diff remove.otus.xml @ 2:45d51905b3b5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

--- a/remove.otus.xml	Tue Sep 05 17:11:20 2017 -0400
+++ b/remove.otus.xml	Tue Mar 20 22:21:21 2018 -0400
@@ -1,5 +1,5 @@
 <tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0">
-    <description>Remove otus containing sequences from specified groups</description>
+    <description>Removes OTUs from various file formats</description>
     <macros>
         <import>macros.xml</import>
     </macros>
@@ -7,65 +7,101 @@
     <expand macro="stdio"/>
     <expand macro="version_command"/>
     <command><![CDATA[
-        @SHELL_OPTIONS@
+@SHELL_OPTIONS@
 
-        ## create symlinks to input datasets
-        ln -s "$otu" otu.dat &&
-        ln -s "$group_in" group_in.dat &&
+## create symlinks to input datasets
+ln -s '$infile.otu' infile.otu.dat &&
+ln -s '$accnos' accnos.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
+echo 'remove.otus(
+    #if $infile.otu.is_of_type("mothur.cons.taxonomy"):
+        constaxonomy=infile.otu.data,
+    #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 $infile.label:
+        label=${ str($infile.label).replace(",","-") },
+    #end if
+    accnos=accnos.dat
+)'
+| 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>
+        <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>
+        <expand macro="param-savelog"/>
     </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 ${on_string}: pick.list"/>
+        <data name="pick_out" format_source="otu" from_work_dir="infile.otu*.pick.dat" label="${tool.name} on ${on_string}: pick"/>
     </outputs>
     <tests>
-        <test>
+        <test><!-- test with shared/list input and label selection -->
+            <param name="accnos" value="amazon.accnos.otulabels"/>
+            <param name="intype" value="in_shared"/>
             <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"/>
+            <param name="label" value="0.22"/>
+            <output name="pick_out" ftype="mothur.list">
+                <assert_contents>
+                    <expand macro="test-list-format"/>
+                    <has_text text="U68686"/>
+                    <has_text text="0.22"/>
+                    <not_has_text text="0.03"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with constaxonomy/otucorr/corraxes file -->
+            <param name="accnos" value="amazon.accnos.otulabels"/>
+            <param name="intype" value="in_other"/>
+            <param name="otu" value="amazon.pcoa.axes" ftype="mothur.axes"/>
+            <output name="pick_out" ftype="mothur.axes">
+                <assert_contents>
+                    <expand macro="test-axes-format"/>
+                    <has_text text="U68686"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
             <expand macro="logfile-test"/>
         </test>
     </tests>
-    <help>
-<![CDATA[
+    <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.
+The remove.otus command removes otu labels from cons.taxonomy, corr.axes, otu.corr, shared and list files. This can be useful especially with subsampled datasets or when groups have been selected.
 
-.. _list: https://www.mothur.org/wiki/List_file
 .. _remove.otus: https://www.mothur.org/wiki/Remove.otus
 
-]]>
-    </help>
+    ]]></help>
     <expand macro="citations"/>
 </tool>