# HG changeset patch
# User thanhlv
# Date 1589993503 14400
# Node ID f9d845c8d9250903cbb52473d3c66c878dbb5d1a

"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/scagaire commit d581c0ded2cfa7dde2d501c5368b055bd7333eb1"

diff -r 000000000000 -r f9d845c8d925 scagaire.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scagaire.xml	Wed May 20 12:51:43 2020 -0400
@@ -0,0 +1,65 @@
+<tool id="scagaire" name="scagaire" version="@VERSION@">
+    <description>Filter AMR results by species</description>
+    <macros>
+        <token name="@VERSION@">0.0.4</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">scagaire</requirement>
+    </requirements>
+    <version_command>scagaire --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        #import re
+        #set $clean_species = re.sub("_"," ",$scagaire_species.fields.name)
+        scagaire
+        -n $db_name
+        #if str($amr_type) != "auto"
+            -t $amr_type
+        #end if
+        '$clean_species'
+        -m $minimum_occurances
+        $debug
+        $verbose
+        $amr > $output
+    ]]>    </command>
+
+    <inputs>
+        <param name="amr" type="data" format="tabular,text" label="Select AMR result"/>
+        <param name="amr_type" type="select" optional="false" label="Source of AMR results">
+            <option value="auto">auto</option>
+            <option value="abricate">abricate</option>
+            <option value="rgi">rgi</option>
+            <option value="staramr">staramr</option>
+        </param>
+        <param name="db_name" type="select" optional="false" label="Database">
+            <option value="argannot">argannot</option>
+            <option value="card">card</option>
+            <option value="ncbi">ncbi</option>
+            <option value="plasmidfinder">plasmidfinder</option>
+            <option value="resfinder" selected="True">resfinder</option>
+            <option value="vfdb">vfdb</option>
+        </param>
+        <!-- DATABASE INPUT-->
+        <param label="Select a species" name="scagaire_species" type="select">
+            <options from_data_table="scagaire_species">
+                <validator message="No species is available" type="no_options" />
+            </options>
+        </param>
+        <param name="minimum_occurances" type="integer" min="0" value="0" label="Minimum number of occurances of a gene in the database"/>
+        <param name="debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Turn on debugging" />
+        <param name="verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="false" label="Turn on verbose output" />
+    </inputs>
+
+    <outputs>
+        <data name="output" format="tabular" label="${tool.name} on ${on_string} Output"/>
+        <data name="summary" format="tabular" label="${tool.name} on ${on_string} Summary" from_work_dir="gene_summary.tsv"/>
+        <data name="log" format="text" label="${tool.name} on ${on_string} Log">
+            <filter>debug is True</filter>
+        </data>
+    </outputs>
+
+    <help><![CDATA[
+
+    Documentation can be found at `<https://github.com/quadram-institute-bioscience/scagaire>`_.
+
+    ]]>    </help>
+</tool>
diff -r 000000000000 -r f9d845c8d925 tool-data/scagaire.loc
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/scagaire.loc	Wed May 20 12:51:43 2020 -0400
@@ -0,0 +1,44 @@
+# This file defines databases and their folder location. Each database is a line with 
+# two columns: value{tab}{name}
+Acinetobacter_baumannii	Acinetobacter_baumannii
+Bacillus_anthracis	Bacillus_anthracis
+Campylobacter_jejuni	Campylobacter_jejuni
+Chlamydia_trachomatis	Chlamydia_trachomatis
+Citrobacter_freundii	Citrobacter_freundii
+Citrobacter_koseri	Citrobacter_koseri
+Clostridioides_difficile	Clostridioides_difficile
+Clostridium_botulinum	Clostridium_botulinum
+Enterobacter_cloacae	Enterobacter_cloacae
+Enterococcus_faecalis	Enterococcus_faecalis
+Enterococcus_faecium	Enterococcus_faecium
+Escherichia_coli	Escherichia_coli
+Francisella_tularensis	Francisella_tularensis
+Haemophilus_influenzae	Haemophilus_influenzae
+Klebsiella_aerogenes	Klebsiella_aerogenes
+Klebsiella_oxytoca	Klebsiella_oxytoca
+Klebsiella_pneumoniae	Klebsiella_pneumoniae
+Legionella_pneumophila	Legionella_pneumophila
+Listeria_monocytogenes	Listeria_monocytogenes
+Moraxella_catarrhalis	Moraxella_catarrhalis
+Morganella_morganii	Morganella_morganii
+Mycoplasma_pneumoniae	Mycoplasma_pneumoniae
+Proteus_mirabilis	Proteus_mirabilis
+Pseudomonas_aeruginosa	Pseudomonas_aeruginosa
+Raoultella_ornithinolytica	Raoultella_ornithinolytica
+Salmonella_enterica	Salmonella_enterica
+Serratia_liquefaciens	Serratia_liquefaciens
+Serratia_marcescens	Serratia_marcescens
+Shigella_dysenteriae	Shigella_dysenteriae
+Shigella_flexneri	Shigella_flexneri
+Shigella_sonnei	Shigella_sonnei
+Staphylococcus_aureus	Staphylococcus_aureus
+Stenotrophomonas_maltophilia	Stenotrophomonas_maltophilia
+Streptococcus_agalactiae	Streptococcus_agalactiae
+Streptococcus_pneumoniae	Streptococcus_pneumoniae
+Streptococcus_pyogenes	Streptococcus_pyogenes
+Vibrio_cholerae	Vibrio_cholerae
+Vibrio_parahaemolyticus	Vibrio_parahaemolyticus
+Yersinia_enterocolitica	Yersinia_enterocolitica
+Yersinia_pestis	Yersinia_pestis
+gut	gut
+skin	skin
\ No newline at end of file
diff -r 000000000000 -r f9d845c8d925 tool-data/scagaire.loc.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/scagaire.loc.sample	Wed May 20 12:51:43 2020 -0400
@@ -0,0 +1,44 @@
+# This file defines databases and their folder location. Each database is a line with 
+# two columns: value{tab}{name}
+Acinetobacter_baumannii	Acinetobacter_baumannii
+Bacillus_anthracis	Bacillus_anthracis
+Campylobacter_jejuni	Campylobacter_jejuni
+Chlamydia_trachomatis	Chlamydia_trachomatis
+Citrobacter_freundii	Citrobacter_freundii
+Citrobacter_koseri	Citrobacter_koseri
+Clostridioides_difficile	Clostridioides_difficile
+Clostridium_botulinum	Clostridium_botulinum
+Enterobacter_cloacae	Enterobacter_cloacae
+Enterococcus_faecalis	Enterococcus_faecalis
+Enterococcus_faecium	Enterococcus_faecium
+Escherichia_coli	Escherichia_coli
+Francisella_tularensis	Francisella_tularensis
+Haemophilus_influenzae	Haemophilus_influenzae
+Klebsiella_aerogenes	Klebsiella_aerogenes
+Klebsiella_oxytoca	Klebsiella_oxytoca
+Klebsiella_pneumoniae	Klebsiella_pneumoniae
+Legionella_pneumophila	Legionella_pneumophila
+Listeria_monocytogenes	Listeria_monocytogenes
+Moraxella_catarrhalis	Moraxella_catarrhalis
+Morganella_morganii	Morganella_morganii
+Mycoplasma_pneumoniae	Mycoplasma_pneumoniae
+Proteus_mirabilis	Proteus_mirabilis
+Pseudomonas_aeruginosa	Pseudomonas_aeruginosa
+Raoultella_ornithinolytica	Raoultella_ornithinolytica
+Salmonella_enterica	Salmonella_enterica
+Serratia_liquefaciens	Serratia_liquefaciens
+Serratia_marcescens	Serratia_marcescens
+Shigella_dysenteriae	Shigella_dysenteriae
+Shigella_flexneri	Shigella_flexneri
+Shigella_sonnei	Shigella_sonnei
+Staphylococcus_aureus	Staphylococcus_aureus
+Stenotrophomonas_maltophilia	Stenotrophomonas_maltophilia
+Streptococcus_agalactiae	Streptococcus_agalactiae
+Streptococcus_pneumoniae	Streptococcus_pneumoniae
+Streptococcus_pyogenes	Streptococcus_pyogenes
+Vibrio_cholerae	Vibrio_cholerae
+Vibrio_parahaemolyticus	Vibrio_parahaemolyticus
+Yersinia_enterocolitica	Yersinia_enterocolitica
+Yersinia_pestis	Yersinia_pestis
+gut	gut
+skin	skin
\ No newline at end of file
diff -r 000000000000 -r f9d845c8d925 tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample	Wed May 20 12:51:43 2020 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of ariba database in the required format -->
+    <table name="scagaire_species" comment_char="#" allow_duplicate_entries="False">
+        <columns>value, name</columns>
+        <file path="tool-data/scagaire.loc" />
+    </table>
+</tables>
\ No newline at end of file
diff -r 000000000000 -r f9d845c8d925 tool_data_table_conf.xml.test
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test	Wed May 20 12:51:43 2020 -0400
@@ -0,0 +1,7 @@
+<tables>
+    <!-- Locations of ariba database in the required format -->
+    <table name="scagaire_species" comment_char="#">
+        <columns>value, name, path</columns>
+        <file path="${__HERE__}/test-data/scagaire.loc" />
+    </table>
+</tables>
\ No newline at end of file