Mercurial > repos > ximgchess > hexrd

changeset 3:54513f5fc836 draft

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"planemo upload for repository https://github.com/ximg-chess/galaxytools/tools/hexrd commit f29a6f52c76e068908ab2e1161314eb3edcfe4c9"
author ximgchess
date Wed, 31 Mar 2021 14:56:35 +0000
parents f0db3e3b9d99
children b49a8ef3351d
files datatypes_conf.xml hexrd_find_orientations.xml hexrd_fit_grains.xml macros.xml
diffstat 4 files changed, 10 insertions(+), 9 deletions(-) [+]
line wrap: on
line diff
--- a/datatypes_conf.xml	Mon Dec 07 22:32:14 2020 +0000
+++ b/datatypes_conf.xml	Wed Mar 31 14:56:35 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <datatypes>
   <registration>
-    <datatype extension="material.hexrd" type="galaxy.datatypes.binary:Binary" subclass="true" display_in_upload="true"/>
+    <datatype extension="hexrd.materials.h5" type="galaxy.datatypes.binary:H5" subclass="true" display_in_upload="true"/>
     <datatype extension="hexrd.npz" type="galaxy.datatypes.binary:CompressedZipArchive" subclass="true" display_in_upload="true"/>
     <datatype extension="hexrd.yml" type="galaxy.datatypes.data:Text" subclass="true" display_in_upload="true"/>
   </registration>
--- a/hexrd_find_orientations.xml	Mon Dec 07 22:32:14 2020 +0000
+++ b/hexrd_find_orientations.xml	Wed Mar 31 14:56:35 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hexrd_find_orientations" name="HEXRD find-orientations" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+<tool id="hexrd_find_orientations" name="HEXRD find-orientations" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
     <description>Process rotation image series to find grain orientations</description>
     <macros>
         <import>macros.xml</import>
@@ -39,7 +39,7 @@
                 <param name="panel_assignment" value="infer_from_name"/>
             </conditional>
             <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
-            <param name="material" ftype="material.hexrd" value="materials_py38.hexrd"/>
+            <param name="material" ftype="hexrd.materials.h5" value="materials.h5"/>
             <param name="active_material" value="ruby"/>
             <section name="orientation_maps">
                 <param name="threshold" value="25"/>
--- a/hexrd_fit_grains.xml	Mon Dec 07 22:32:14 2020 +0000
+++ b/hexrd_fit_grains.xml	Wed Mar 31 14:56:35 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="hexrd_fit_grains" name="HEXRD fit-grains" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+<tool id="hexrd_fit_grains" name="HEXRD fit-grains" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5">
     <description>Extracts G vectors, grain position and strain</description>
     <macros>
         <import>macros.xml</import>
@@ -36,7 +36,7 @@
                 <param name="panel_assignment" value="infer_from_name"/>
             </conditional>
             <param name="instrument" ftype="hexrd.yml" value="ge_detector.yml"/>
-            <param name="material" ftype="material.hexrd" value="materials_py38.hexrd"/>
+            <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="accepted_orientations" ftype="tabular" value="accepted_orientations_analysis_ruby.dat"/>
--- a/macros.xml	Mon Dec 07 22:32:14 2020 +0000
+++ b/macros.xml	Wed Mar 31 14:56:35 2021 +0000
@@ -1,5 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.8.0</token>
+    <token name="@TOOL_VERSION@">0.8.4</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
         <requirement type="package" version="@TOOL_VERSION@">hexrd</requirement>
@@ -72,7 +73,7 @@
             </when>
         </conditional>
         <param name="instrument" type="data" format="hexrd.yml" label="instrument"/>
-        <param name="material" type="data" format="material.hexrd" label="material"/>
+        <param name="material" type="data" format="hexrd.materials.h5" label="material"/>
         <param name="active_material" type="text" value="" label="active material name">
             <validator type="empty_field" />
         </param>
@@ -80,7 +81,7 @@
 
     <token name="@CMD_LINKS@"><![CDATA[@CMD_IMPORTS@
 mkdir -p imageseries &&
-ln -s '$material' $ln_name($material,'hexrd') &&
+ln -s '$material' $ln_name($material,'h5') &&
 ln -s '$instrument' $ln_name($instrument,'yml') &&
 #for $input in $inputs
 ln -s '$input' imageseries/$ln_name($input,'npz') &&
@@ -103,7 +104,7 @@
 multiprocessing: -1
 
 material:
-  definitions: $ln_name($material,'hexrd')
+  definitions: $ln_name($material,'h5')
   active: $active_material
 
 instrument: $ln_name($instrument,'yml')