Mercurial > repos > iuc > ncbi_datasets

diff datasets_genome.xml @ 8:b2ae7186d41f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ncbi_datasets commit c204867781d8755c7469a88c11478b15caec57b2
author iuc
date Thu, 23 Jun 2022 17:33:12 +0000
parents 0622d99c2619
children 18eed8fa7f23
line wrap: on
line diff
--- a/datasets_genome.xml	Tue Jun 07 17:39:19 2022 +0000
+++ b/datasets_genome.xml	Thu Jun 23 17:33:12 2022 +0000
@@ -35,9 +35,9 @@
     --search '$filters.search_term'
 #end for
 #if $uncompressed
-&& unzip ncbi_dataset.zip
+&& 7z x -y ncbi_dataset.zip
 #else
-&& unzip -l ncbi_dataset.zip > ncbi_dataset.txt
+&& 7z l ncbi_dataset.zip > ncbi_dataset.txt
 #end if
 ]]></command>
     <inputs>
@@ -233,7 +233,11 @@
             <param name="uncompressed" value="true"/>
             <param name="released_before" value="01/02/2007"></param>
             <output_collection name="sequence_report">
-                <element name="GCF_000001405.40" file="GCF_000001405.40.seq.rpt.jsonl" compare="contains"/>
+                <element name="GCF_000001405.40">
+                    <assert_contents>
+                        <has_text text="assignedMoleculeLocationType"/>
+                    </assert_contents>
+                 </element>
             </output_collection>
         </test>
         <test expect_num_outputs="5">
@@ -260,6 +264,37 @@
                 </element>
             </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 GCF_000002945.1"></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="2">
+                <element name="GCF_000146045.2">
+                    <element name="chrI">
+                        <assert_contents>
+                            <has_text text=">NC_001133.9"/>
+                        </assert_contents>
+                    </element>
+                </element>
+                <element name="GCF_000002945.1">
+                    <element name="chrI">
+                        <assert_contents>
+                            <has_text text=">NC_003424.3"/>
+                        </assert_contents>
+                    </element>
+                </element>
+            </output_collection>
+        </test>
     </tests>
     <help>
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