diff homova.xml @ 0:d891666964ad 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/homova.xml	Fri May 19 04:55:33 2017 -0400
@@ -0,0 +1,96 @@
+<tool profile="16.07" id="mothur_homova" name="Homova" version="@WRAPPER_VERSION@.0">
+    <description>Homogeneity of molecular variance</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 "$dist" dist.dat &&
+        ln -s "$design" design.dat &&
+
+        echo 'homova(
+            phylip=dist.dat,
+            design=design.dat,
+            #if $sets:
+                sets=${ str($sets).replace(",","-") },
+            #end if
+            iters=$iters,
+            alpha=$alpha
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+        <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
+        <param name="alpha" type="float" optional="true" value="0.05" min="0.0" label="alpha - acceptable stopping precision (default 0.05)"/>
+        <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
+        <param name="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze. The set names are separated by dashes. The default is all sets in designfile">
+            <options>
+                <filter type="data_meta" ref="design" key="groups"/>
+            </options>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="homova" format="tabular" from_work_dir="dist*.homova" label="${tool.name} on ${on_string}: homova"/>
+    </outputs>
+    <tests>
+        <test><!-- test default settings -->
+            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
+            <param name="design" value="amazon.design" ftype="tabular"/>
+            <output name="homova" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
+                    <has_text text="A-B"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with subsets -->
+            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
+            <param name="design" value="amazon.design" ftype="mothur.design"/>
+            <param name="sets" value="A"/>
+            <output name="homova" ftype="tabular">
+                <assert_contents>
+                    <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
+                    <has_line_matching expression="A\t.*$"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The homova_ command calculates the homogeneity of molecular variance (HOMOVA) from a phylip_distance_matrix_, a nonparametric analog of Bartlett's test for homo- geneity of variance, which has been used in population genetics to test the hypothesis that the genetic diversity within two or more populations is homogeneous.
+
+A design file partitions a list of names into groups.  It is a tab-delimited file with 2 columns: name and group, e.g. :
+        ======= =======
+        duck    bird
+        cow     mammal
+        pig     mammal
+        goose   bird
+        cobra   reptile
+        ======= =======
+
+The Make_Design tool can construct a design file from a Mothur dataset that contains group names.
+
+.. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _homova: https://www.mothur.org/wiki/Homova
+
+v.1.20.0: Updated to Mothur 1.33, added sets parameter
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>