Mercurial > repos > iuc > ncbi_datasets

changeset 6:5a2656cc84cb draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit 3f6e22f12ae0fe27cfc1d3dab576d0c10017f41e
author iuc
date Mon, 06 Jun 2022 13:41:05 +0000
parents 6c829a430475
children 0622d99c2619
files datasets_genome.xml macros.xml
diffstat 2 files changed, 28 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/datasets_genome.xml	Wed May 04 13:15:43 2022 +0000
+++ b/datasets_genome.xml	Mon Jun 06 13:41:05 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@">
     <description>download genome sequence, annotation and metadata</description>
     <macros>
         <import>macros.xml</import>
@@ -88,8 +88,8 @@
             <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/sequence_report.jsonl" ext="json" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
             <filter>uncompressed</filter>
         </collection>
-        <collection name="genome_fasta" label="NCBI Genome Datasets: genome fasta" type="list">
-            <discover_datasets pattern="(?P&lt;identifier_0&gt;.*?)\/.*(?&lt;!cds_from)(chr|unplaced|_genomic)*fna" ext="fasta" directory="ncbi_dataset/data" recurse="true" match_relative_path="true"></discover_datasets>
+        <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>
             <filter>uncompressed and not file_choices['exclude_seq']</filter>
         </collection>
         <collection name="genomic_cds" label="NCBI Genome Datasets: genomic cds fasta" type="list">
@@ -236,6 +236,30 @@
                 <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/>
             </output_collection>
         </test>
+        <test expect_num_outputs="3">
+            <conditional name="query|subcommand">
+                <param name="download_by" value="accession"></param>
+                <conditional name="text_or_file">
+                    <param name="text_or_file" value="text"></param>
+                    <param name="accession" value="GCF_000146045.2"></param>
+                </conditional>
+            </conditional>
+            <param name="exclude_protein" value="true"/>
+            <param name="exclude_rna" value="true"/>
+            <param name="exclude_seq" value="false"/>
+            <param name="exclude_genomic_cds" value="true"/>
+            <param name="exclude_gff3" value="true"/>
+            <param name="uncompressed" value="true"/>
+            <output_collection name="genome_fasta" type="list:list" count="1">
+                <element name="GCF_000146045.2">
+                    <element name="chrI">
+                        <assert_contents>
+                            <has_text text=">NC_001133.9"/>
+                        </assert_contents>
+                    </element>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help>
 <![CDATA[
--- a/macros.xml	Wed May 04 13:15:43 2022 +0000
+++ b/macros.xml	Mon Jun 06 13:41:05 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">13.14.0</token>
+    <token name="@TOOL_VERSION@">13.21.0</token>
     <token name="@PROFILE@">20.01</token>
     <token name="@LICENSE@">MIT</token>
     <token name="@PROFILE_AND_LICENSE@">profile="@PROFILE@" license="@LICENSE@"</token>