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changeset 1:15197951a756 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 626b990b38e0585abfb6a06a2516ff498dc2257b
author iuc
date Fri, 03 Mar 2017 14:56:09 -0500
parents 862f5a86854d
children 2aa02d2a6af3
files abricate.xml abricate_list.xml test-data/output_cull100.txt test-data/output_minid100.txt test-data/output_mrsa.txt test-data/output_noheader.txt tool_dependencies.xml
diffstat 7 files changed, 62 insertions(+), 83 deletions(-) [+]
line wrap: on
line diff
--- a/abricate.xml	Tue Nov 29 14:52:34 2016 -0500
+++ b/abricate.xml	Fri Mar 03 14:56:09 2017 -0500
@@ -1,28 +1,26 @@
-<tool id="abricate" name="ABRicate" version="0.1.0">
+<tool id="abricate" name="ABRicate" version="0.3">
     <requirements>
         <requirement type="package" version="0.3">abricate</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
-        <requirement type="package" version="2.2.31">blast+</requirement>
     </requirements>
 
     <version_command>abricate --version</version_command>
 
     <command detect_errors="exit_code"><![CDATA[
-        abricate "$fasta_input"
+        abricate '$fasta_input'
         #if $settings.advanced == "advanced"
             $settings.no_header
-            #if $settings.min_dna_id
+            #if str($settings.min_dna_id)
                 --minid=$settings.min_dna_id
             #end if
-            #if $settings.cull_limit
+            #if str($settings.cull_limit)
                 --cull=$settings.cull_limit
             #end if
         #end if
-        > "$report"
+        > '$report'
     ]]></command>
 
     <inputs>
-        <param name="fasta_input" type="data" format="fasta" label="Select fasta file" help="Specify fasta file to screen for antibiotic resistant genes"/>
+        <param name="fasta_input" type="data" format="fasta" label="FASTA file" help="To screen for antibiotic resistant genes" />
         <conditional name="settings">
             <param name="advanced" type="select" label="Specify advanced parameters">
                 <option value="simple" selected="true">No, use program defaults.</option>
@@ -31,18 +29,15 @@
             <when value="simple">
             </when>
             <when value="advanced">
-                <param name="no_header" type="boolean" label="Suppress header" truevalue="--noheader" falsevalue=""
-                  help="Suppress output file's column headings" optional="true" />
-                <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="75" min="0" max="100" help="Minimum DNA identity (default 75, must be between 0-100)" optional="true" />
-                <param name="cull_limit" type="integer" label="Culling limit" value="1" min="0" help="Culling limit (encompassing hits) (default 1, must be a positive number)" optional="true">
-                    <validator type="in_range" message="This value must be greater than or equal to 0" min="0" max="2147483647"/>
-                </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" />
+                <param name="cull_limit" argument="--cull" type="integer" value="1" min="0" optional="true" label="Culling limit (encompassing hits)" />
             </when>
         </conditional>
     </inputs>
 
     <outputs>
-        <data format="tabular" name="report" label="${tool.name} on ${on_string} report file"/>
+        <data name="report" format="tabular" label="${tool.name} on ${on_string} report file" />
     </outputs>
 
     <tests>
@@ -130,17 +125,16 @@
 	Klebsiella.fna  NC_021232.1 872545  872964  fosA    1-420/420   =============== 0   100.00  100.00
 	Klebsiella.fna  NC_021232.1 1381252 1382427 oqxA    1-1176/1176 =============== 0   100.00  99.32
 	Klebsiella.fna  NC_021232.1 2584899 2585759 blaSHV1 1-861/861   =============== 0   100.00  99.88
-
-
     ]]></help>
 
     <citations>
-      <citation type="bibtex">
-        @UNPUBLISHED{Seemann2016,
-        author = "Seemann T",
-        title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
-        year = "2016",
-        note = "https://github.com/tseemann/abricate"}
-      </citation>
+        <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>
 </tool>
--- a/abricate_list.xml	Tue Nov 29 14:52:34 2016 -0500
+++ b/abricate_list.xml	Fri Mar 03 14:56:09 2017 -0500
@@ -1,22 +1,19 @@
-<tool id="abricate_list" name="ABRicate List" version="0.1.0">
+<tool id="abricate_list" name="ABRicate List" version="0.3">
     <requirements>
         <requirement type="package" version="0.3">abricate</requirement>
-        <requirement type="package" version="5.18.1">perl</requirement>
-        <requirement type="package" version="2.2.31">blast+</requirement>
     </requirements>
 
     <version_command>abricate --version</version_command>
 
     <command detect_errors="exit_code"><![CDATA[
-        abricate --list 2> "$report"
+        abricate --list 2> '$report'
     ]]></command>
 
     <inputs>
-
     </inputs>
 
     <outputs>
-        <data format="txt" name="report" label="${tool.name} - list of databases"/>
+        <data name="report" format="txt" label="${tool.name} - list of databases"/>
     </outputs>
 
     <tests>
@@ -29,16 +26,16 @@
 **What it does**
 
 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 T",
-        title = "ABRicate: mass screening of contigs for antiobiotic resistance genes",
-        year = "2016",
-        note = "https://github.com/tseemann/abricate"}
-      </citation>
+        <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>
 </tool>
--- a/test-data/output_cull100.txt	Tue Nov 29 14:52:34 2016 -0500
+++ b/test-data/output_cull100.txt	Fri Mar 03 14:56:09 2017 -0500
@@ -1,12 +1,12 @@
 #FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY
-gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.741
-gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	55983	56576	erm(A)	1-594/594	===============	0	100.00	85.522
-gi|49482253|ref|NC_002952.2|	1796606	1797199	erm(A)	1-594/594	===============	0	100.00	85.522
-gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	44919	46925	mecA	1-2007/2007	===============	0	100.00	99.950
-gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.688
-gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.000
+gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.74
+gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	55983	56576	erm(A)	1-594/594	===============	0	100.00	85.52
+gi|49482253|ref|NC_002952.2|	1796606	1797199	erm(A)	1-594/594	===============	0	100.00	85.52
+gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	44919	46925	mecA	1-2007/2007	===============	0	100.00	99.95
+gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.69
+gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.00
--- a/test-data/output_minid100.txt	Tue Nov 29 14:52:34 2016 -0500
+++ b/test-data/output_minid100.txt	Fri Mar 03 14:56:09 2017 -0500
@@ -1,7 +1,7 @@
 #FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY
-gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.000
+gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.00
--- a/test-data/output_mrsa.txt	Tue Nov 29 14:52:34 2016 -0500
+++ b/test-data/output_mrsa.txt	Fri Mar 03 14:56:09 2017 -0500
@@ -1,9 +1,9 @@
 #FILE	SEQUENCE	START	END	GENE	COVERAGE	COVERAGE_MAP	GAPS	%COVERAGE	%IDENTITY
-gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.741
-gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.688
-gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.000
+gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.74
+gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.69
+gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.00
--- a/test-data/output_noheader.txt	Tue Nov 29 14:52:34 2016 -0500
+++ b/test-data/output_noheader.txt	Fri Mar 03 14:56:09 2017 -0500
@@ -1,8 +1,8 @@
-gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.741
-gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.688
-gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.000
-gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.000
+gi|49482253|ref|NC_002952.2|	40786	41556	aadD	1-771/771	===============	0	100.00	99.74
+gi|49482253|ref|NC_002952.2|	1913827	1914672	blaZ	1-846/846	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	55890	56621	erm(A)	1-732/732	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	1796513	1797244	erm(A)	1-732/732	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	44919	46928	mecA	1-2010/2010	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	782414	783580	norA	1-1167/1167	===============	0	100.00	91.69
+gi|49482253|ref|NC_002952.2|	1797370	1798152	spc	1-783/783	===============	0	100.00	100.00
+gi|49482253|ref|NC_002952.2|	56747	57529	spc	1-783/783	===============	0	100.00	100.00
--- a/tool_dependencies.xml	Tue Nov 29 14:52:34 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,12 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="abricate" version="0.3">
-        <repository changeset_revision="8c7976eed9c3" name="package_abricate_0_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="blast+" version="2.2.31">
-        <repository changeset_revision="921d2963a177" name="package_blast_plus_2_2_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
-    </package>
-</tool_dependency>