# HG changeset patch
# User ximgchess
# Date 1688132059 0
# Node ID 262b81603e4e8bd398cdab457e243d121b1e46ca
# Parent  b2e914633e614f9b05f02a87bee8a0a1c2dea3a1
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit bd55c86b9f7bfabff0bbec1f10704850fec82f02-dirty

diff -r b2e914633e61 -r 262b81603e4e chapbook_demo/chapbook_demo.xml
--- a/chapbook_demo/chapbook_demo.xml	Fri Jun 30 13:21:22 2023 +0000
+++ b/chapbook_demo/chapbook_demo.xml	Fri Jun 30 13:34:19 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy6" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
+<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy7" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
   <macros>
     <import>../macros.xml</import>
   </macros>
@@ -9,11 +9,20 @@
     <requirement type="package" version="1.10.7">pydantic</requirement>
   </requirements>
   <command detect_errors="exit_code"><![CDATA[
+      ## certif-pyspec is not available over any conda channels, so
+      ## pip install the package the first time this tool is run
       pip --exists-action i install certif-pyspec==1.5.3 &&
 
-      indir=$(realpath )
-      ln -s \$(realpath '$indir')/* '$__tool_directory__' &&
+      ## Create symlinks in the tool directory to all items in the
+      ## input directory provided by the user
+      #import os.path
+      #set $norm_indir = os.path.normpath('$indir')
+      ln -s '$norm_indir'/* '$__tool_directory__' &&
+
+      ## Run the pipeline provided
       CHAP --config '$config' &&
+
+      ## Unlink the symlinks created previously
       find '$__tool_directory__' -type l -exec unlink {} \;
 ]]></command>
   <environment_variables>