diff classify.seqs.xml @ 0:2a0d8b8c3ade draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/classify.seqs.xml	Fri May 19 05:13:36 2017 -0400
@@ -0,0 +1,189 @@
+<tool profile="16.07" id="mothur_classify_seqs" name="Classify.seqs" version="@WRAPPER_VERSION@.0">
+    <description>Assign sequences to taxonomy</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## enable mothur to find blast
+        loc=`which mothur` && ln -s "\${loc%/mothur}"/* . &&
+
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+        ln -s "$alignment.template" alignment.template.dat &&
+        ln -s "$tax.taxonomy" tax.taxonomy.dat &&
+        ln -s "$count" count.dat &&
+        ln -s "$name" name.dat &&
+
+        echo 'classify.seqs(
+            fasta=fasta.dat,
+            reference=alignment.template.dat,
+            taxonomy=tax.taxonomy.dat,
+            method=$classify.method,
+            #if $classify.method == "wang":
+                ksize=$classify.ksize,
+                iters=$classify.iters,
+                cutoff=$classify.cutoff,
+                probs=$classify.probs,
+            #elif $classify.method == "knn":
+                numwanted=$classify.numwanted,
+                search=$classify.search.algorithm,
+                #if $classify.search.algorithm == "kmer":
+                    ksize=$classify.search.ksize,
+                #elif $classify.search.algorithm == "blast":
+                    match=$classify.search.match,
+                    mismatch=$classify.search.mismatch,
+                    gapopen=$classify.search.gapopen,
+                    gapextend=$classify.search.gapextend,
+                #end if
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            #if $name:
+                name=name.dat,
+            #end if
+            relabund=$relabund,
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | ./mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Candiate 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" 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" label="reference - Reference to align with" help=""/>
+            </when>
+        </conditional>
+        <conditional name="tax">
+            <param name="source2" type="select" label="Select Taxonomy from" help="">
+                <option value="ref">Cached Reference</option>
+                <option value="hist">History</option>
+            </param>
+            <when value="ref">
+                <param name="taxonomy" type="select" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference">
+                    <options from_data_table="mothur_taxonomy"/>
+                </param>
+            </when>
+            <when value="hist">
+                <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy reference"/>
+            </when>
+        </conditional>
+        <conditional name="classify">
+            <param name="method" type="select" label="method - Select a classification method" help="">
+                <option value="wang" selected="true">Bayesian (default)</option>
+                <option value="knn">K-Nearest Neighbor (knn)</option>
+            </param>
+            <when value="wang">
+                <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
+                <param name="iters" type="integer" value="100" min="1" label="iters - iterations to do when calculating the bootstrap confidence score"/>
+                <param name="cutoff" type="integer" value="0" min="0" label="cutoff - specify a bootstrap confidence threshold for your taxonomy"/>
+                <param name="probs" type="boolean" falsevalue="false" truevalue="true" checked="true" label="probs - Show probabilities"/>
+            </when>
+            <when value="knn">
+                <param name="numwanted" type="integer" value="10" label="numwanted - the number of sequence matches you want with the knn method"/>
+                <conditional name="search">
+                    <param name="algorithm" type="select" label="algorithm - " help="">
+                        <option value="kmer" selected="true">Kmer (default)</option>
+                        <option value="blast">BLAST</option>
+                        <option value="suffix">Suffix Tree</option>
+                        <option value="distance">Distance</option>
+                    </param>
+                    <when value="kmer">
+                        <param name="ksize" type="integer" value="8" min="1" label="ksize - kmer length"/>
+                    </when>
+                    <when value="blast">
+                        <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/>
+                        <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/>
+                        <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/>
+                        <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/>
+                    </when>
+                    <when value="suffix"/>
+                    <when value="distance"/>
+                </conditional>
+            </when>
+        </conditional>
+        <param name="count" type="data" format="mothur.count_table" label="count file" optional="true"/>
+        <param name="name" type="data" format="mothur.names" label="names file" optional="true"/>
+        <param name="relabund" type="boolean" falsevalue="false" truevalue="true" checked="false" label="relabund - allows you to indicate that you want the summary files to be relative abundances rather than raw abundances. default=f"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="fasta*.taxonomy" label="${tool.name} on ${on_string}: taxonomy"/>
+        <data name="tax_summary" format="mothur.tax.summary" from_work_dir="fasta*.tax.summary" label="${tool.name} on ${on_string}: tax.summary"/>
+        <data name="tree_sum" format="tabular" from_work_dir="tax.taxonomy*.tree.sum" label="${tool.name} on ${on_string}: tree.sum"/>
+    </outputs>
+    <tests>
+        <test><!-- test with wang method -->
+            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
+            <param name="source" value="hist"/>
+            <param name="template" value="abrecovery.fasta" ftype="fasta"/>
+            <param name="source2" value="hist"/>
+            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <output name="tax_summary" md5="d6f02a20cdf415fb84e394d0dab2314f" ftype="mothur.tax.summary"/>
+            <output name="taxonomy_out" ftype="mothur.seq.taxonomy">
+                <assert_contents>
+                    <has_text text="Bacteria"/>
+                    <has_text text="U68589"/>
+                </assert_contents>
+            </output>
+            <output name="tree_sum" md5="a6ae5cc82edd181082dd23f348b621d9" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with knn method -->
+            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
+            <param name="source" value="hist"/>
+            <param name="template" value="abrecovery.fasta" ftype="fasta"/>
+            <param name="source2" value="hist"/>
+            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <param name="method" value="knn"/>
+            <output name="tax_summary" md5="4931072238dcf29344f4a1e3332f3415" ftype="mothur.tax.summary"/>
+            <output name="taxonomy_out" md5="1080c7676c1a1f4f429c7d8df6a62f47" ftype="mothur.seq.taxonomy"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with knn method and blast algorithm -->
+            <param name="fasta" value="abrecovery.fasta" ftype="fasta"/>
+            <param name="source" value="hist"/>
+            <param name="template" value="abrecovery.fasta" ftype="fasta"/>
+            <param name="source2" value="hist"/>
+            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
+            <param name="method" value="knn"/>
+            <param name="algorithm" value="blast"/>
+            <output name="tax_summary" md5="4d6e1fa3be9abe5f57b0660fe5ae5887" ftype="mothur.tax.summary"/>
+            <output name="taxonomy_out" md5="1296e2a2c8efd58f9c840760bed55042" ftype="mothur.seq.taxonomy"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The classify.seqs_ command assigns sequences to chosen taxonomy outline.
+
+.. _classify.seqs: https://www.mothur.org/wiki/Classify.seqs
+
+
+v1.22.0: Updated for Mothur 1.33. Added count parameter (1.28), added relabund parameter (1.33), bayesian term changed to wang.
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>