# HG changeset patch
# User dfornika
# Date 1576789574 0
# Node ID 109b9d1e2e991dc4c95c619b2bb00edea59e5978
# Parent  50640b06fca54fd5466c7b6aeb7ea5392d6e3d57
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/pick_plasmids_containing_genes commit 0f3fff91eb329adf437224eb8f7449853083b01e-dirty"

diff -r 50640b06fca5 -r 109b9d1e2e99 pick_plasmids_containing_genes.py
--- a/pick_plasmids_containing_genes.py	Sat Nov 02 01:36:30 2019 -0400
+++ b/pick_plasmids_containing_genes.py	Thu Dec 19 21:06:14 2019 +0000
@@ -3,14 +3,12 @@
 from __future__ import print_function
 
 import argparse
+import csv
 import errno
-import csv
 import os
 import re
 import shutil
-import sys
 
-from pprint import pprint
 
 def parse_screen_file(screen_file):
     screen = []
@@ -20,6 +18,7 @@
             screen.append(row)
     return screen
 
+
 def main(args):
     # create output directory
     try:
@@ -47,7 +46,7 @@
             f.seek(0)
             next(abricate_report_reader)
 
-    # copy the corresponding plasmid fasta files into outdir        
+    # copy the corresponding plasmid fasta files into outdir
     for contig in contigs_with_genes_of_interest:
         for plasmid in args.plasmids:
             copy_plasmid = False
@@ -59,6 +58,7 @@
                 print("\t".join([plasmid, "True"]))
                 shutil.copy2(plasmid, args.outdir)
 
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser()
     parser.add_argument("--plasmids", nargs='+', help="plasmid assemblies (fasta)")
diff -r 50640b06fca5 -r 109b9d1e2e99 pick_plasmids_containing_genes.xml
--- a/pick_plasmids_containing_genes.xml	Sat Nov 02 01:36:30 2019 -0400
+++ b/pick_plasmids_containing_genes.xml	Thu Dec 19 21:06:14 2019 +0000
@@ -1,4 +1,4 @@
-<tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.1.0">
+<tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.2.0">
     <description>Pick plasmids containing specific genes</description>
     <requirements>
     </requirements>
@@ -9,24 +9,79 @@
           '${plasmid}'
         #end for
         --concatenated_abricate_reports '${concatenated_abricate_reports}'
-        --abricate_report_screening_file '${screening_file.fields.path}'
-        --outdir outdir
+        #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table":
+          #set $input_screening_file = str( $screening_file_source.screening_file.fields.path )
+        #else:
+          #set $input_screening_file = str( $screening_file_source.screening_file )
+        #end if
+        --abricate_report_screening_file '${input_screening_file}'
+        --outdir outdir &&
+        cp '${input_screening_file}' '${output_screening_file}'
     ]]></command>
     <inputs>
+        <conditional name="screening_file_source">
+            <param name="screening_file_source_selector" type="select" label="Select a gene screening file from your history or use one from a tool data table?"
+                   help="Screening files must be stored in the 'abricate_report_screening_files' tool data table">
+                <option value="tool_data_table">From tool data table</option>
+                <option value="history">From history</option>
+            </param>
+            <when value="tool_data_table">
+                <param name="screening_file" type="select" format="tabular">
+	            <options from_data_table="abricate_report_screening_files">
+	                <validator type="no_options" message="No abricate report screening files are available" />
+                    </options>
+	        </param>
+            </when>
+            <when value="history">
+                <param name="screening_file" type="data" format="tabular" label="Gene screening file" help="A two-column tab-delimited file with gene names and regular expressions" />
+            </when>
+        </conditional>
         <param name="plasmids" type="data_collection" collection_type="list" format="fasta" />
         <param name="concatenated_abricate_reports" type="data" format="tabular" />
-        <param name="screening_file" type="select" format="tabular">
-	    <options from_data_table="abricate_report_screening_files">
-	        <validator type="no_options" message="No abricate report screening files are available" />
-            </options>
-	</param>
     </inputs>
     <outputs>
         <collection name="output" type="list" label="Output plasmids">
             <discover_datasets pattern="__name__" format="fasta" directory="outdir" />
         </collection>
+        <data name="output_screening_file" format="tabular" />
     </outputs>
     <tests>
+        <test>
+	    <param name="plasmids">
+                <collection type="list">
+                    <element name="SRR9113487_plasmid_1068" value="SRR9113487_plasmid_1068.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_1550" value="SRR9113487_plasmid_1550.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_2719" value="SRR9113487_plasmid_2719.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_739" value="SRR9113487_plasmid_739.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" />
+                </collection>
+            </param>
+            <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/>
+            <param name="screening_file_source.screening_file_source_selector" value="tool_data_table" />
+            <param name="screening_file_source.screening_file" value="screening_file_1"/>
+            <output_collection name="output" type="list">
+                <element file="outdir/SRR9113487_plasmid_2719.fasta" ftype="fasta"/>
+            </output_collection>
+        </test>
+        <test>
+	    <param name="plasmids">
+                <collection type="list">
+                    <element name="SRR9113487_plasmid_1068" value="SRR9113487_plasmid_1068.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_1550" value="SRR9113487_plasmid_1550.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_2719" value="SRR9113487_plasmid_2719.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_739" value="SRR9113487_plasmid_739.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" />
+                    <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" />
+                </collection>
+            </param>
+            <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/>
+            <param name="screening_file_source.screening_file_source_selector" value="history" />
+            <param name="screening_file_source.screening_file" value="abricate_report_screening_file_1.tsv"/>
+            <output_collection name="output" type="list">
+                <element file="outdir/SRR9113487_plasmid_2719.fasta" ftype="fasta"/>
+            </output_collection>
+        </test>
     </tests>
     <help><![CDATA[
     ]]></help>
diff -r 50640b06fca5 -r 109b9d1e2e99 test-data/abricate_report_screening_file_1.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abricate_report_screening_file_1.tsv	Thu Dec 19 21:06:14 2019 +0000
@@ -0,0 +1,4 @@
+gene_name	regex
+KPC	KPC
+NDM	NDM
+OXA-48	OXA\-48
diff -r 50640b06fca5 -r 109b9d1e2e99 test-data/abricate_report_screening_files.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/abricate_report_screening_files.loc	Thu Dec 19 21:06:14 2019 +0000
@@ -0,0 +1,6 @@
+# Tab separated with three columns:
+# - value (Galaxy records this in the Galaxy DB)
+# - name (Galaxy shows this in the UI)
+# - path (folder name containing the Kraken DB)
+#
+screening_file_1	"Carbapenemase Genes"	${__HERE__}/abricate_report_screening_file_1.tsv
diff -r 50640b06fca5 -r 109b9d1e2e99 test-data/outdir-test/SRR9113487_plasmid_2719.fasta
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/outdir-test/SRR9113487_plasmid_2719.fasta	Thu Dec 19 21:06:14 2019 +0000
@@ -0,0 +1,4 @@
+>SRR9113487.fasta|53_length=9674_depth=5.42x
+GTTTACTCATACCTAGATTCTACGTCAGTACTTCAAAAAGCATAATCAAAGCCTTGATAAATATGCATTCCTTCGAAATTCAGCTTTCACCCATTGGGTGAAAGAAAAGTGCTCAACATAAAATACTCGAAGAAGATTTAGGCATAGATGTATATTTCTGTGACCCACATTCACCCTGGCAAAAAGGCACATGCGAAAATATGAATGGTTTAATTAGGCAATATTTACCTAAAGGGATTGATTTAAATCAGGCAGATCAGCATTATTTAAATCAAGTTGCCATGTCACTGAATACTCGTCCTAGAAAGGCGTTAGATTGGCTTACACCATTAGAGAAATTTGCTCAGCTTGTTGATTATCATATGGCTTTTGAAACTGTCGCACCTCATGTTTGAATTCGCCCCATATTTTTGCTACAGTGAACCAAATTAAGATCATCTATTTACTAGGCCTCGCATTTGCGGGGTTTTTAATGCTGAATAAAAGGAAAACTTGATGGAATTGCCCAATATTATGCACCCGGTCGCGAAGCTGAGCACCGCATTAGCCGCTGCATTGATGCTGAGCGGGTGCATGCCCGGTGAAATCCGCCCGACGATTGGCCAGCAAATGGAAACTGGCGACCAACGGTTTGGCGATCTGGTTTTCCGCCAGCTCGCACCGAATGTCTGGCAGCACACTTCCTATCTCGACATGCCGGGTTTCGGGGCAGTCGCTTCCAACGGTTTGATCGTCAGGGATGGCGGCCGCGTGCTGTTGGTCGATACCGCCTGGACCGATGACCAGACCGCCCAGATCCTCAACTGGATCAAGCAGGAGATCAACCTGCCGGTCGCGCTGGCGGTGGTGACTCACGCGCATCAGGACAAGATGGGCGGTATGGACGCGCTGCATGCGGCGGGGATTGCGACTTATGCCAATGCGTTGTCGAACCAGCTTGCCCCGCAAGAGGGGCTGGTTGCGGCGCAACACAGCCTGACTTTCGCCGCCAATGGCTGGGTCGAACCAGCAACCGCGCCCAACTTTGGCCCGCTCAAGGTATTTTACCCCGGCCCCGGCCACACCAGTGACAATATCACCGTTGGGATCGACGGCACCGACATCGCTTTTGGTGGCTGCCTGATCAAGGACAGCAAGGCCAAGTCGCTCGGCAATCTCGGTGATGCCGACACTGAGCACTACGCCGCGTCAGCGCGCGCGTTTGGTGCGGCGTTCCCCAAGGCCAGCATGATCGTGATGAGCCATTCCGCCCCCGATAGCCGCGCCGCAATCACTCATACGGCCCGCATGGCCGACAAGCTGCGCTGAGCCATGGCTGACCACGTCACCCCCAATCTGCCATCGCGCGATTTCGATGTGACAGAGGCGTTTTATGCGAAGCTGGGCTTTGCGACGAGTTGGAAGGATCGCGGCTGGATGATCCTGCAGCGCGGCGGTTTGCAGCTCGAATTCTTCCCCTATCCTGACCTCGACCCAGCTACGAGCTCGTTCGGCTGTTGCCTGCGGTTGGATGATCTCGATGCCATGGTGGCATTGGTGAACGCGGCGGGAGCCGAGGAAAAAAGCACCGGCTGGCCGCGCTTCAAAGCTCCGCAACTGGAGGCGAGCGGCCTGAGGATCGGCTACCTGATCGATCCCGACTGCACGCTGGTGCGGCTGATCCAGAACCCCGACTGACCGCATGCCCGCGAAAATCAAGATTTGCGGGATCAGCACACCCGAGGCGCTCGATGCGACCATCGCGGCGCGGGCGGACTATGCCGGGTTGGTGTTCTATCCAGCGTCGCCCCGTGCGGTTACGTCGAATGTCGCGGGCGCTTTGACATCGCGCGCAGCTGGCCAGATCGCCATGGTCGGTTTGTTCGTCGATGCGGATGATGCTGTCATCGCCGACGCACTGGTGGCAGCCAAGCTGAACGCGCTGCAGCTGCACGGTTCGGAATCGCCCGAACGCGTGGCCCAGTTGCGCGCGCGGTTTGGCAAGCCGGTGTGGAAGGCGCTGCCCGTCGCCAGCGCCAGCGATGTCGCACGCGCCGCAGCCTATGCCGGGGCGGCGGACTTGATCTTGTTCGACGCCAAGACCCCCAAAGGCGCGCTGCCCGGCGGCATGGGGTTGGCGTTCGACTGGTCGCTGCTGGCCGGATATCGCGGTGCCTTGCCGTGGGGGCTGGCAGGCGGGCTAAATCCGACGAATGTTGCCGAGGCGATTGCGCGCACCGGAGCGCCGCTGGTCGATACCTCCAGCGGCGTCGAAAGCGCGCCGGGCGTCAAGGATACCGACAAGATTACCAATTTCGCCTTTGCGGTGCGCTTGGCCTAAATCGCGTCGATCAATAGGCGTCGTTCAGCGCAAAGATCGGCTTGCGGGTGCGCCACTGCCCTCGGGTGAAGTCGGGAAAATCTAACGTGCGATTGCCCTCAGCAATCGATTGTTCCGACAGAGGCGTGATCGCGCTCCAGGCCAGCGCGTCGTAAATGTCGATTGGCATCGGGGCCTTGGCCTTCAGCGCCTCGACAAAAGCGTGGATCACGAACCAGTCCATCCCGCCATGCCCGGCCCCTGCCGCCAGATCGGCGTAGCGTTTCCATAGCGGGTGATCGTATTTCGCAAACCAGCCCTCGGCAGGCTCCCAGCGGTGCGGCTGTGGGCTCTTGCCCTCCAGATAGATCGACTTGTTGACGTCCATCCACAGCCCCTCGGTGCCTTGCACCCGAAAGCCGAGAGAATAGGGGCGCGGCAGCGAGGTGTCGTGGCACAGCATGATCGTTTCACCATTAGTGCAGCCGATCATGGTGTTGACCACATCACCCAGTGCGAATTTCACCTCGGCGTTGGGATGATCGGCAGAGCCGTTCTTGACGACATAATCATGCAGCCCGCGCGCCTTACAGCCGAAGCCGCCAGCGCCCGCTTCGCCCGGCAACGCGACCTTCAGGGTGCGGGTCTGCGGCGGGTAGCACACGCCGGCATCGGCGCAGCCCTGGTACTTCACGGTCAGGGTGGTCGCGCTCGCGCCGGCCGCGGGCGTGCCGGTGAGGGTGCCGAGCAATTCCTTGCGGTAGGTTTCGACGTCGCCGAAGAATTCGTCGCGGTAGGCCTTGCCCTTCGGCAGCGCCATGGTCGCGCCGGTGAAGGCGGCATCGGCCTTGACCGAGGTGCGGTGCCGGTACAGGTAATAGCCGTCGGCGATCCGCCAGCGCACCTCGATGCGGTCCGGCGCGGTGGCCTGCGCGGACAGGACGAAGACCTCGTCGACCGGCGGCAGTTCGAAGTCCTGGGCGACGGCCGAGGTCGCGGGCAGCGCAAGCAGCAGGGCGAGCCCGGCCAGCCAGCGGCGCAGGCGGATCGTGGATGCGGTCATTGGCTCAGTTTACCGGTCGGCTCTCGGCGGCCAGCCATTGCAGGTATTCGGGCAGGCCGGACGCGGCTTCGACCGCGAGCGGGTATAGGAAGTATAAACCACCTTTTTGCTCCTCATCCGAAGTATCTTACCTGAAATTCCCTCACTCGTTTACCGCTCAAGCCCCAATTTTAACTGCCGGTCCAGCCTAAACCGCTCTAATAAGGTTCGATTTGGCGGTAAAATCTCTAGCCTGATAGCTCGAGAGATACAAACTGCCCCACCGCCCCGTTTAAAAGTTGGCAGTGTTGAGCAGTGTTGGATTTGGGGTCGTCAGTCAAAGAGACGACTCTGTGATGGATCGAACAGGCTGGGAGTCAGTGGCGGCGCTCGTTCTGGTGGCAGCTCACGCTGCTTGGCGGCATTCGCCTTGGCTGTTTTCTGTTTCAGATGCTTGAGAATCTGCTCAATGACCTTCGGATCTTCGATGCTGGCAATCACTTTGACGTGACCGCCGCAGTGTTCGCAGACTTCAATATCAATATTGAAGACTCGCTTGAGGCGTTGCATCCAGGTCATGGCGCGGTGGCGCTCTGCAGGACTCTTGTCACGCCAGTTAGTATCGAGACCTTCCGATTTGTCGGGCTTCTTGCCCCGCTTGGCGGGTGTTACTTGAACTCGGTGTTTGCTGTTCGGTGCAAAGACGCCGTGGAAGCGTGTGAGGTTGACTCGCGGCTTAGGTACCAACGCAGCGAGTTTGGCGATGAAGTCCAGCGGCTCGAAGATCACATGGGTGGTGCCATTGCGGTACGGAGTTTTGAGCTCGTAACGCACCTGCCCATTGGCGGTTAATGCCAGACGTTTTTCTGAAACCGCTGGCCGACTAATGTAGCGACACAAGCGCTCAAGCTTATCCCGCTGATGCGCTTCGGCCATCACACCGGCGTGTAGCGAGAAACCAGCATGGTTGGCTACTCGACTGCTTGAGTCGGCTTTATCCTCACGCCCTGGCAAGGTTTGCAGGGTGAAGACTTTGCGCCCTTGCTGGGGGCCGACGGCAATGCGATACGTAACCGAAGCACCATGTAATTGAGTCAGCGTATCGTCTTCGCCCTCTTCCAGTGTCAACCACGTATTCTCGGCATCACGCTCCAAAATCCCACGCTTTTCCATGCAGCGAGCGATGCGATGGCTGAGGGTGTGAGCGAGCGTATTCAGCTCATCGTAAGTGGGTGCCTTGACACGATGGAAGCGTTGCTTGCCATAGTCATCTTCGGCATAGACACCATCGAGAAACAGCATGTGGTAGTGGACATTGAGATTTAGCGCGGAGCCAAAGCGTTGGATAAGAGTCACTGAGCCAGTTTGTGCAGAGGCTTTGGTGTAACCGGCTTTTTTGATCAGATGAGTTGAGAGTGTACGATAGACGATACTCAAGACCTGGCCCATCAGCTGGGGATGGCGAGCCAGCAAAAAGCGTAGCTGGAAAGGAAAGCTGAGCACCCACTGGCGAATGGGCTCCTTGGGGAAGACTTCGTCTATCAGCAGCGCCGCACTCTCGGCCATCCGGCGGGCACCGCAGCTAGGGCAAAAGCCGCGTCGTTTACAGCTGAAGGCGACCAGACGCTCGTGATGACAATCCTCGCAGCGAACCCGCATGAAACCATACTCCAGACGGCCACATTGGAGGAGGTCGTTGAATTCTTGTTGGATGTAGCGAGGCAGGTGTTGACCTTGGGCTTCGAGTGAGGCTTTGAAGGCTGGGTAGTGCTGCTCAACCAGCTGGTAGAGCAGCGTCTGGTCGGGTTGGTGGCGTTCGTAACCGTTTGTTTGAGTGGGCGATTGACTCGCCGTGGCGTTCCTTGCCAGCGACATGGGTATCCTCCGCTGATACTGTGGTTATGTACAGTATCAGCGGCTTGCGTTCAGACGTCCAGTCTGGCCCTAGACATCGCTAAATGCTTAACCCGCAATAGCCCTCACGAGTTGTTATCAGCCACTACCGGTTGAGCGAGAAGGTTTTGGGTTCAGGGTGCTATTGCTCCACCAATCACAATACTGAAGCCCCAACTGTTATCAGTTGGGGCTTTTTCTTGTCTGTTTGCGGCGGTTGCGTTTTATCGGTAGTCGTCGAGCTCTGCACCATCCCACATAAGAGCTTAACGGTGCGATCTTCAACGCCATCACACAAAACTTTCTTTTTCACGCACAGTCAACTTATTGGATGTTTTATTAACAACCCAAAAGGAGATATTTAGCGGGCGGCCGGAAGGTGAATGCTAGGCATGATCTAACCCTCGGTCTCTGGCGTCGCGACTGCGAAATTTCGCGAGGGTTTCCGAGAAGGTGATTGCGCTTCGCAGATCTCCAGGCGCGTGGGTGCGGACGTAGTCAGCGCCATTGCCGATCGCGTGAAGTTCCGCCGCAAGGCTCGCTGGACCCAGATCCTTTACAGGAAGGCCAACGGTGGCGCCCAAGAAGGATTTCCGCGACACCGAGACCAATAGCGGAAGCCCCAACGCCGACTTCAGCTTTTGAAGGTTCGACAGCACGTGCAGCGATGTTTCCGGTGCGGGGCTCAAGAAAAATCCCATCCCCGGATCGAGGATGAGCCGGTCGGCAGCGACCCCGCTCCGTCGCAAGGCGGAAACCCGCGCCTCGAAGAACCGCACAATCTCGTCGAGCGCGTCTTCGGGTCGAAGGTGACCGGTGCGGGTGGCGATGCCATCCCGCTGCGCTGAGTGCATAACCACCAGCCTGCAGTCCGCCTCAGCAATATCGGGATAGAGCGCAGGGTCAGGAAATCCTTGGATATCGTTCAGGTAGCCCACGCCGCGCTTGAGCGCATAGCGCTGGGTTTCCGGTTGGAAGCTGTCGATTGAAACACGGTGCATCTGATCGGACAGGGCGTCTAAGAGCGGCGCAATACGTCTGATCTCATCGGCCGGCGATACAGGCCTCGCGTCCGGATGGCTGGCGGCCGGTCCGACATCCACGACGTCTGATCCGACTCGCAGCATTTCGATCGCCGCGGTGACAGCGCCGGCGGGGTCTAGCCGCCGGCTCTCATCGAAGAAGGAGTCCTCGGTGAGATTCAGAATGCCGAACACCGTCACCATGGCGTCGGCCTCCGCAGCGACTTCCACGATGGGGATCGGGCGAGCAAAAAGGCAGCAATTATGAGCCCCATACCTACAAAGCCCCACGCATCAAGCTTTTGCCCATGAAGCAACCAGGCAATGGCTGTAATTATGACGACGCCGAGTCCCGACCAGACTGCATAAGCAACACCGACAGGGATGGATTTCAGAACCAGAGAAAGAAAATAAAATGCGATGCCATAACCGATTATGACAACGGCGGAAGGGGCAAGCTTAGTAAAGCCCTCGCTAGATTTTAATGCGGATGTTGCGATTACTTCGCCAACTATTGCGATAACAAGAAAAAGCCAGCCTTTCATGATATATCTCCCAATTTGTGTAGGGCTTATTATGCACGCTTAAAAATAATAAAAGCAGACTTGACCTGATAGTTTGGCTGTGAGCAATTATGTGCTTAGTGCATCTAACGCCGGAGTTAAGCCGCCGCGCGTAGCGCGGTCGGCTTGAACGAATTGTTAGACATCATTTACCAACTGACTTGATGATCTCGCCTTTCACAAAGCGAATAAATTCTTCCAAGTGATCTGCGCGTGAGGCCAAGTGATCTTCTTTTTGTCCCAGATAAGCTTGCTTAGCTTCAAGTAAGACGGGCTGATACTGGGCAGGTAGGCGTTTTATTGCCCAGTCGGCAGCGACATCCTTCGGCGCGATTTTGCCGGTTATTGCGCTGTACCAAATGCGGGACAACGTAAGCACTACATTTCGCTCATCGCCGGCCCAGTCGGGCTGCGAGTTCCATAGCTTCAAGGTTTCCCTCAGCGCCTCGAATAGATCCTGTTCAGGAACCGGGTCAAAGAATTCCTCCGCTGCCGGACCTACCAAGGCAACGCTATGTTCTCTTGCTTTTGTAAGCAGGATAGCTAGATCAATGTCGATCATGGCTGGCTCGAAGATACCCGCAAGAATGTCATTGCGCTGCCATTCTCCAAATTGCAGCTCGCGCTTAGCCGGATAACGCCACGGGATGATGTCGTCATGCACGACAAGGGTGACTTCTATAGCGCGGAGCGTCTCGCTCTCGCCAGGGAAAGCCGAAGCCTCCATAAGATCATTGAGCAATGCTCGCCGCGTCGTTTCATCAAGCTTTACGGCCACAGTAACCAACAAATCAATATCGCTGTATGGCTTCAGGCCGCCATCCACTGCGGAGCCGTACAAATGCACGGCCAGCAACGTTGATTCCAGATGGCGCTCAATGACGCTTAGCACCTCTGATAGTTGGTTCGAAATTTCGATGGTCACCGCTTCCCTCATGATGTCTAACGGGCGAGGTAAGCCGACCGCAGAATGCGGGTCGGCTTGACCGAAATGTTAGAACCAGAAGCCAAAACGGATAACTTGAATTTGGCGACGGGCGCTAACCGTGAAAAAACGCTGCGCCACCGAGGCGGCACAGCACTGCAAAAACGATAGCTGCTTGCGCTTGCTACGCAAGGGCTAGAGGCCAAAAAGACTGAAAACCTGCGCAGCCCATGCAGGCGAAGCCCGGAAAAAAGGCAAAACAGGCACTGAATAACGCCTGAAAAGCTAAATGCCGTTTGAATAAACATGAGCTAAATAAAGCTGGGTTTAAGTGGTGCTAACGTTGGACGTAACGAGAGCCGGAGCGCAGCGGAGGGAACCAAAATGCGCAGCATTTTGGCGTCCCGTTGACGGAATGGTTAGCCGTTTCGACGCGCATAAACGGAGTGGGTGTACGGAATTACAGCTTGAATGGTTTCGGTTGAGACAAGCTCGAATTCTGTTTCGTTGAGCATTGGGAAGAAGGCGTCACCCTCGAAGGTTTGATGTACCTCAGATAGAAACACGCCGTGGGCGTGAGGTAGTGCCAGAGTGTATATCTCAGCTCCGCCCGCGACGTAGAGTTCATTGCCGAGTTCGGATGCCAAAGCGATAGCGTGCGACAGCGTTGAAACAACTACGCAGCCAGTGGCGCGGTAGTTAGCTTGGCGTGAGATTACCAATGTGTGACGGTTCGGTAGAGGCTTGCCGATAGACTCAAAGGTCTTTCGCCCCATGACAACGACTTTTCCCTCAGTGAGTCTGCGAAAAATCTTCTGCTCACCCGGAATTTTCCAGGGGATATTAGGACCATTGCCAATAACCCGATTGGCTCCCATCGCAGCAACGAGATAAATGCGTACTGATTCCGAGTTCATATGGCTAACTTTGTTTTAGGGCGACTGCCCTGCTGCGTAACATCGTTGCTGCTCCATAACATCAAACATCGACCCACGGCGTAACGCGCTTGCTGCTTGGATGCCCGAGGCATAGACTGTACAAAAAAACAGTCATAACAAGCCATGAAAACCGCCACTGCGCCGTTACCACCGCTGCGTTCGGTCAAGGTTCTGGACCAGTTGCGTGAGCGCATACGCTACTTGCATTACAGCTTACCAACCGAACAGGCTTATGTCCACTGGGTTCGTGCCTTCATCCGTTTCCACGGTGTGCGTCACCCGGCAACCTTGGGCAGCAGCGAAGTCGAGGCATTTCTGTCCTGGCTGGCGAACGAGCGCAAGGTTTCGGTCTCCACGCATCGTCAGGCATTGGCGGCCTTGCTGTTCTTCTACGGCAAGGTGCTGTGCACGGATCTGCCCTGGCTTCAGGAGATCGGAAGACCTCGGCCGTCGCGGCGCTTGCCGGTGGTGCTGACCCCGGATGAAGTGGTTCGCATCCTCGGTTTTCTGGAAGGCGAGCATCGTTTGTTCGCCCAGCTTCTGTATGGAACGGGCATGCGGATCAGTGAGGGTTTGCAACTGCGGGTCAAGGATCTGGATTTCGATCACGGCACGATCATCGTGCGGGAGGGCAAGGGCTCCAAGGATCGGGCCTTGATGTTACCCGAGAGCTTGGCACCCAGCCTGCGCGAGCAGCTGTCGCGTGCACGGGCATGGTGGCTGAAGGACCAGGCCGAGGGCCGCAGCGGCGTTGCGCTTCCCGACGCCCTTGAGCGGAAGTATCCGCGCGCCGGGCATTCCTGGCCGTGGTTCTGGGTTTTTGCGCAGCACACGCATTCGACCGATCCACGGAGCGGTGTCGTGCGTCGCCATCACATGTATGACCAGACCTTTCAGCGCGCCTTCAAACGTGCCGTAGAACAAGCAGGCATCACGAAGCCCGCCACACCGCACACCCTCCGCCACTCGTTCGCGACGGCCTTGCTCCGCAG
+>SRR9113487.fasta|93_length=1443_depth=2.74x
+TGTACTGACCCCAAAAAGTTGGACAGTTAAACACGAGGCATATAGGTCTGATTCCGATATTCAATTGGAGTCAGACCTTTTAATTTCAGGCTAATTCTTCTGCTGTTGTAGTATTCAATATATTCCGTAACAGCATCCTTCAGTTCGCTTATATTACTGAACTCATCAAGATAAAAACACTCCGACTTTAAGGTTCCAAAGAAACACTCCACCACAGCATTATCCAGACAATTGCCTTTTCTGGACATGCTTTGTTTAATACCATGTTCTTTAAGGATATTTTGATATCTTCTCATACGATACTGCCATCCCTGGTCAGAGTGCAGAACAGGATGCTCGTGAGGATTAAGCTTTTTGAATGCCTGATCGAGCATATTCTCAACCATGTTCATCACTGGTCTTTCCGAAAGGCTGTAAGAAATAACTTCGTTGTTGAAGAGATCTATTACTGGAGACAAATACAGCTTGCGCCCATTGACTGCAAATTCAGTAACATCGGTAACCCACTTCTCGTTTGGCCGCGTAGCCTTGAAATCTCTTTGGAGAACATTAGGGGCGGTTTGCCCTACCTCTCCTCTGTAAGAGCGGTATCGCTTGACCTTAATCGCTGCTTTAAGTGAGAGGGTTCCCATCAGGCGCTGAACAGCTTTATGGTTAATCTGTTTCCCTTCTCGATGAAGAGACAGCGTTACCCTACGGTATCCGTATCGGCCTCTATTCTCGTGATAAATCTCACTAATACGCTTTTTAACGTCCGCATACTTGTCAGGCTTGCTGAGAGCCTTTAGATGATAATAAAACGTACTGCGCGGTATCTCCGCAGCCCTGAGAAGCTCATCAAGAGGATAAAACTGCCTTAGCTCGTTGAGTACTTTCACTTTTTCGTGGGATGAGCTAAGGCTTTCAGCTTTTTTAGATACATAAGCCGCGTTTCAAGAAATCGAACTTGCCTTTCAAGATCCTCAATGCGTCGGTCTTTTGACAGCTCCAATGCTGATGCCGCTTTTTCTGGATCAACTGATATTGCAATGTTTCTTTTGGTGCCAATCTTGAGCGCGCGTAAACCAGCTTCTCCGCGCTCTTCATAGACCTTCAGCCACCTGGCTACAGAACCACTACCAGCAAGCATAAAGTGAGCAGCAGCCTGATTAAGGGACATGTGCTGCTCGATCACAGCTTTCACGACCTTAATACGCAACTCTGGATCAGCACTAACGCCTTTAGGTTTGGGAATTAAACCTTTTTCTCCATGTTTTTCATAGAGGGCAACCCATGTCCTGACCTGGGTTCGGGGGACACCAAAACGTGCCGAGATGATCCTGTAACCATCATCAGTTGTGAAGTAGTGATTCACGACTTCAAGGCGCTTTTCAAAAGGGTATTTTGGCTTTGACATATTAGGGGCTATTCCATTTCATCGTCCAACAAAATGGGTGCAGTACA
diff -r 50640b06fca5 -r 109b9d1e2e99 test-data/screening_file.tsv
--- a/test-data/screening_file.tsv	Sat Nov 02 01:36:30 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-gene_name	regex
-KPC	KPC
-NDM	NDM
-OXA-48	OXA\-48
diff -r 50640b06fca5 -r 109b9d1e2e99 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Thu Dec 19 21:06:14 2019 +0000
@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<tables>
+    <!-- Locations of abricate report screening files in the required format -->
+    <table name="abricate_report_screening_files" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/abricate_report_screening_files.loc" />
+    </table>
+</tables>