diff abricate.xml @ 0:862f5a86854d draft

planemo upload commit 3fdc0150310db0a67769f9ce6ea85695d595b2ba-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/abricate.xml	Tue Nov 29 14:52:34 2016 -0500
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+<tool id="abricate" name="ABRicate" version="0.1.0">
+    <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"
+        #if $settings.advanced == "advanced"
+            $settings.no_header
+            #if $settings.min_dna_id
+                --minid=$settings.min_dna_id
+            #end if
+            #if $settings.cull_limit
+                --cull=$settings.cull_limit
+            #end if
+        #end if
+        > "$report"
+    ]]></command>
+
+    <inputs>
+        <param name="fasta_input" type="data" format="fasta" label="Select fasta file" help="Specify fasta file to screen for antibiotic resistant genes"/>
+        <conditional name="settings">
+            <param name="advanced" type="select" label="Specify advanced parameters">
+                <option value="simple" selected="true">No, use program defaults.</option>
+                <option value="advanced">Yes, see full parameter list.</option>
+            </param>
+            <when value="simple">
+            </when>
+            <when value="advanced">
+                <param name="no_header" type="boolean" label="Suppress header" truevalue="--noheader" falsevalue=""
+                  help="Suppress output file's column headings" optional="true" />
+                <param name="min_dna_id" type="integer" label="Minimum DNA identity" value="75" min="0" max="100" help="Minimum DNA identity (default 75, must be between 0-100)" optional="true" />
+                <param name="cull_limit" type="integer" label="Culling limit" value="1" min="0" help="Culling limit (encompassing hits) (default 1, must be a positive number)" optional="true">
+                    <validator type="in_range" message="This value must be greater than or equal to 0" min="0" max="2147483647"/>
+                </param>
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="report" label="${tool.name} on ${on_string} report file"/>
+    </outputs>
+
+    <tests>
+        <!-- Basic test - will produce no results. -->
+        <test>
+            <param name="fasta_input" value="Acetobacter.fna"/>
+            <param name="advanced" value="simple"/>
+            <output name="report" ftype="tabular" file="output_noresults.txt" />
+        </test>
+
+        <!-- Basic test - will produce results. -->
+        <test>
+            <param name="fasta_input" value="MRSA0252.fna"/>
+            <param name="advanced" value="simple"/>
+            <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
+        </test>
+
+        <!-- Advanced test - No header. -->
+        <test>
+            <param name="fasta_input" value="MRSA0252.fna"/>
+            <param name="advanced" value="advanced"/>
+            <param name="no_header" value="True"/>
+            <output name="report" ftype="tabular" file="output_noheader.txt" compare="contains"/>
+        </test>
+
+        <!-- Advanced test - Cull limit 100 -->
+        <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"/>
+        </test>
+
+        <!-- Advanced test - Min DNA ID 100 -->
+        <test>
+            <param name="fasta_input" value="MRSA0252.fna"/>
+            <param name="advanced" value="advanced"/>
+            <param name="min_dna_id" value="100"/>
+            <output name="report" ftype="tabular" file="output_minid100.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.
+
+**Output**
+
+ABRicate will produce a tab-seperated output file with the following outputs:
+
++---------------+------------------------------------------------+
+|  Column       | Description                                    |
++===============+================================================+
+|  FILE         | The filename this hit came from                |
++---------------+------------------------------------------------+
+|  SEQUENCE     | The sequence in the filename                   |
++---------------+------------------------------------------------+
+|  START        | Start coordinate in the sequence               |
++---------------+------------------------------------------------+
+|  END          | End coordinate                                 |
++---------------+------------------------------------------------+
+|  GENE         | ABR gene                                       |
++---------------+------------------------------------------------+
+|  COVERAGE     | What proportion of the gene is in our sequence |
++---------------+------------------------------------------------+
+|  COVERAGE_MAP | A visual represenation                         |
++---------------+------------------------------------------------+
+|  GAPS         | Was there any gaps in the                      |
+|               | alignment - possible pseudogene?               |
++---------------+------------------------------------------------+
+|  %COVERAGE    | Proportion of gene covered                     |
++---------------+------------------------------------------------+
+|  %IDENTITY    | Proportion of exact nucleotide matches         |
++---------------+------------------------------------------------+
+
+
+**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
+
+
+    ]]></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>
+    </citations>
+</tool>