Mercurial > repos > tduigou > domestication

diff domestication.xml @ 1:bf8cd9487e33 draft

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planemo upload for repository https://github.com/Edinburgh-Genome-Foundry/Examples/blob/master/templates/template1.ipynb commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae
author tduigou
date Tue, 13 May 2025 07:22:36 +0000
parents 8fd9af4cb080
children f730b81671fb
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--- a/domestication.xml	Mon May 12 10:21:24 2025 +0000
+++ b/domestication.xml	Tue May 13 07:22:36 2025 +0000
@@ -1,7 +1,7 @@
 <tool id="domestication" name="domestication" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
     <description>Enables rapid and accurate preparation of DNA parts for modular cloning systems, such as Golden Gate Assembly</description>
     <macros>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
         <token name="@TOOL_VERSION@">0.1.0</token>
     </macros>
     <requirements>
@@ -12,14 +12,15 @@
         <requirement type="package" version="2.2.3">pandas</requirement>
         <requirement type="package" version="2.0.11">dnacauldron</requirement>
         <requirement type="package" version="0.3.9">pdf-reports</requirement>
-        <requirement type="package" version="0.1.7">sequenticon</requirement>
+        <requirement type="package" version="0.1.8">sequenticon</requirement>
         <requirement type="package" version="3.1.4">dna_features_viewer</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
+        #set genbank_file_paths = ','.join([str(f) for f in $genbank_files])
         #set $file_name_mapping = ",".join(["%s:%s" % (file.file_name, file.name) for file in $genbank_files])
         mkdir 'outdir_gb' && mkdir 'outdir_zip' &&
         python '$__tool_directory__/domestication.py'
-            --files_to_domestication '$genbank_files'
+            --files_to_domestication '$genbank_file_paths'
             --csv_file '$domestication_csv'
             --file_name_mapping '$file_name_mapping'
             --use_file_names_as_id '$adv.use_file_names_as_ids'
@@ -30,7 +31,7 @@
         cp 'output_zip.zip' '$output_zip'
     ]]></command>
     <inputs>
-        <param name="genbank_files" type="data" format="genbank" multiple="true" label="GenBank File(s)"/>
+        <param name="genbank_files" type="data_collection" collection_type="list" format="genbank" label="GenBank File(s)"/>
         <param name="domestication_csv" type="data" format="csv" label="deomestication csv"/>
         <param name="methylation_protection" type="boolean" checked="False" label="Enabel Methylation Protection"/>
         <section name="adv" title="Advanced Options" expanded="false">
@@ -51,7 +52,17 @@
     <tests>
         <!--test without methylation protection-->
         <test expect_num_outputs="1"> 
-            <param name="genbank_files" value="EMMA_undomesticated_parts/p3_2_CAG.gb,EMMA_undomesticated_parts/p7_gfp_sequence.gb,EMMA_undomesticated_parts/p14_CMVp.gb,EMMA_undomesticated_parts/p16_bGHpolyA.gb,EMMA_undomesticated_parts/p18_CMVp.gb,EMMA_undomesticated_parts/p19_mNeoGreen.gb,EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
+            <param name="genbank_files">
+                <collection type="list">
+                    <element name="p3_2_CAG" value="EMMA_undomesticated_parts/p3_2_CAG.gb" />
+                    <element name="p7_gfp_sequence" value="EMMA_undomesticated_parts/p7_gfp_sequence.gb" />
+                    <element name="p14_CMVp" value="EMMA_undomesticated_parts/p14_CMVp.gb" />
+                    <element name="p16_bGHpolyA" value="EMMA_undomesticated_parts/p16_bGHpolyA.gb" />
+                    <element name="p18_CMVp" value="EMMA_undomesticated_parts/p18_CMVp.gb" />
+                    <element name="p19_mNeoGreen" value="EMMA_undomesticated_parts/p19_mNeoGreen.gb" />
+                    <element name="p22_PGKpolyA" value="EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
+                </collection>
+            </param>
             <param name="domestication_csv" value="EMMA.csv" />
             <param name='methylation_protection' value='false' />
             <param name="adv|use_file_names_as_ids" value="True" />
@@ -67,7 +78,17 @@
         </test>
         <!--test with methylation protection-->
         <test expect_num_outputs="2"> 
-            <param name="genbank_files" value="EMMA_undomesticated_parts/p3_2_CAG.gb,EMMA_undomesticated_parts/p7_gfp_sequence.gb,EMMA_undomesticated_parts/p14_CMVp.gb,EMMA_undomesticated_parts/p16_bGHpolyA.gb,EMMA_undomesticated_parts/p18_CMVp.gb,EMMA_undomesticated_parts/p19_mNeoGreen.gb,EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
+            <param name="genbank_files">
+                <collection type="list">
+                    <element name="p3_2_CAG" value="EMMA_undomesticated_parts/p3_2_CAG.gb" />
+                    <element name="p7_gfp_sequence" value="EMMA_undomesticated_parts/p7_gfp_sequence.gb" />
+                    <element name="p14_CMVp" value="EMMA_undomesticated_parts/p14_CMVp.gb" />
+                    <element name="p16_bGHpolyA" value="EMMA_undomesticated_parts/p16_bGHpolyA.gb" />
+                    <element name="p18_CMVp" value="EMMA_undomesticated_parts/p18_CMVp.gb" />
+                    <element name="p19_mNeoGreen" value="EMMA_undomesticated_parts/p19_mNeoGreen.gb" />
+                    <element name="p22_PGKpolyA" value="EMMA_undomesticated_parts/p22_PGKpolyA.gb" />
+                </collection>
+            </param>
             <param name="domestication_csv" value="EMMA.csv" />
             <param name="methylation_protection" value="true" />
             <param name="adv|use_file_names_as_ids" value="True" />