diff remove.otus.xml @ 0:4b07bc776ccb 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/remove.otus.xml	Fri May 19 05:53:16 2017 -0400
@@ -0,0 +1,71 @@
+<tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0">
+    <description>Remove otus containing sequences from specified groups</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 "$otu" otu.dat &&
+        ln -s "$group_in" group_in.dat &&
+
+        echo 'remove.otus(
+            list=otu.dat,
+            label=$label,
+            group=group_in.dat
+            #if $groups:
+                ,groups=${ str($groups).replace(",","-") }
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+        <param name="label" type="select" label="label - OTU Labels" help="Select exactly one label">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
+        <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" help="At least one group must be selected">
+            <options>
+                <filter type="data_meta" ref="group_in" key="groups"/>
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.dat" label="${tool.name} on ${on_string}: pick.groups"/>
+        <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.dat" label="${tool.name} on ${on_string}: pick.list"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
+            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="groups" value="forest"/>
+            <param name="label" value="0.05"/>
+            <output name="list_out" md5="fa5b954ad8e8235dbb700af1a9d8a091" ftype="mothur.list"/>
+            <output name="group_out" md5="3c9f6e88de0f60f2a870c8d4a9d61db8" ftype="mothur.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups.
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _remove.otus: https://www.mothur.org/wiki/Remove.otus
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>