changeset 144:807ef54fdc76 draft

planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty

--- a/chap/chap.xml	Mon Jun 26 12:10:59 2023 +0000
+++ b/chap/chap.xml	Mon Jun 26 12:18:09 2023 +0000
@@ -1,32 +1,25 @@
-<tool id="CHAP_test" name="CHESS Analysis Pipeline" version="@TOOL_VERSION@+galaxy2" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
+<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" />
-    <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 &&
-      cd '$indir' &&
+      cp '$input' data.csv &&
       CHAP --config '$config' &&
   ]]></command>
-  <environment_variables>
-    <environment_variable name="PYTHONPATH">/home/chess_chapaas/chess/chap/</environment_variable>
-  </environment_variables>
   <inputs>
-      <param type="data" name="config" format="yaml" label="Pipeline Configuration File" />
-      <param type="text" name="indir" label="Input Directory" />
+      <param type="data" name="config" format="yaml" />
+      <param type="data" name="input" format="csv" />
   </inputs>
-  <!-- <outputs> -->
-  <!--     <data name="output" format="json" /> -->
-  <!-- </outputs> -->
+  <outputs>
+      <data name="output" format="json" />
+  </outputs>
   <tests>
       <test>
           <param name="config" value="config.yaml"/>
-	  <param name="indir" value="/tmp/"/>
+          <param name="input" value="data.csv"/>
       </test>
   </tests>
   <help><![CDATA[

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chapbook_demo/chapbook_demo.xml	Mon Jun 26 12:18:09 2023 +0000
@@ -0,0 +1,45 @@
+<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy0" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
+  <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 &&
+      cd '$indir' &&
+      CHAP --config '$config' &&
+]]></command>
+  <environment_variables>
+    <environment_variable name="PYTHONPATH">/home/chess_chapaas/chess/chap/</environment_variable>
+  </environment_variables>
+  <inputs>
+      <param type="data" name="config" format="yaml" label="Pipeline Configuration File" />
+      <param type="text" name="indir" label="Input Directory" />
+  </inputs>
+  <outputs>
+      <data name="data" format="nex" />
+      <data name="plot" format="png">
+  </outputs>
+  <tests>
+      <test>
+          <param name="config" value="config.yaml"/>
+	  <param name="indir" value="/tmp/"/>
+      </test>
+  </tests>
+  <help><![CDATA[
+      CHESS Analysis Pipeline (CHAP):
+
+      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>
+    <expand macro="chap-citation" />
+  </citations>
+</tool>