Mercurial > repos > ximgchess > chap_test_20230411

diff saxswaxs/reduce.xml @ 61:a560d5143348 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit e280dd942513f966a9a61a3af68ee7972fb8992f-dirty
author kls286
date Thu, 13 Apr 2023 12:18:11 +0000
parents 47d2a1f087d1
children be4a6ceb0a3d
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--- a/saxswaxs/reduce.xml	Wed Apr 12 19:04:05 2023 +0000
+++ b/saxswaxs/reduce.xml	Thu Apr 13 12:18:11 2023 +0000
@@ -1,6 +1,6 @@
 <tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
     <requirements>
-      <requirement type="package" version="0.0.3">chessanalysispipeline</requirement>
+      <requirement type="package" version="0.0.5">chessanalysispipeline</requirement>
       <requirement type="package" version="2.28.1">requests</requirement>
       <requirement type="package" version="2023.3.0">pyfai</requirement>
       <requirement type="package" version="1.10.7">pydantic</requirement>
@@ -9,9 +9,11 @@
         pip --exists-action i install certif-pyspec==1.5.3 &&
         cp '$mapconfig' map.yaml &&
 	cp '$integrationconfig' integration.yaml &&
-	CHAP --config '$__tool_directory__/pipeline.yaml'
+	sed 's/GITLABTOKEN/$token/' '$__tool_directory__/pipeline.yaml' > pipeline.yaml
+	CHAP --config pipeline.yaml
     ]]></command>
     <inputs>
+        <param type="text" name="token" />
         <param type="data" name="mapconfig" format="yaml" />
         <param type="data" name="integrationconfig" format="yaml" />
     </inputs>