Mercurial > repos > ximgchess > chap_test_20230411

changeset 132:81838550bb4d draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit dfe15e79689bca8ddcd843f9cf47eff29f6ee2e4-dirty
author ximgchess
date Tue, 20 Jun 2023 12:13:58 +0000
parents 905acff8ffdb
children 49985da419b8
files macros.xml saxswaxs/reduce.xml
diffstat 2 files changed, 41 insertions(+), 37 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Tue Jun 20 12:01:34 2023 +0000
+++ b/macros.xml	Tue Jun 20 12:13:58 2023 +0000
@@ -1,6 +1,7 @@
 <macros>
+  <token name="@TOOL_VERSION@">0.0.8</token>
   <xml name="chap-requirement">
-    <requirement type="package" version="PACKAGE_VERSION">chessanalysispipeline</requirement>
+    <requirement type="package" version="@TOOL_VERSION@">chessanalysispipeline</requirement>
   </xml>
   <xml name="chap-citation">
     <citation type="doi">10.5281/zenodo.7963532</citation>
--- a/saxswaxs/reduce.xml	Tue Jun 20 12:01:34 2023 +0000
+++ b/saxswaxs/reduce.xml	Tue Jun 20 12:13:58 2023 +0000
@@ -1,40 +1,43 @@
-<tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.1+galaxy0" python_template_version="3.5" profile="21.05">
-    <requirements>
-      <requirement type="package" version="0.0.8">chessanalysispipeline</requirement>
-      <requirement type="package" version="1.0.1">nexusformat</requirement>
-      <requirement type="package" version="2023.3.0">pyfai</requirement>
-      <requirement type="package" version="1.10.7">pydantic</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        pip --exists-action i install certif-pyspec==1.5.3 &&
-        cp '$mapconfig' map.yaml &&
-	cp '$integrationconfig' integration.yaml &&
-	CHAP --config '$__tool_directory__/pipeline.yaml'
-    ]]></command>
-    <inputs>
-        <param type="data" name="mapconfig" format="yaml" />
-        <param type="data" name="integrationconfig" format="yaml" />
-    </inputs>
-    <outputs>
-	<data name="reduceddata" label="Map of reduced data" format="nex" from_work_dir="map_reduceddata.nxs"/>
-    </outputs>
-    <tests>
-        <test>
-            <param name="mapconfig" value="map.yaml"/>
-            <param name="integrationconfig" value="integration.yaml"/>
-            <output name="reduceddata" value="map_reduceddata.nxs"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-        usage: PROG [-h] [--config CONFIG] [--verbose]
+<tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+  <macros>
+    <import>../macros.xml</import>
+  </macros>
+  <requirements>
+    <expand macro="chap-requirement" />
+    <requirement type="package" version="1.0.1">nexusformat</requirement>
+    <requirement type="package" version="2023.3.0">pyfai</requirement>
+    <requirement type="package" version="1.10.7">pydantic</requirement>
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+      pip --exists-action i install certif-pyspec==1.5.3 &&
+      cp '$mapconfig' map.yaml &&
+      cp '$integrationconfig' integration.yaml &&
+      CHAP --config '$__tool_directory__/pipeline.yaml'
+  ]]></command>
+  <inputs>
+      <param type="data" name="mapconfig" format="yaml" />
+      <param type="data" name="integrationconfig" format="yaml" />
+  </inputs>
+  <outputs>
+  	<data name="reduceddata" label="Map of reduced data" format="nex" from_work_dir="map_reduceddata.nxs"/>
+  </outputs>
+  <tests>
+      <test>
+          <param name="mapconfig" value="map.yaml"/>
+          <param name="integrationconfig" value="integration.yaml"/>
+          <output name="reduceddata" value="map_reduceddata.nxs"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+      usage: PROG [-h] [--config CONFIG] [--verbose]
 
 options:
-  -h, --help       show this help message and exit
-  --config CONFIG  Input configuration file
-  --verbose        verbose output
+  , --help       show this help message and exit
+  config CONFIG  Input configuration file
+  verbose        verbose output
 
-    ]]></help>
-    <citations>
-        <citation type="doi">10.5281/zenodo.7963532</citation>
-    </citations>
+  ]]></help>
+  <citations>
+    <expand macro="chap-citation" />
+  </citations>
 </tool>