diff mlst_cpo.xml @ 0:917a05a03ac9 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mlst_cpo.xml	Tue Aug 14 17:18:49 2018 -0400
@@ -0,0 +1,132 @@
+<tool id="mlst" name="MLST" version="2.11">
+    <requirements>
+        <requirement type="package" version="2.11">mlst</requirement>
+    </requirements>
+
+    <version_command>mlst --version</version_command>
+
+    <command detect_errors="exit_code"><![CDATA[
+        mlst "$input_file" --nopath
+        #if $settings.advanced == "advanced"
+            #if $settings.min_dna_id
+                --minid=$settings.min_dna_id
+            #end if
+            #if $settings.min_dna_cov
+                --mincov=$settings.min_dna_cov
+            #end if
+            #if $settings.scheme
+                --scheme=$settings.scheme
+            #end if
+        #end if
+        > "$report"
+    ]]></command>
+
+    <inputs>
+        <param type="data" name="input_file" format="fasta,genbank" />
+        <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="min_dna_id" type="integer" label="Minimum DNA identity" value="95" min="0" max="100" help="Minimum DNA identity of full allelle to consider 'similar' (default 95, must be between 0-100)" optional="true" />
+                <param name="min_dna_cov" type="integer" label="Minimum DNA coverage" value="10" help="Minimum DNA coverage to report partial allele at all (default 10)" optional="true" />
+                <param name="scheme" type="text" area="false" label="PubMLST Scheme" help="Turn off auto-detection and only use this scheme" optional="true" />
+            </when>
+        </conditional>
+    </inputs>
+
+    <outputs>
+        <data name="report" format="tabular" />
+    </outputs>
+
+    <tests>
+        <!-- Basic test - will produce no results. -->
+        <test>
+            <param name="input_file" value="Acetobacter.fna"/>
+            <param name="advanced" value="simple"/>
+            <output name="report" ftype="tabular" file="output_noresults.txt" compare="contains"/>
+        </test>
+
+        <!-- Basic test - will produce results. -->
+        <test>
+            <param name="input_file" value="MRSA0252_trimmed.fna"/>
+            <param name="advanced" value="simple"/>
+            <output name="report" ftype="tabular" file="output_mrsa.txt" compare="contains"/>
+        </test>
+
+        <!-- Advanced test - Min DNA Coverage 100 -->
+        <test>
+            <param name="input_file" value="MRSA0252_trimmed.fna"/>
+            <param name="advanced" value="advanced"/>
+            <param name="min_dna_cov" value="100"/>
+            <output name="report" ftype="tabular" file="output_mincov100.txt" compare="contains"/>
+        </test>
+
+        <!-- Advanced test - Min DNA ID 100 -->
+        <test>
+            <param name="input_file" value="MRSA0252_trimmed.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 genome file in FASTA or Genbank format, MLST will scan the file against PubMLST typing schemes.
+
+**Output**
+
+MLST will produce a tab-seperated output file which contains:
+- the filename
+- the closest PubMLST scheme name
+- the ST (sequence type)
+- the allele IDs
+
+**Example Output**
+
+::
+
+genomes/6008.fna        saureus         239  arcc(2)   aroe(3)   glpf(1)   gmk_(1)   pta_(4)   tpi_(4)   yqil(3)
+
+**Without auto-detection**
+
+If you provide the 'scheme' parameter, it will print a fixed tabular output with a heading containing allele names specific to that scheme. To view a list of schemes, use the MLST List tool.
+
+::
+
+FILE      SCHEME     ST    abcZ  adk  aroE  fumC  gdh  pdhC  pgm
+NM003.fa  neisseria  11    2     3    4     3       8     4    6
+
+**Missing data**
+MLST does not just look for exact matches to full length alleles. It attempts to tell you as much as possible about what it found using the notation below:
+
++--------+---------------------------+
+| Symbol | Meaning                   |
++========+===========================+
+| n      | Exact intact allele       |
++--------+---------------------------+
+| ~n     | Novel allele similar to n |
++--------+---------------------------+
+| n,m    | Multiple alleles          |
++--------+---------------------------+
+|  *-*   | Allele missing            |
++--------+---------------------------+
+
+Galaxy wrapper maintained by Simon Gladman.
+    ]]></help>
+
+    <citations>
+        <citation type="bibtex">
+            @UNPUBLISHED{Seemann2016,
+            author = "Seemann T",
+            title = "MLST: Scan contig files against PubMLST typing schemes",
+            year = "2016",
+            note = "https://github.com/tseemann/mlst"}
+        </citation>
+    </citations>
+</tool>