Mercurial > repos > iuc > ncbi_datasets

changeset 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
files datasets_genome.xml macros.xml test-data/GCF_000001405.40.seq.rpt.jsonl
diffstat 3 files changed, 39 insertions(+), 195 deletions(-) [+]
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>
 <![CDATA[
--- a/macros.xml	Tue Jun 07 17:39:19 2022 +0000
+++ b/macros.xml	Thu Jun 23 17:33:12 2022 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">13.21.0</token>
+    <token name="@TOOL_VERSION@">13.24.1</token>
     <token name="@PROFILE@">20.01</token>
     <token name="@LICENSE@">MIT</token>
     <token name="@VERSION_SUFFIX@">1</token>
--- a/test-data/GCF_000001405.40.seq.rpt.jsonl	Tue Jun 07 17:39:19 2022 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,191 +0,0 @@
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","gcCount":"103674491","genbankAccession":"CM000663.2","length":248956422,"refseqAccession":"NC_000001.11","role":"assembled-molecule","sortOrder":1,"ucscStyleName":"chr1"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270706.1","length":175055,"refseqAccession":"NT_187361.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270706v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270707.1","length":32032,"refseqAccession":"NT_187362.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270707v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270708.1","length":127682,"refseqAccession":"NT_187363.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270708v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270709.1","length":66860,"refseqAccession":"NT_187364.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270709v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270710.1","length":40176,"refseqAccession":"NT_187365.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270710v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270711.1","length":42210,"refseqAccession":"NT_187366.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270711v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270712.1","length":176043,"refseqAccession":"NT_187367.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270712v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270713.1","length":40745,"refseqAccession":"NT_187368.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270713v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"1","genbankAccession":"KI270714.1","length":41717,"refseqAccession":"NT_187369.1","role":"unlocalized-scaffold","sortOrder":1,"ucscStyleName":"chr1_KI270714v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"10","gcCount":"59342366","genbankAccession":"CM000672.2","length":133797422,"refseqAccession":"NC_000010.11","role":"assembled-molecule","sortOrder":10,"ucscStyleName":"chr10"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"11","gcCount":"70204082","genbankAccession":"CM000673.2","length":135086622,"refseqAccession":"NC_000011.10","role":"assembled-molecule","sortOrder":11,"ucscStyleName":"chr11"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"12","gcCount":"58038673","genbankAccession":"CM000674.2","length":133275309,"refseqAccession":"NC_000012.12","role":"assembled-molecule","sortOrder":12,"ucscStyleName":"chr12"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"13","gcCount":"38619357","genbankAccession":"CM000675.2","length":114364328,"refseqAccession":"NC_000013.11","role":"assembled-molecule","sortOrder":13,"ucscStyleName":"chr13"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","gcCount":"45815948","genbankAccession":"CM000676.2","length":107043718,"refseqAccession":"NC_000014.9","role":"assembled-molecule","sortOrder":14,"ucscStyleName":"chr14"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000009.2","length":201709,"refseqAccession":"NT_113796.3","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_GL000009v2_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000194.1","length":191469,"refseqAccession":"NT_113888.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_GL000194v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"GL000225.1","length":211173,"refseqAccession":"NT_167219.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_GL000225v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270722.1","length":194050,"refseqAccession":"NT_187377.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270722v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270723.1","length":38115,"refseqAccession":"NT_187378.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270723v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270724.1","length":39555,"refseqAccession":"NT_187379.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270724v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270725.1","length":172810,"refseqAccession":"NT_187380.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270725v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"14","genbankAccession":"KI270726.1","length":43739,"refseqAccession":"NT_187381.1","role":"unlocalized-scaffold","sortOrder":14,"ucscStyleName":"chr14_KI270726v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"15","gcCount":"46742416","genbankAccession":"CM000677.2","length":101991189,"refseqAccession":"NC_000015.10","role":"assembled-molecule","sortOrder":15,"ucscStyleName":"chr15"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"15","genbankAccession":"KI270727.1","length":448248,"refseqAccession":"NT_187382.1","role":"unlocalized-scaffold","sortOrder":15,"ucscStyleName":"chr15_KI270727v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"16","gcCount":"48251436","genbankAccession":"CM000678.2","length":90338345,"refseqAccession":"NC_000016.10","role":"assembled-molecule","sortOrder":16,"ucscStyleName":"chr16"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"16","genbankAccession":"KI270728.1","length":1872759,"refseqAccession":"NT_187383.1","role":"unlocalized-scaffold","sortOrder":16,"ucscStyleName":"chr16_KI270728v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"17","gcCount":"46714680","genbankAccession":"CM000679.2","length":83257441,"refseqAccession":"NC_000017.11","role":"assembled-molecule","sortOrder":17,"ucscStyleName":"chr17"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"GL000205.2","length":185591,"refseqAccession":"NT_113930.2","role":"unlocalized-scaffold","sortOrder":17,"ucscStyleName":"chr17_GL000205v2_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"KI270729.1","length":280839,"refseqAccession":"NT_187384.1","role":"unlocalized-scaffold","sortOrder":17,"ucscStyleName":"chr17_KI270729v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"17","genbankAccession":"KI270730.1","length":112551,"refseqAccession":"NT_187385.1","role":"unlocalized-scaffold","sortOrder":17,"ucscStyleName":"chr17_KI270730v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"18","gcCount":"40613699","genbankAccession":"CM000680.2","length":80373285,"refseqAccession":"NC_000018.10","role":"assembled-molecule","sortOrder":18,"ucscStyleName":"chr18"}
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-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"2","gcCount":"101284083","genbankAccession":"CM000664.2","length":242193529,"refseqAccession":"NC_000002.12","role":"assembled-molecule","sortOrder":2,"ucscStyleName":"chr2"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"2","genbankAccession":"KI270715.1","length":161471,"refseqAccession":"NT_187370.1","role":"unlocalized-scaffold","sortOrder":2,"ucscStyleName":"chr2_KI270715v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"2","genbankAccession":"KI270716.1","length":153799,"refseqAccession":"NT_187371.1","role":"unlocalized-scaffold","sortOrder":2,"ucscStyleName":"chr2_KI270716v1_random"}
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-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270737.1","length":103838,"refseqAccession":"NT_187392.1","role":"unlocalized-scaffold","sortOrder":22,"ucscStyleName":"chr22_KI270737v1_random"}
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-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"22","genbankAccession":"KI270739.1","length":73985,"refseqAccession":"NT_187394.1","role":"unlocalized-scaffold","sortOrder":22,"ucscStyleName":"chr22_KI270739v1_random"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"3","gcCount":"91922884","genbankAccession":"CM000665.2","length":198295559,"refseqAccession":"NC_000003.12","role":"assembled-molecule","sortOrder":3,"ucscStyleName":"chr3"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"3","genbankAccession":"GL000221.1","length":155397,"refseqAccession":"NT_167215.1","role":"unlocalized-scaffold","sortOrder":3,"ucscStyleName":"chr3_GL000221v1_random"}
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-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"5","genbankAccession":"GL000208.1","length":92689,"refseqAccession":"NT_113948.1","role":"unlocalized-scaffold","sortOrder":5,"ucscStyleName":"chr5_GL000208v1_random"}
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-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270302.1","length":2274,"refseqAccession":"NT_187396.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270302v1"}
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-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270304.1","length":2165,"refseqAccession":"NT_187397.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270304v1"}
-{"assemblyUnit":"GCF_000001305.16","assignedMoleculeLocationType":"Chromosome","chrName":"Un","genbankAccession":"KI270305.1","length":1472,"refseqAccession":"NT_187399.1","role":"unplaced-scaffold","sortOrder":9999,"ucscStyleName":"chrUn_KI270305v1"}
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