Mercurial > repos > iuc > ncbi_datasets

changeset 7:0622d99c2619 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 7fc0becfda6c41c95d4aa9ee32ae0539be9b6210
author iuc
date Tue, 07 Jun 2022 17:39:19 +0000
parents 5a2656cc84cb
children b2ae7186d41f
files datasets_genome.xml macros.xml
diffstat 2 files changed, 6 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/datasets_genome.xml	Mon Jun 06 13:41:05 2022 +0000
+++ b/datasets_genome.xml	Tue Jun 07 17:39:19 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@">
+<tool id="datasets_download_genome" name="NCBI Datasets Genomes" profile="@PROFILE@" license="@LICENSE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>download genome sequence, annotation and metadata</description>
     <macros>
         <import>macros.xml</import>
@@ -89,7 +89,7 @@
             <filter>uncompressed</filter>
         </collection>
         <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list:list">
-            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/(?P&lt;identifier_1&gt;.*?)\.(?&lt;!cds_from)(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/(?!rna|cds_from)(?P&lt;identifier_1&gt;.*?)\.(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
             <filter>uncompressed and not file_choices['exclude_seq']</filter>
         </collection>
         <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
@@ -236,7 +236,7 @@
                 <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/>
             </output_collection>
         </test>
-        <test expect_num_outputs="3">
+        <test expect_num_outputs="5">
             <conditional name="query|subcommand">
                 <param name="download_by" value="accession"></param>
                 <conditional name="text_or_file">
@@ -245,9 +245,9 @@
                 </conditional>
             </conditional>
             <param name="exclude_protein" value="true"/>
-            <param name="exclude_rna" value="true"/>
+            <param name="exclude_rna" value="false"/>
             <param name="exclude_seq" value="false"/>
-            <param name="exclude_genomic_cds" value="true"/>
+            <param name="exclude_genomic_cds" value="false"/>
             <param name="exclude_gff3" value="true"/>
             <param name="uncompressed" value="true"/>
             <output_collection name="genome_fasta" type="list:list" count="1">
--- a/macros.xml	Mon Jun 06 13:41:05 2022 +0000
+++ b/macros.xml	Tue Jun 07 17:39:19 2022 +0000
@@ -2,6 +2,7 @@
     <token name="@TOOL_VERSION@">13.21.0</token>
     <token name="@PROFILE@">20.01</token>
     <token name="@LICENSE@">MIT</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>
     <token name="@SETUP_CERTIFICATES@"><![CDATA[
 ## If running in container use certificate from ca-certificates instead of outdated / missing container certificates