diff abricate.xml @ 2:2aa02d2a6af3 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/abricate/ commit 0ccab47582f8bc88f9ebc836c4c70d4ce495960c

--- a/abricate.xml	Fri Mar 03 14:56:09 2017 -0500
+++ b/abricate.xml	Tue Jul 18 13:56:16 2017 -0400
@@ -1,39 +1,34 @@
-<tool id="abricate" name="ABRicate" version="0.3">
+<tool id="abricate" name="ABRicate" version="0.5">
     <requirements>
-        <requirement type="package" version="0.3">abricate</requirement>
+        <requirement type="package" version="0.5">abricate</requirement>
     </requirements>
 
     <version_command>abricate --version</version_command>
 
     <command detect_errors="exit_code"><![CDATA[
-        abricate '$fasta_input'
-        #if $settings.advanced == "advanced"
-            $settings.no_header
-            #if str($settings.min_dna_id)
-                --minid=$settings.min_dna_id
-            #end if
-            #if str($settings.cull_limit)
-                --cull=$settings.cull_limit
-            #end if
+        abricate '$file_input'
+        $adv.no_header
+        #if $adv.min_dna_id
+            --minid=$adv.min_dna_id
         #end if
+        --db=$adv.db
         > '$report'
     ]]></command>
 
     <inputs>
-        <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>
-                <option value="advanced">Yes, see full parameter list.</option>
+        <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>
             </param>
-            <when value="simple">
-            </when>
-            <when value="advanced">
-                <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>
+            <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" />
+        </section>
     </inputs>
 
     <outputs>
@@ -41,49 +36,51 @@
     </outputs>
 
     <tests>
-        <!-- Basic test - will produce no results. -->
+        <!-- Basic test 0 - will produce no results. -->
         <test>
-            <param name="fasta_input" value="Acetobacter.fna"/>
-            <param name="advanced" value="simple"/>
+            <param name="file_input" value="Acetobacter.fna"/>
             <output name="report" ftype="tabular" file="output_noresults.txt" />
         </test>
 
-        <!-- Basic test - will produce results. -->
+        <!-- Basic test 1 - will produce results. -->
         <test>
-            <param name="fasta_input" value="MRSA0252.fna"/>
-            <param name="advanced" value="simple"/>
+            <param name="file_input" value="MRSA0252.fna"/>
             <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
         </test>
 
-        <!-- Advanced test - No header. -->
+        <!-- Advanced test 2 - No header. -->
         <test>
-            <param name="fasta_input" value="MRSA0252.fna"/>
-            <param name="advanced" value="advanced"/>
+            <param name="file_input" value="MRSA0252.fna"/>
             <param name="no_header" value="True"/>
             <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
         </test>
 
-        <!-- Advanced test - Cull limit 100 -->
+        <!-- Advanced test 3 - Changed DB to card -->
         <test>
-            <param name="fasta_input" value="MRSA0252.fna"/>
-            <param name="advanced" value="advanced"/>
-            <param name="cull_limit" value="100"/>
-            <output name="report" ftype="tabular" file="output_cull100.txt" compare="contains"/>
+            <param name="file_input" value="MRSA0252.fna"/>
+            <param name="db" value="card"/>
+            <output name="report" ftype="tabular" file="output_db-card.txt" compare="contains"/>
         </test>
 
-        <!-- Advanced test - Min DNA ID 100 -->
+        <!-- Advanced test 4 - Min DNA ID 100 -->
         <test>
-            <param name="fasta_input" value="MRSA0252.fna"/>
-            <param name="advanced" value="advanced"/>
+            <param name="file_input" value="MRSA0252.fna"/>
             <param name="min_dna_id" value="100"/>
             <output name="report" ftype="tabular" file="output_minid100.txt" compare="contains"/>
         </test>
+
+        <!-- Filetype test 5 - input a gbk -->
+        <test>
+            <param name="file_input" value="test.gbk"/>
+            <output name="report" ftype="tabular" file="output_gbk.txt" compare="contains"/>
+        </test>
+
     </tests>
 
     <help><![CDATA[
 **What it does**
 
-Given a FASTA contig file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The database of these genes is built from ResFinder.
+Given a FASTA contig file or a genbank file, ABRicate will perform a mass screening of contigs and identify the presence of antibiotic resistance genes. The user can choose which database to search from a list of available AMR databases.
 
 **Output**
 
@@ -113,18 +110,20 @@
 +---------------+------------------------------------------------+
 |  %IDENTITY    | Proportion of exact nucleotide matches         |
 +---------------+------------------------------------------------+
+|  DATABASE     | The database this sequence comes from          |
++---------------+------------------------------------------------+
+|  ACCESSION    | The genomic source of the sequence             |
++---------------+------------------------------------------------+
 
 
 **Example Output**
 
 ::
 
-	#FILE   SEQUENCE    START   END GENE    COVERAGE    COVERAGE_MAP    GAPS    %COVERAGE   %IDENTITY
-	Processing: 6008.fna
-	Found 12 ABR genes in 6008.fna
-	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
+        #FILE     SEQUENCE     START   END     GENE     COVERAGE     COVERAGE_MAP     GAPS  %COVERAGE  %IDENTITY  DATABASE   ACCESSION
+        6159.fna  NC_017338.1  39177   41186   mecA_15  1-2010/2010  ===============  0/0   100.00     100.000    resfinder  AB505628
+        6159.fna  NC_017338.1  727191  728356  norA_1   1-1166/1167  ===============  0/0   99.91      92.367     resfinder  M97169
+        6159.fna  NC_017339.1  10150   10995   blaZ_32  1-846/846    ===============  0/0   100.00     100.000    resfinder  AP004832
     ]]></help>
 
     <citations>