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changeset 133:49985da419b8 draft

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planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 85285b9b70eaf7c5db051ed50b000339023ccdf2-dirty
author ximgchess
date Tue, 20 Jun 2023 12:45:50 +0000
parents 81838550bb4d
children 96f74c637a36
files chap/chap.xml inference/chapmlaas.xml macros.xml 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 9 files changed, 96 insertions(+), 99 deletions(-) [+]
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line diff
--- a/chap/chap.xml	Tue Jun 20 12:13:58 2023 +0000
+++ b/chap/chap.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,42 +1,37 @@
-<tool id="CHAP_test" name="CHESS Analysis Pipeline" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
-    <requirements>
-        <requirement type="package" version="0.0.2">ChessAnalysisPipeline</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        cp '$input' data.csv &&
-        CHAP --config '$config' &&
-    ]]></command>
-    <inputs>
-        <param type="data" name="config" format="yaml" />
-        <param type="data" name="input" format="csv" />
-    </inputs>
-    <outputs>
-        <data name="output" format="json" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="config" value="config.yaml"/>
-            <param name="input" value="data.csv"/>
-        </test>
-    </tests>
-    <help><![CDATA[
-        CHESS Analysis Pipeline (CHAP):
+<tool id="CHAP_test" name="CHESS Analysis Pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
+  <macros>
+    <import>../macros.xml</import>
+  </macros>
+  <requirements>
+    <expand macro="chap-requirement" />
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+      cp '$input' data.csv &&
+      CHAP --config '$config' &&
+  ]]></command>
+  <inputs>
+      <param type="data" name="config" format="yaml" />
+      <param type="data" name="input" format="csv" />
+  </inputs>
+  <outputs>
+      <data name="output" format="json" />
+  </outputs>
+  <tests>
+      <test>
+          <param name="config" value="config.yaml"/>
+          <param name="input" value="data.csv"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+      CHESS Analysis Pipeline (CHAP):
 
-        To run it on command line you'll use:
-        CHAP --config CONFIG
+      To run it on command line you'll use:
+      CHAP --config CONFIG
 
-        To run it within galaxy you'll only need to upload your
-        required configuration pipeline and necessary data.
-    ]]></help>
-    <citations>
-        <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>
+      To run it within galaxy you'll only need to upload your
+      required configuration pipeline and necessary data.
+  ]]></help>
+  <citations>
+    <expand macro="chap-citation" />
+  </citations>
 </tool>
--- a/inference/chapmlaas.xml	Tue Jun 20 12:13:58 2023 +0000
+++ b/inference/chapmlaas.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,30 +1,33 @@
-<tool id="CHAP_inference_demo" name="CHAP MLaaS" version="0.1.0+galaxy0" python_template_version="3.5" profile="21.05">
-    <requirements>
-        <requirement type="package" version="2.28.2">requests</requirement>
-        <requirement type="package" version="0.0.2">chessanalysispipeline</requirement>
-    </requirements>
-    <command detect_errors="exit_code"><![CDATA[
-        cp '$input' data.csv &&
-        cp '$image' img.png &&
-        CHAP --config '$config' &&
-        cp preds.json '$output'
-    ]]></command>
-    <inputs>
-        <param type="data" name="config" format="yaml" />
-        <param type="data" name="input" format="csv" />
-        <param type="data" name="image" format="png" />
-    </inputs>
-    <outputs>
-        <data name="output" format="json" />
-    </outputs>
-    <tests>
-        <test>
-            <param name="config" value="config.yaml"/>
-            <param name="input" value="data.csv"/>
-            <param name="image" value="img.png"/>
-        </test>
-    </tests>
-    <help><![CDATA[
+<tool id="CHAP_inference_demo" name="CHAP MLaaS" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
+  <macros>
+    <import>../macros.xml</import>
+  </macros>
+  <requirements>
+    <requirement type="package" version="2.28.2">requests</requirement>
+    <expand macro="chap-requirement" />
+  </requirements>
+  <command detect_errors="exit_code"><![CDATA[
+      cp '$input' data.csv &&
+      cp '$image' img.png &&
+      CHAP --config '$config' &&
+      cp preds.json '$output'
+  ]]></command>
+  <inputs>
+    <param type="data" name="config" format="yaml" />
+    <param type="data" name="input" format="csv" />
+    <param type="data" name="image" format="png" />
+  </inputs>
+  <outputs>
+    <data name="output" format="json" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="config" value="config.yaml"/>
+      <param name="input" value="data.csv"/>
+      <param name="image" value="img.png"/>
+    </test>
+  </tests>
+  <help><![CDATA[
 CHESS Analysis Pipeline (CHAP) with Machine Learning as a Service (MLaaS)
 
 To run it you need the following:
@@ -45,15 +48,7 @@
       filename: preds.json
 
     ]]></help>
-    <citations>
-        <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>
+  <citations>
+    <expand macro="chap-citation" />
+  </citations>
 </tool>
--- a/macros.xml	Tue Jun 20 12:13:58 2023 +0000
+++ b/macros.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,5 +1,8 @@
 <macros>
   <token name="@TOOL_VERSION@">0.0.8</token>
+  <token name="@VERSION_SUFFIX@">0</token>
+  <token name="@PROFILE@">21.09</token>
+  <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>
   <xml name="chap-requirement">
     <requirement type="package" version="@TOOL_VERSION@">chessanalysispipeline</requirement>
   </xml>
--- a/saxswaxs/reduce.xml	Tue Jun 20 12:13:58 2023 +0000
+++ b/saxswaxs/reduce.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5" profile="21.05">
+<tool id="CHAP_saxswaxs_reduce" name="SAXSWAXS Reduce Map" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
   <macros>
     <import>../macros.xml</import>
   </macros>
--- a/tomo/tomo_combine.xml	Tue Jun 20 12:13:58 2023 +0000
+++ b/tomo/tomo_combine.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="CHAP_tomo_combine" name="Tomo Combine" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
+<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>tomo_macros.xml</import>
--- a/tomo/tomo_find_center.xml	Tue Jun 20 12:13:58 2023 +0000
+++ b/tomo/tomo_find_center.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="CHAP_tomo_find_center" name="Tomo Find Center" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
+<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>tomo_macros.xml</import>
--- a/tomo/tomo_macros.xml	Tue Jun 20 12:13:58 2023 +0000
+++ b/tomo/tomo_macros.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,10 +1,13 @@
 <macros>
-    <token name="@TOOL_VERSION@">0.1.0</token>
-    <token name="@PROFILE@">21.09</token>
-    <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>
+    <macros>
+      <import>../macros.xml</import>
+    </macros>
+    <!-- <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>
-            <requirement type="package" version="0.0.8">chessanalysispipeline</requirement>
+	    <expand macro="chap-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>
@@ -14,19 +17,20 @@
     </xml>
     <xml name="citations">
         <citations>
-            <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 12:13:58 2023 +0000
+++ b/tomo/tomo_reconstruct.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="CHAP_tomo_reconstruct" name="Tomo Reconstruct" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
+<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>tomo_macros.xml</import>
--- a/tomo/tomo_reduce.xml	Tue Jun 20 12:13:58 2023 +0000
+++ b/tomo/tomo_reduce.xml	Tue Jun 20 12:45:50 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="CHAP_tomo_reduce" name="Tomo Reduce" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@" python_template_version="@PYTHON_TEMPLATE_VERSION@">
+<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>tomo_macros.xml</import>