# HG changeset patch
# User ximgchess
# Date 1686856918 0
# Node ID 0823bbfb0a78058e70cdd0aa5adaa0d2ffb561eb
# Parent  d8baf7dafbd80c6ce43c6dcff256c26bb920e266
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit dfe15e79689bca8ddcd843f9cf47eff29f6ee2e4

diff -r d8baf7dafbd8 -r 0823bbfb0a78 chap/chap.xml
--- a/chap/chap.xml	Thu Jun 15 19:08:58 2023 +0000
+++ b/chap/chap.xml	Thu Jun 15 19:21:58 2023 +0000
@@ -1,9 +1,6 @@
 <tool id="CHAP_test" name="CHESS Analysis Pipeline" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
-    <macros>
-        <import>../macros.xml</import>
-    </macros>
     <requirements>
-        <expand macro="chap-requirement" />
+        <requirement type="package" version="0.0.2">ChessAnalysisPipeline</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         cp '$input' data.csv &&
@@ -32,6 +29,14 @@
         required configuration pipeline and necessary data.
     ]]></help>
     <citations>
-        <expand macro="chap-citation" />
+        <citation type="bibtex">
+@misc{githubChessAnalysisPipeline,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {ChessAnalysisPipeline},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
+}</citation>
     </citations>
 </tool>
diff -r d8baf7dafbd8 -r 0823bbfb0a78 inference/chapmlaas.xml
--- a/inference/chapmlaas.xml	Thu Jun 15 19:08:58 2023 +0000
+++ b/inference/chapmlaas.xml	Thu Jun 15 19:21:58 2023 +0000
@@ -1,10 +1,7 @@
 <tool id="CHAP_inference_demo" name="CHAP MLaaS" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
-    <macros>
-        <import>../macros.xml</import>
-    </macros>
     <requirements>
         <requirement type="package" version="2.28.2">requests</requirement>
-	<expand macro="chap-requirement" />
+        <requirement type="package" version="0.0.2">chessanalysispipeline</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         cp '$input' data.csv &&
@@ -49,6 +46,14 @@
 
     ]]></help>
     <citations>
-        <expand macro="chap-citation" />
+        <citation type="bibtex">
+@misc{githubChessAnalysisPipeline,
+  author = {Kuznetsov, Valentin},
+  year = {2023},
+  title = {ChessAnalysisPipeline},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
+}</citation>
     </citations>
 </tool>
diff -r d8baf7dafbd8 -r 0823bbfb0a78 saxswaxs/reduce.xml
--- a/saxswaxs/reduce.xml	Thu Jun 15 19:08:58 2023 +0000
+++ b/saxswaxs/reduce.xml	Thu Jun 15 19:21:58 2023 +0000
@@ -1,9 +1,6 @@
 <tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
-    <macros>
-      <import>../macros.xml</import>
-    </macros>
     <requirements>
-      <expand macro="chap-requirement" />
+      <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>
@@ -38,6 +35,14 @@
 
     ]]></help>
     <citations>
-        <expand macro="chap-citation" />
+        <citation type="bibtex">
+@misc{githubChessAnalysisPipeline,
+  author = {LastTODO, FirstTODO},
+  year = {TODO},
+  title = {CHAPSAXSWAXSdemo},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/CHESSComputing/ChessAnalysisPipeline},
+}</citation>
     </citations>
 </tool>
diff -r d8baf7dafbd8 -r 0823bbfb0a78 tomo/tomo_macros.xml
--- a/tomo/tomo_macros.xml	Thu Jun 15 19:08:58 2023 +0000
+++ b/tomo/tomo_macros.xml	Thu Jun 15 19:21:58 2023 +0000
@@ -1,12 +1,10 @@
 <macros>
-    <import>../macros.xml</import>
     <token name="@TOOL_VERSION@">0.1.0</token>
     <token name="@PROFILE@">21.09</token>
     <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>
     <xml name="requirements">
         <requirements>
-	    <expand macro="chap-requirement" />
-            <!-- <requirement type="package" version="0.0.8">chessanalysispipeline</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>
             <requirement type="package" version="1.0.1">nexusformat</requirement>
@@ -16,20 +14,19 @@
     </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> -->
+            <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>