diff get.otulabels.xml @ 0:ca0c577f910d 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/get.otulabels.xml	Fri May 19 05:43:09 2017 -0400
@@ -0,0 +1,98 @@
+<tool profile="16.07" id="mothur_get_otulabels" name="Get.otulabels" version="@WRAPPER_VERSION@.0">
+    <description>Selects OTU labels</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 "$infile.otu" infile.otu.dat &&
+        ln -s "$accnos" accnos.dat &&
+
+        echo 'get.otulabels(
+            #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
+                constaxonomy=infile.otu.dat,
+            #end if
+            #if $infile.otu.is_of_type("mothur.otu.corr"):
+                otucorr=infile.otu.dat,
+            #end if
+            #if $infile.otu.is_of_type("mothur.axes"):
+                corraxes=infile.otu.dat,
+            #end if
+            #if $infile.otu.is_of_type("mothur.list"):
+                list=infile.otu.dat,
+            #end if
+            #if $infile.otu.is_of_type("mothur.shared"):
+                shared=infile.otu.dat,
+            #end if
+            #if $infile.intype == "in_shared" and $infile.label:
+                label=$infile.label,
+            #end if
+            accnos=accnos.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="accnos" type="data" format="mothur.otulabels" label="accnos - otulabels" help="Required"/>
+        <conditional name="infile">
+            <param name="intype" type="select" label="Which type of files will you be supplying?" help="">
+                <option value="in_shared">Shared or List file</option>
+                <option value="in_other">Constaxonomy / OtuCorr / CorrAxes file</option>
+            </param>
+            <when value="in_shared">
+                <param name="otu" type="data" format="mothur.list,mothur.shared" label="shared/list - allows you to input a list file you wish to select OTUs from. "/>
+                <param name="label" type="select" label="label - pick (one) OTU Label" optional="true" help="By default first label in your file is used">
+                    <expand macro="labeloptions"/>
+                </param>
+            </when>
+            <when value="in_other">
+                <param name="otu" type="data" format="mothur.cons.taxonomy,mothur.otu.corr,mothur.axes" label="cons.taxonomy/otu.corr/axes file" help="constaxonomy file can be obtained by the running classify.otu tool, otucorr from otu.association tool, and corraxes from corr.axes command"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="intype" value="in_shared"/>
+            <param name="accnos" value="amazon.accnos.otulabels"/>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="label" value="0.22"/>
+            <output name="pick_out" md5="1868b58c69f48fe0ae14113d1fc50b33" ftype="mothur.shared"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="intype" value="in_other"/>
+            <param name="accnos" value="amazon.accnos.otulabels"/>
+            <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
+            <output name="pick_out" md5="c5f9d1a80b85cce640f25eb89cb67509" ftype="mothur.axes"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+
+**Command Documentation**
+
+The get.otulabels_ command selects otu labels from the output from classify.otu_, corr.axes_ and otu.association_. This can be useful especially with subsampled datasets or when groups have been selected.
+
+.. _classify.otu: https://www.mothur.org/wiki/Classify.otu
+.. _corr.axes: https://www.mothur.org/wiki/Corr.axes
+.. _otu.association: https://www.mothur.org/wiki/Otu.association
+
+v.1.27.0: Added list and shared parameters, updated to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>