# HG changeset patch
# User ximgchess
# Date 1692815608 0
# Node ID 7883df4af8ab4f1dc5b509e047c8485de84652e7
# Parent  50fb82e1213a313c46a95afd9e78f08d6194d761
planemo upload for repository https://github.com/CHESSComputing/ChessAnalysisPipeline commit 509f8f9b035d9dc3f4878cea2d14769819fe2349-dirty

diff -r 50fb82e1213a -r 7883df4af8ab chapbook_demo/chapbook_demo.xml
--- a/chapbook_demo/chapbook_demo.xml	Wed Jul 05 13:37:14 2023 +0000
+++ b/chapbook_demo/chapbook_demo.xml	Wed Aug 23 18:33:28 2023 +0000
@@ -1,4 +1,4 @@
-<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy13" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
+<tool id="CHAP_chapbook_demo" name="CHAPbook" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="@PYTHON_TEMPLATE_VERSION@" profile="@PROFILE@">
   <macros>
     <import>../macros.xml</import>
   </macros>
@@ -9,17 +9,8 @@
     <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 &&
-
-      ## Create symlinks in the tool directory to all items in the
-      ## input directory provided by the user
-      #import os.path
-      #set $norm_indir = os.path.normpath(str($indir))
-      ln -s $norm_indir/* . &&
-
-      ## Run the pipeline provided
+      cd '$indir' &&
       CHAP --config '$config'
 ]]></command>
   <environment_variables>
@@ -30,8 +21,8 @@
       <param type="text" name="indir" label="Input Directory" />
   </inputs>
   <outputs>
-      <data name="data" format="nex" label="Reduced data" from_work_dir="data.nex"/>
-      <data name="plot" format="png" label="Plot" from_work_dir="plot.png"/>
+      <data name="data" format="nex" label="Reduced data"/>
+      <data name="plot" format="png" label="Plot"/>
   </outputs>
   <tests>
       <test>
diff -r 50fb82e1213a -r 7883df4af8ab macros.xml
--- a/macros.xml	Wed Jul 05 13:37:14 2023 +0000
+++ b/macros.xml	Wed Aug 23 18:33:28 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-  <token name="@TOOL_VERSION@">0.0.10</token>
+  <token name="@TOOL_VERSION@">0.0.11</token>
   <token name="@VERSION_SUFFIX@">0</token>
   <token name="@PROFILE@">21.09</token>
   <token name="@PYTHON_TEMPLATE_VERSION@">3.11</token>
diff -r 50fb82e1213a -r 7883df4af8ab tomo/tomo_macros.xml
--- a/tomo/tomo_macros.xml	Wed Jul 05 13:37:14 2023 +0000
+++ b/tomo/tomo_macros.xml	Wed Aug 23 18:33:28 2023 +0000
@@ -2,7 +2,6 @@
     <xml name="requirements">
         <requirements>
 	    <expand macro="chap-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>