Mercurial > repos > tduigou > icfree_instructor

changeset 10:b3b05bfd58a8 draft

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planemo upload for repository https://github.com/brsynth/icfree-ml commit 08614ac872d03dfb266e405d5ff6c18f85e11117
author tduigou
date Thu, 12 Sep 2024 06:54:30 +0000
parents 25a9788e84ba
children e3747a8d8999
files instructor.xml macros.xml
diffstat 2 files changed, 5 insertions(+), 12 deletions(-) [+]
line wrap: on
line diff
--- a/instructor.xml	Tue Sep 10 15:02:42 2024 +0000
+++ b/instructor.xml	Thu Sep 12 06:54:30 2024 +0000
@@ -4,12 +4,11 @@
         <import>macros.xml</import>
     </macros>
     <expand macro="requirements"/>
-    <expand macro="stdio"/>
     <command detect_errors="exit_code"><![CDATA[
         python -m icfree.instructor
             '$source_plate_file'
             '$destination_plate_file'
-            'instructor.csv'
+            'instructions.csv'
             --source_plate_type '$adv.source_plate_type'
             #if str($adv.max_transfer_volume) != ''
                 --max_transfer_volume '$adv.max_transfer_volume'
@@ -35,7 +34,7 @@
         </section>
     </inputs>
     <outputs>
-        <collection name="output_instructor" type="list" label="${tool.name} - Instructor">
+        <collection name="output_instructor" type="list" label="${tool.name} - Instructions">
             <discover_datasets pattern="__designation_and_ext__" format="csv" directory="."/>
         </collection>
     </outputs>
@@ -45,7 +44,7 @@
             <param name="source_plate_file" value="plates_designer.source_plate.test-2.csv" />
             <param name="destination_plate_file" value="plates_designer.destination_plate.test-2.csv" />
             <output_collection name="output_instructor" type="list" count="1">
-                <element name="instructor" file="instructor.test-1.csv" ftype="csv" compare="diff" />
+                <element name="instructions" file="instructor.test-1.csv" ftype="csv" compare="diff" />
             </output_collection>
         </test>
         <test>
@@ -55,8 +54,8 @@
             <param name="source_plate_type" value="Hela lysate:384PP_AQ_CP,Access prot 50%:384PP_AQ_GP3,Reaction mix:384PP_AQ_GP3,RNA 1ug/uL:384PP_AQ_GP3" />
             <param name="split_components" value="Hela lysate,Access prot 50%" />
             <output_collection name="output_instructor" type="list" count="3">
-                <element name="instructor" file="instructor.test-2.csv" ftype="csv" compare="diff" />
-                <element name="instructor_Hela lysate" file="instructor.hela.test-2.csv" ftype="csv" compare="diff" />
+                <element name="instructions" file="instructor.test-2.csv" ftype="csv" compare="diff" />
+                <element name="instructions_Hela lysate" file="instructor.hela.test-2.csv" ftype="csv" compare="diff" />
                 <!--
                     <element name="instructor_Access prot 50X" file="instructor.access.test-2.csv" ftype="csv" compare="diff" />
                 -->
--- a/macros.xml	Tue Sep 10 15:02:42 2024 +0000
+++ b/macros.xml	Thu Sep 12 06:54:30 2024 +0000
@@ -7,12 +7,6 @@
             <yield/>
         </requirements>
     </xml>
-    <xml name="stdio">
-        <stdio>
-            <regex match="WARNING" level="warning" />
-            <regex match="ERROR" level="fatal" />
-        </stdio>
-    </xml>
     <xml name="citation">
         <citations>
             <citation type="bibtex">