# HG changeset patch
# User ximgchess
# Date 1687780457 0
# Node ID 47b86f77fa59834a121e94e65d06aca0d1137814
# Parent  59d672fde7fd853ee0dd1dc436f23991cf5dbabc
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 819e366e63ba35d3f50f8fc2bd163ce60293b59c-dirty

diff -r 59d672fde7fd -r 47b86f77fa59 chap/chap.xml
--- a/chap/chap.xml	Thu Jun 22 14:45:11 2023 +0000
+++ b/chap/chap.xml	Mon Jun 26 11:54:17 2023 +0000
@@ -1,17 +1,24 @@
-<tool id="CHAP_test" name="CHESS Analysis Pipeline" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
+<tool id="CHAP_test" name="CHESS Analysis Pipeline" version="@TOOL_VERSION@+galaxy1" 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[
-      cp '$input' data.csv &&
+      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" />
-      <param type="data" name="input" format="csv" />
+      <param type="data" name="config" format="yaml" label="Pipeline Configuration File" />
+      <param type="text" name="indir" label="Input Directory" />
   </inputs>
   <outputs>
       <data name="output" format="json" />
@@ -19,7 +26,7 @@
   <tests>
       <test>
           <param name="config" value="config.yaml"/>
-          <param name="input" value="data.csv"/>
+	  <param name="indir" value="/tmp/"/>
       </test>
   </tests>
   <help><![CDATA[
diff -r 59d672fde7fd -r 47b86f77fa59 macros.xml
--- a/macros.xml	Thu Jun 22 14:45:11 2023 +0000
+++ b/macros.xml	Mon Jun 26 11:54:17 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@TOOL_VERSION@">v0.0.8</token>
+  <token name="@TOOL_VERSION@">PACKAGE_VERSION</token>
   <token name="@VERSION_SUFFIX@">0</token>
   <token name="@PROFILE@">21.09</token>
   <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>