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changeset 4:78c75f134c16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 1127a471ad5d1a75c311fa3be581476f5d8f9339
author iuc
date Mon, 19 Mar 2018 10:42:19 -0400
parents 6e9aea89e388
children f9bf6a8d8547
files abricate.xml abricate_list.xml macros.xml test-data/output_gbk.txt test-data/output_list.txt test-data/output_mrsa.txt test-data/output_noheader.txt test-data/output_noresults.txt
diffstat 8 files changed, 80 insertions(+), 65 deletions(-) [+]
line wrap: on
line diff
--- a/abricate.xml	Mon Sep 04 02:47:12 2017 -0400
+++ b/abricate.xml	Mon Mar 19 10:42:19 2018 -0400
@@ -1,9 +1,12 @@
-<tool id="abricate" name="ABRicate" version="0.7">
-    <requirements>
-        <requirement type="package" version="0.7">abricate</requirement>
-    </requirements>
-
-    <version_command>abricate --version</version_command>
+<tool id="abricate" name="ABRicate" version="@VERSION@">
+    <description>
+        Mass screening of contigs for antimicrobial and virulence genes
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
 
     <command detect_errors="exit_code"><![CDATA[
         abricate '$file_input'
@@ -19,12 +22,13 @@
         <param name="file_input" type="data" format="fasta,genbank,embl" label="Input file (Fasta, Genbank or EMBL file)" help="To screen for antibiotic resistant genes, can be a fasta file, a genbank file or an EMBL file." />
         <section name="adv" title="Advanced options" expanded="False">
             <param argument="--db" type="select" label="Database to use - default is 'resfinder'" help="Option to switch to other AMR/other database">
-                <option value="argannot">argannot</option>
-                <option value="card">card</option>
-                <option value="ncbibetalactamase">ncbi betalactamase</option>
-                <option value="resfinder" selected="true">resfinder</option>
-                <option value="plasmidfinder">plasmidfinder</option>
-                <option value="vfdb">vfdb</option>
+                <option value="argannot">ARG-ANNOT</option>
+                <option value="card">CARD</option>
+                <option value="ecoh">EcOH</option>
+                <option value="ncbi">NCBI Bacterial Antimicrobial Resistance Reference Gene Database</option>
+                <option value="resfinder" selected="true">Resfinder</option>
+                <option value="plasmidfinder">PlasmidFinder</option>
+                <option value="vfdb">VFDB</option>
             </param>
             <param name="no_header" argument="--noheader" type="boolean" truevalue="--noheader" falsevalue="" label="Suppress header" help="Suppress output file's column headings" />
             <param name="min_dna_id" argument="--minid" type="float" value="75" min="0" max="100" optional="true" label="Minimum DNA identity" />
@@ -126,14 +130,5 @@
         6159.fna  NC_017339.1  10150   10995   blaZ_32  1-846/846    ===============  0/0   100.00     100.000    resfinder  AP004832
     ]]></help>
 
-    <citations>
-        <citation type="bibtex">
-@UNPUBLISHED{Seemann2016,
-    author = {Seemann, Torsten},
-    title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
-    year = {2016},
-    url = {https://github.com/tseemann/abricate},
-}
-        </citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>
--- a/abricate_list.xml	Mon Sep 04 02:47:12 2017 -0400
+++ b/abricate_list.xml	Mon Mar 19 10:42:19 2018 -0400
@@ -1,9 +1,12 @@
-<tool id="abricate_list" name="ABRicate List" version="0.7">
-    <requirements>
-        <requirement type="package" version="0.7">abricate</requirement>
-    </requirements>
-
-    <version_command>abricate --version</version_command>
+<tool id="abricate_list" name="ABRicate List" version="@VERSION@">
+    <description>
+        List all of abricate's available databases.
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
 
     <command detect_errors="exit_code"><![CDATA[
         abricate --list > '$report'
@@ -28,14 +31,5 @@
 ABRicate List will list all the antibiotic databases used by ABRicate. The database of these genes is built from ResFinder.
     ]]></help>
 
-    <citations>
-        <citation type="bibtex">
-@UNPUBLISHED{Seemann2016,
-    author = {Seemann, Torsten},
-    title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
-    year = {2016},
-    url = {https://github.com/tseemann/abricate},
-}
-        </citation>
-    </citations>
+    <expand macro="citations"/>
 </tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Mar 19 10:42:19 2018 -0400
@@ -0,0 +1,27 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@VERSION@">abricate</requirement>
+            <yield />
+        </requirements>
+    </xml>
+
+    <xml name="version_command">
+        <version_command><![CDATA[abricate --version]]></version_command>
+    </xml>
+
+    <token name="@VERSION@">0.8</token>
+
+    <xml name="citations">
+      <citations>
+          <citation type="bibtex">
+  @UNPUBLISHED{Seemann2016,
+      author = {Seemann, Torsten},
+      title = {ABRicate: mass screening of contigs for antiobiotic resistance genes},
+      year = {2016},
+      url = {https://github.com/tseemann/abricate},
+  }
+          </citation>
+      </citations>
+    </xml>
+</macros>
--- a/test-data/output_gbk.txt	Mon Sep 04 02:47:12 2017 -0400
+++ b/test-data/output_gbk.txt	Mon Mar 19 10:42:19 2018 -0400
@@ -1,2 +1,1 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
-STANORAX	246	1412	norA_1	1-1167/1167	===============	0/0	100.00	100.00	resfinder	M97169
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT
--- a/test-data/output_list.txt	Mon Sep 04 02:47:12 2017 -0400
+++ b/test-data/output_list.txt	Mon Mar 19 10:42:19 2018 -0400
@@ -1,8 +1,8 @@
 DATABASE	SEQUENCES	DATE
-argannot	1749	
-card	2153	
-ncbi	4124	
-ncbibetalactamase	1557	
-plasmidfinder	263	
-resfinder	2228	
-vfdb	2597	
+argannot	1749
+card	2220
+ecoh	597
+ncbi	4324
+plasmidfinder	263
+resfinder	2280
+vfdb	2597
--- a/test-data/output_mrsa.txt	Mon Sep 04 02:47:12 2017 -0400
+++ b/test-data/output_mrsa.txt	Mon Mar 19 10:42:19 2018 -0400
@@ -1,9 +1,9 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
-NC_002952.2	40786	41556	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950
-NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628
-NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
-NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
-NC_002952.2	782414	783580	norA_1	1-1167/1167	===============	0/0	100.00	91.69	resfinder	M97169
-NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
-NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
-NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT
+	NC_002952.2	40786	41556	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950	Alternate name; ant(4')-Ia and aadD2
+	NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628	mecA_15
+	NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)_1
+	NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	Alternate name; aad9 ant(9)-Ia
+	NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)_1
+	NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	Alternate name; aad9 ant(9)-Ia
+	NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722	blaZ_36
+	NC_002952.2	2488459	2488878	fosD_1	1-420/420	===============	0/0	100.00	79.05	resfinder	KC989517	fosD_1
--- a/test-data/output_noheader.txt	Mon Sep 04 02:47:12 2017 -0400
+++ b/test-data/output_noheader.txt	Mon Mar 19 10:42:19 2018 -0400
@@ -1,8 +1,8 @@
-NC_002952.2	40786	41556	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950
-NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628
-NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
-NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
-NC_002952.2	782414	783580	norA_1	1-1167/1167	===============	0/0	100.00	91.69	resfinder	M97169
-NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216
-NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588
-NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722
+	NC_002952.2	40786	41556	aadD_1	1-771/771	===============	0/0	100.00	99.74	resfinder	AF181950	Alternate name; ant(4')-Ia and aadD2
+	NC_002952.2	44919	46928	mecA_15	1-2010/2010	===============	0/0	100.00	100.00	resfinder	AB505628	mecA_15
+	NC_002952.2	55890	56621	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)_1
+	NC_002952.2	56747	57529	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	Alternate name; aad9 ant(9)-Ia
+	NC_002952.2	1796513	1797244	erm(A)_1	1-732/732	===============	0/0	100.00	100.00	resfinder	X03216	erm(A)_1
+	NC_002952.2	1797370	1798152	spc_1	1-783/783	===============	0/0	100.00	100.00	resfinder	X02588	Alternate name; aad9 ant(9)-Ia
+	NC_002952.2	1913827	1914672	blaZ_36	1-846/846	===============	0/0	100.00	100.00	resfinder	AJ400722	blaZ_36
+	NC_002952.2	2488459	2488878	fosD_1	1-420/420	===============	0/0	100.00	79.05	resfinder	KC989517	fosD_1
--- a/test-data/output_noresults.txt	Mon Sep 04 02:47:12 2017 -0400
+++ b/test-data/output_noresults.txt	Mon Mar 19 10:42:19 2018 -0400
@@ -1,1 +1,1 @@
-#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION
+#FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY	DATABASE	ACCESSION	PRODUCT