diff create.database.xml @ 0:9ab5ebae3fb2 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/create.database.xml	Fri May 19 05:56:16 2017 -0400
@@ -0,0 +1,97 @@
+<tool profile="16.07" id="mothur_create_database" name="Create.database" version="@WRAPPER_VERSION@.0">
+    <description>creates a database file from a list, repnames, repfasta and contaxonomy file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="stdio"/>
+    <expand macro="version_command"/>
+    <command><![CDATA[
+        @SHELL_OPTIONS@
+
+        ## create symlinks to input datasets
+        ln -s "$otu" otu.dat &&
+        ln -s "$repfasta" repfasta.dat &&
+        ln -s "$nameOrCount" nameOrCount.dat &&
+        ln -s "$constaxonomy" constaxonomy.dat &&
+        ln -s "$group" group.dat &&
+
+        echo 'create.database(
+            #if $otu.is_of_type("mothur.list"):
+                list=otu.dat
+            #elif $otu.is_of_type("mothur.shared"):
+                shared=otu.dat
+            #end if
+            ,repfasta=repfasta.dat
+            #if $nameOrCount.is_of_type("mothur.names"):
+                ,repname=nameOrCount.dat
+            #elif $nameOrCount.is_of_type("mothur.count_table"):
+                ,count=nameOrCount.dat
+            #end if
+            ,constaxonomy=constaxonomy.dat
+            #if $group:
+                ,group=group.dat
+            #end if
+            #if $label:
+                ,label=$label
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.list,mothur.shared" label="list or shared - OTU List of Shared"/>
+        <param name="repfasta" type="data" format="fasta" label="repfasta - rep.fasta" help="rep.fasta file generated by get.oturep"/>
+        <param name="nameOrCount" type="data" format="mothur.names,mothur.count_table" label="repname/count - Representative sequences" help="rep.name file or rep.count_table file generated by get.oturep"/>
+        <param name="constaxonomy" type="data" format="mothur.cons.taxonomy" label="constaxonomy - Consensus Taxonomy" help="consensus taxonomy file output by classify.otu"/>
+        <param name="group" type="data" format="mothur.groups" optional="true" label="group - Groups for summary file"/>
+        <param name="label" type="select" label="label - OTU Labels" optional="true" help="Select exactly one label. If none selected, first label in your list or shared file will be used">
+            <expand macro="labeloptions"/>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="database" format="tabular" from_work_dir="otu*.database" label="${tool.name} on ${on_string}: database"/>
+    </outputs>
+    <tests>
+        <!-- Test with a mothur.names file -->
+        <test>
+            <param name="otu" value="cd-test.list" ftype="mothur.list"/>
+            <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
+            <param name="nameOrCount" value="cd-test.repname" ftype="mothur.names"/>
+            <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
+            <param name="label" value="unique"/>
+            <output name="database" file="cd-test.database" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <!-- Test with a mothur.count_table file -->
+        <test>
+            <param name="otu" value="cd-test.list" ftype="mothur.list"/>
+            <param name="repfasta" value="cd-test.repfasta" ftype="fasta"/>
+            <param name="nameOrCount" value="cd-test.count_table" ftype="mothur.count_table"/>
+            <param name="constaxonomy" value="cd-test.constaxonomy" ftype="mothur.cons.taxonomy"/>
+            <param name="label" value="unique"/>
+            <output name="database" file="cd-test.database" ftype="tabular"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The create.database_ command reads a list_ or shared_ file, .cons.taxonomy, .rep.fasta, .rep.names and optional group file, and creates a database file.
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _create.database: https://www.mothur.org/wiki/Create.database
+
+v.1.28.0: Updated to Mothur 1.33, added count paramter.
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>