diff data_manager/vsnp_excel_filter_fetcher.xml @ 0:58cd557a53a0 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/vsnp_excel_filter_fetcher.xml	Tue Mar 10 07:37:23 2020 -0400
@@ -0,0 +1,101 @@
+<?xml version="1.0"?>
+<tool id="vsnp_excel_filter_fetcher" name="vSNP Excel Filter data manager" tool_type="manage_data" profile="18.09" version="0.0.8">
+    <description>Download vSNP Excel files</description>
+    <requirements>
+        <requirement type="package" version="3.7">python</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+    python '$__tool_directory__/vsnp_excel_filter_fetcher.py'
+    --dbkey '${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 Excel Filter file associated with the selected FASTA reference" optional="False" />
+    </inputs>
+    <outputs>
+        <data name="out_file" format="data_manager_json" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool fetches a vSNP Excel Filter file associated with each supported genome reference to populate the vsnp_excel_filter 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 Excel Filter files are available in GitHub at https://github.com/USDA-VS/vSNP_reference_options.  Note that the file names
+are a bit confusing.  This tool must be used for Excel files with the pattern "remove_from_analysis" in the name.
+
+ * **Mycobacterium bovis AF2122/97**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_AF2122/Mbovis_remove_from_analysis.xlsx
+
+ * **Brucella abortus bv. 1 str. 9-941**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus1/Bab1_remove_from_analysis.xlsx
+
+ * **Brucella abortus strain BER**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_abortus3/Bab3_remove_from_analysis.xlsx
+
+ * **Brucella canis ATCC 23365**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_canis/Bcanis_remove_from_analysis.xlsx
+
+ * **Brucella ceti TE10759-12**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ceti2/Bceti2_remove_from_analysis.xlsx
+
+ * **Brucella melitensis bv. 1 str. 16M**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1/Bmelbv1_remove_from_analysis.xlsx
+
+ * **Brucella melitensis bv. 3 str. Ether**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv3/Bmelbv3_remove_from_analysis.xlsx
+
+ * **Brucella melitensis BwIM_SOM_36b**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv1b/Bmelbv1b_remove_from_analysis.xlsx
+
+ * **Brucella melitensis ATCC 23457**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_melitensis-bv2/Bmelbv2_remove_from_analysis.xlsx
+
+ * **Brucella ovis ATCC 25840**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_ovis/B_ovis_remove_from_analysis.xlsx
+
+ * **Brucella suis 1330**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis1/Bsuis1_remove_from_analysis.xlsx
+
+ * **Mycobacterium tuberculosis H37Rv**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Mycobacterium_H37/H37_remove_from_analysis.xlsx
+
+ * **Mycobacterium avium subsp. paratuberculosis strain Telford**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-CP033688/CP033688_remove_from_analysis.xlsx
+
+ * **Mycobacterium avium subsp. paratuberculosis K-10**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/para-NC002944/NC_002944_remove_from_analysis.xlsx
+
+ * **Brucella suis ATCC 23445**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis2/Bsuis2_remove_from_analysis.xlsx
+
+ * **Brucella suis bv. 3 str. 686**
+
+   * **Excel file**    https://github.com/USDA-VS/vSNP_reference_options/raw/master/Brucella_suis3/Bsuis3_remove_from_analysis.xlsx
+
+    ]]></help>
+    <citations>
+    </citations>
+</tool>