Mercurial > repos > ximgchess > chap_test_20230411

changeset 137:0bd8fb3aae96 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
author ximgchess
date Tue, 20 Jun 2023 18:13:36 +0000
parents dd3ed024679c
children 326d9fb7301b
files saxswaxs/reduce.xml tomo/tomo_combine.xml tomo/tomo_find_center.xml tomo/tomo_macros.xml tomo/tomo_reconstruct.xml tomo/tomo_reduce.xml
diffstat 6 files changed, 26 insertions(+), 22 deletions(-) [+]
line wrap: on
line diff
--- a/saxswaxs/reduce.xml	Tue Jun 20 13:39:31 2023 +0000
+++ b/saxswaxs/reduce.xml	Tue Jun 20 18:13:36 2023 +0000
@@ -32,9 +32,9 @@
       usage: PROG [-h] [--config CONFIG] [--verbose]
 
 options:
-  , --help       show this help message and exit
-  config CONFIG  Input configuration file
-  verbose        verbose output
+  -h, --help       show this help message and exit
+  --config CONFIG  Input configuration file
+  --verbose        verbose output
 
   ]]></help>
   <citations>
--- a/tomo/tomo_combine.xml	Tue Jun 20 13:39:31 2023 +0000
+++ b/tomo/tomo_combine.xml	Tue Jun 20 18:13:36 2023 +0000
@@ -1,6 +1,7 @@
 <tool id="CHAP_tomo_combine" name="Tomo Combine" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
     <description>Combine tomography stacks</description>
     <macros>
+        <import>../macros.xml</import>
         <import>tomo_macros.xml</import>
     </macros>
     <expand macro="requirements"/>
--- a/tomo/tomo_find_center.xml	Tue Jun 20 13:39:31 2023 +0000
+++ b/tomo/tomo_find_center.xml	Tue Jun 20 18:13:36 2023 +0000
@@ -1,6 +1,7 @@
 <tool id="CHAP_tomo_find_center" name="Tomo Find Center" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
     <description>Find rotation axis centers for the tomography stacks</description>
     <macros>
+        <import>../macros.xml</import>
         <import>tomo_macros.xml</import>
     </macros>
     <expand macro="requirements"/>
--- a/tomo/tomo_macros.xml	Tue Jun 20 13:39:31 2023 +0000
+++ b/tomo/tomo_macros.xml	Tue Jun 20 18:13:36 2023 +0000
@@ -2,13 +2,13 @@
     <!-- <macros> -->
     <!--   <import>../macros.xml</import> -->
     <!-- </macros> -->
-    <token name="@TOOL_VERSION@">0.1.1</token>
-    <token name="@VERSION_SUFFIX@">0</token>
-    <token name="@PROFILE@">21.09</token>
-    <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>
+    <!-- <token name="@TOOL_VERSION@">0.1.1</token> -->
+    <!-- <token name="@VERSION_SUFFIX@">0</token> -->
+    <!-- <token name="@PROFILE@">21.09</token> -->
+    <!-- <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token> -->
     <xml name="requirements">
         <requirements>
-	    <!-- <expand macro="chap-requirement" /> -->
+	    <expand macro="chap-requirement" />
 	    <requirement type="package" version="0.0.8">chessanalysispipeline</requirement>
             <requirement type="package" version="1.1.0">lmfit</requirement>
             <requirement type="package" version="3.7.1">matplotlib</requirement>
@@ -19,20 +19,20 @@
     </xml>
     <xml name="citations">
         <citations>
-            <!-- <expand macro="chap-citation" /> -->
-            <citation type="bibtex">
-@software{keara_soloway_2023_7963605,
-  author       = {Keara Soloway and
-                  Valentin Kuznetsov and
-                  Rolf Verberg},
-  title        = {CHESSComputing/ChessAnalysisPipeline: v0.0.8},
-  month        = may,
-  year         = 2023,
-  publisher    = {Zenodo},
-  version      = {v0.0.8},
-  doi          = {10.5281/zenodo.7963605},
-  url          = {https://doi.org/10.5281/zenodo.7963605}
-}</citation>
+            <expand macro="chap-citation" />
+<!--             <citation type="bibtex"> -->
+<!-- @software{keara_soloway_2023_7963605, -->
+<!--   author       = {Keara Soloway and -->
+<!--                   Valentin Kuznetsov and -->
+<!--                   Rolf Verberg}, -->
+<!--   title        = {CHESSComputing/ChessAnalysisPipeline: v0.0.8}, -->
+<!--   month        = may, -->
+<!--   year         = 2023, -->
+<!--   publisher    = {Zenodo}, -->
+<!--   version      = {v0.0.8}, -->
+<!--   doi          = {10.5281/zenodo.7963605}, -->
+<!--   url          = {https://doi.org/10.5281/zenodo.7963605} -->
+<!-- }</citation> -->
         </citations>
     </xml>
 </macros>
--- a/tomo/tomo_reconstruct.xml	Tue Jun 20 13:39:31 2023 +0000
+++ b/tomo/tomo_reconstruct.xml	Tue Jun 20 18:13:36 2023 +0000
@@ -1,6 +1,7 @@
 <tool id="CHAP_tomo_reconstruct" name="Tomo Reconstruct" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
     <description>Reconstruct tomography stacks</description>
     <macros>
+        <import>../macros.xml</import>
         <import>tomo_macros.xml</import>
     </macros>
     <expand macro="requirements"/>
--- a/tomo/tomo_reduce.xml	Tue Jun 20 13:39:31 2023 +0000
+++ b/tomo/tomo_reduce.xml	Tue Jun 20 18:13:36 2023 +0000
@@ -1,6 +1,7 @@
 <tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
     <description>Reduce tomography images</description>
     <macros>
+        <import>../macros.xml</import>
         <import>tomo_macros.xml</import>
     </macros>
     <expand macro="requirements"/>