Mercurial > repos > iuc > dimet_metabologram

changeset 6:c7ff01bd331b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/DIMet commit 3dba8748fbc8cc8e89ffc08e5febe0a0527a96a5
author iuc
date Fri, 21 Jun 2024 18:49:45 +0000
parents 82fbf955bb0f
children 06f8d9ba09cd
files dimet_metabologram.xml macros.xml
diffstat 2 files changed, 6 insertions(+), 8 deletions(-) [+]
line wrap: on
line diff
--- a/dimet_metabologram.xml	Tue May 21 13:42:49 2024 +0000
+++ b/dimet_metabologram.xml	Fri Jun 21 18:49:45 2024 +0000
@@ -16,10 +16,9 @@
     @INIT_PATHWAYS@
     @INIT_STAT_TEST@
     HYDRA_FULL_ERROR=1 python -m dimet
-    -cp '$__new_file_path__/config'
+    '++hydra.run.dir=.'
     '++figure_path=figures'
     '++table_path=tables'
-    '++hydra.run.dir=metabologram'
     '++analysis={
         dataset:{
             _target_: dimet.data.DataIntegrationConfig,
@@ -344,4 +343,4 @@
  ]]>
     </help>
     <expand macro="citations" />
-</tool> 
\ No newline at end of file
+</tool> 
--- a/macros.xml	Tue May 21 13:42:49 2024 +0000
+++ b/macros.xml	Fri Jun 21 18:49:45 2024 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">0.2.4</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">dimet</requirement>
@@ -598,16 +598,15 @@
 
     ]]></token>
     <token name="@INIT_CONFIG@"><![CDATA[
-    mkdir -p '$__new_file_path__/config' &&
-    touch '$__new_file_path__/config/config.yaml' &&
+    mkdir -p 'config' &&
+    touch 'config/config.yaml' &&
     ]]></token>
     <token name="@REMOVE_CONFIG@"><![CDATA[
-    && rm -r '$__new_file_path__/config'
+    && rm -r 'config'
     ]]></token>
     <token name="@INIT_ABUNDANCE_PLOT@"><![CDATA[
 
     mkdir -p data &&
-
     #if $metadata_path:
         ln -s '$metadata_path' data/metadata.csv &&
     #end if