diff list.otulabels.xml @ 0:e86c535cf4d1 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/list.otulabels.xml	Fri May 19 05:50:07 2017 -0400
@@ -0,0 +1,92 @@
+<tool profile="16.07" id="mothur_list_otulabels" name="List.otulabels" version="@WRAPPER_VERSION@.0">
+    <description>Lists otu labels from shared or relabund 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 &&
+
+        echo 'list.otulabels(
+            #if $otu.is_of_type("mothur.relabund"):
+                relabund=otu.dat
+            #elif $otu.is_of_type("mothur.shared"):
+                shared=otu.dat
+            #else
+                list=otu.dat
+            #end if
+            #if $label:
+                ,label=${ str($label).replace(",","-") }
+            #end if
+            #if $groups:
+                ,groups=${ str($groups).replace(",","-") }
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared,mothur.relabund,mothur.list" label="list or shared or relabund - OTU List or Shared or Relabund"/>
+        <param name="label" type="select" multiple="true" label="label - OTU Labels">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="groups" type="select" multiple="true" label="groups - Pairwise comparision groups">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="otulabels" type="list" label="${tool.name} on ${on_string}: otulabels">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otulabels" format="mothur.otulabels"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="otulist"/>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <output_collection name="otulabels" count="36">
+                <element name="unique" md5="c901cebfbc87559f1667546111408a22" ftype="mothur.otulabels"/>
+                <element name="0.55" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.otulabels"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with group select -->
+            <param name="infile" value="otulist"/>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="groups" value="forest"/>
+            <output_collection name="otulabels" count="36">
+                <element name="unique" md5="8a4d85496fdcfdf99337129989350e7e" ftype="mothur.otulabels"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otulabels_ or remove.otulabels_ commands.
+
+.. _list.otulabels: https://www.mothur.org/wiki/List.otulabels
+.. _classify.otu: https://www.mothur.org/wiki/Classify.otu
+.. _otu.association: https://www.mothur.org/wiki/Otu.association
+.. _corr.axes: https://www.mothur.org/wiki/Corr.axes
+.. _remove.otulabels: https://www.mothur.org/wiki/Remove.otulabels
+.. _shared: https://www.mothur.org/wiki/Shared_file
+.. _relabund: https://www.mothur.org/wiki/Get.relabund
+
+v.1.27.0: Updated to mothur 1.33, added list file for otu
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>