diff tools/mothur/chimera.check.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/chimera.check.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,104 @@
+<tool profile="16.07" id="mothur_chimera_check" name="Chimera.check" version="@WRAPPER_VERSION@.0">
+    <description>Find putative chimeras using chimeraCheck</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        echo 'chimera.check(
+            fasta=$fasta,
+            reference=$alignment.template,
+            #if $svg.gen == "yes":
+                svg=yes,
+                name=$svg.name,
+            #end if
+            increment=$increment,
+            ksize=$ksize,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$fasta" &&
+        mv mothur.*.logfile "$logfile" &&
+        mv \${prefix%.dat}.chimeracheck.chimeras "$out_file"
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="mothur.align" argument="fasta" label="fasta - Candiate Aligned Sequences"/>
+        <conditional name="alignment">
+            <param name="source" type="select" label="Select Reference Template from" help="">
+                <option value="hist">History</option>
+                <option value="ref">Cached Reference</option>
+            </param>
+            <when value="ref">
+                <param name="template" type="select" argument="reference" label="reference - Select an alignment database" help="">
+                    <options from_data_table="mothur_aligndb">
+                    </options>
+                </param>
+            </when>
+            <when value="hist">
+                <param name="template" type="data" format="fasta" argument="reference" label="reference - Reference to align with" help=""/>
+            </when>
+        </conditional>
+        <param name="ksize" type="integer" value="7" argument="ksize" label="ksize - kmer length to determine differences between sequence fragments (uses default if &lt; 1)"/>
+        <param name="increment" type="integer" value="10" argument="increment" label="increment - Increment for window slide on each iteration (uses default if &lt; 1)" help="Default is 10, but you may set it up to sequence length minus twice the window."/>
+        <conditional name="svg">
+            <param name="gen" type="select" label="svg - Generate a SVG plot for each query sequence" help="">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="no"/>
+            <when value="yes">
+                <param name="name" type="data" format="mothur.names" optional="true" argument="name" label="name - Names of queries for which to generate SVG plot"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="out_file" format="txt" label="${tool.name} on ${on_string}: chimeracheck.chimeras"/>
+        <collection name="images" type="list" label="${tool.name} on ${on_string}: SVG images">
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.chimeracheck\.svg"/>
+            <filter>svg['gen'] == 'yes'</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="source" value="hist"/>
+            <param name="template" value="HMP_MOCK.v35.align"/>
+            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="source" value="hist"/>
+            <param name="template" value="HMP_MOCK.v35.align"/>
+            <param name="gen" value="yes"/>
+            <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names_tiny"/>
+            <output name="out_file" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chimeracheck.chimeras" ftype="txt"/>
+            <output_collection name="images" count="2">
+                <element name="M00967_43_000000000-A3JHG_1_1101_14010_4122" file="M00967_43_000000000-A3JHG_1_1101_14010_4122.chimeracheck.svg"/>
+                <element name="M00967_43_000000000-A3JHG_1_1101_13293_4703" md5="0d99dc17c183dab4efc75c697060a9a5"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The chimera.check_ command identifies putative chimeras using the chimeraCheck approach. It looks at distance of left side of query to it's closest match + distance of right side of query to it's closest match - distance of whole query and its closest match over several windows.
+
+Note: following the RDP model this method does not determine whether or not a sequence is chimeric, but allows you to determine that based on the IS values produced.
+
+.. _chimera.check: http://www.mothur.org/wiki/Chimera.check
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>