diff data_manager/vsnp_genbank_fetcher.xml @ 0:efed56c325da draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_vsnp_genbank commit 31f4453e44da62788efd01736ed57ad483383b09"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/vsnp_genbank_fetcher.xml	Sat May 09 17:27:45 2020 -0400
@@ -0,0 +1,103 @@
+<?xml version="1.0"?>
+<tool id="vsnp_genbank_fetcher" name="vSNP Genbank data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
+    <description>Download vSNP Genbank files</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    python '$__tool_directory__/vsnp_genbank_fetcher.py'
+    --dbkey '${all_fasta_source.fields.dbkey}'
+    --name '${all_fasta_source.fields.name}'
+    --out_file '$out_file'
+    --url '$url'
+    ]]>
+    </command>
+    <inputs>
+        <param name="all_fasta_source" type="select" label="FASTA reference">
+            <options from_data_table="all_fasta"/>
+        </param>
+        <param name="url" type="text" value="" label="URL to download the Genbank file associated with the selected FASTA reference" optional="False" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="all_fasta_source" value="AF2122"/>
+            <param name="url" value="https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk"/>
+            <output name="out_file" value="vsnp_genbank.json" compare="contains"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool fetches a vSNP Genbank file associated with each supported genome reference to populate the vsnp_genbank data table.  The dbkey and name fields
+in the vsnp data table are inherited from the *all_fasta* data table, so no user entry is necessary.  These public vSNP Genbank files are available in GitHub
+at https://github.com/USDA-VS/vSNP_reference_options.
+
+ * **Mycobacterium bovis AF2122/97**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/NC_002945v4.gbk
+
+ * **Brucella abortus bv. 1 str. 9-941**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/NC_006932-NC_006933.gbk
+
+ * **Brucella abortus strain BER**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/NZ_CP007682-NZ_CP007683.gbk
+
+ * **Brucella canis ATCC 23365**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/NC_010103-NC_010104.gbk
+
+ * **Brucella ceti TE10759-12**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/NC_022905-NC_022906.gbk
+
+ * **Brucella melitensis bv. 1 str. 16M**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/NC_003317-NC_003318.gbk
+
+ * **Brucella melitensis bv. 3 str. Ether**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/NZ_CP007760-NZ_CP007761.gbk
+
+ * **Brucella melitensis BwIM_SOM_36b**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/NZ_CP018508-NZ_CP018509.gbk
+
+ * **Brucella melitensis ATCC 23457**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/NC_012441-NC_012442.gbk
+
+ * **Brucella ovis ATCC 25840**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/NC_009505-NC_009504.gbk
+
+ * **Brucella suis 1330**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/NC_017251-NC_017250.gbk
+
+ * **Mycobacterium tuberculosis H37Rv**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/NC_000962.gbk
+
+ * **Mycobacterium avium subsp. paratuberculosis strain Telford**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688.gbk
+
+ * **Mycobacterium avium subsp. paratuberculosis K-10**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944.gbk
+
+ * **Brucella suis ATCC 23445**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/NC_010169-NC_010167.gbk
+
+ * **Brucella suis bv. 3 str. 686**
+
+   * **Genbank file**  https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/NZ_CP007719-NZ_CP007718.gbk
+
+    ]]></help>
+    <citations>
+    </citations>
+</tool>