outputs>
     <tests>
         <test>
-            <param name="inputs" ftype="hexrd.npz" value="RUBY_0000-fc_GE.npz,RUBY_0001-fc_GE.npz,RUBY_0002-fc_GE.npz,RUBY_0003-fc_GE.npz,RUBY_0004-fc_GE.npz,RUBY_0005-fc_GE.npz"/>
+            <param name="inputs" ftype="hexrd.iamges.npz" value="RUBY_0000-fc_GE.npz,RUBY_0001-fc_GE.npz,RUBY_0002-fc_GE.npz,RUBY_0003-fc_GE.npz,RUBY_0004-fc_GE.npz,RUBY_0005-fc_GE.npz"/>
             <conditional name="detector">
                 <param name="panel_assignment" value="infer_from_name"/>
             </conditional>
-            <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
+            <param name="instrument" ftype="yaml" value="ge_detector.yml"/>
             <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
             <param name="active_material" value="ruby"/>
-            <param name="ome_map" ftype="hexrd.npz" value="analysis_ruby_eta-ome_maps.npz"/>
+            <param name="ome_map" ftype="hexrd.eta_ome.npz" value="analysis_ruby_eta-ome_maps.npz"/>
             <param name="accepted_orientations" ftype="tabular" value="accepted_orientations_analysis_ruby.dat"/>
             <param name="grains_estimate" ftype="tabular" value="grains.out"/>
             <param name="do_fit" value="true"/>
--- a/macros.xml	Thu Oct 14 18:03:22 2021 +0000
+++ b/macros.xml	Tue Jan 04 22:07:42 2022 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.8.12</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.09</token>
     <xml name="requirements">
         <requirements>
@@ -73,7 +73,7 @@
                 </param>
             </when>
         </conditional>
-        <param name="instrument" type="data" format="hexrd.yml" label="instrument"/>
+        <param name="instrument" type="data" format="yaml" label="instrument"/>
         <param name="material" type="data" format="hexrd.materials.h5" label="material"/>
         <param name="active_material" type="select" label="active material name">
             <options>
@@ -194,7 +194,7 @@
                     </conditional>
                 </when>
                 <when value="use_quaternion_grid">
-                    <param name="quaternion_grid" type="data" format="hexrd.npz" label="quaterion grid file"/>
+                    <param name="quaternion_grid" type="data" format="npz" label="quaterion grid file"/>
                 </when>
             </conditional>
         </section>
@@ -301,7 +301,7 @@
     <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="hexrd.accepted_orientations" label="accepted_orientations from find_orientations"/>
+        <param name="accepted_orientations" type="data" format="tabular" 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"/>