diff corr.axes.xml @ 0:9961b707d075 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/corr.axes.xml	Fri May 19 06:00:46 2017 -0400
@@ -0,0 +1,118 @@
+<tool profile="16.07" id="mothur_corr_axes" name="Corr.axes" version="@WRAPPER_VERSION@.0">
+    <description>correlation of data to axes</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
+        #if $input.source == "shared":
+            ln -s "$input.otu" input.otu.dat &&
+        #else
+            ln -s "$input.metadata" input.metadata.dat &&
+        #end if
+
+        echo 'corr.axes(
+            #if $input.source == "shared":
+                #if $input.otu.is_of_type("mothur.relabund"):
+                    relabund=input.otu.dat,
+                #elif $input.otu.is_of_type("mothur.shared"):
+                    shared=input.otu.dat,
+                #end if
+                #if $input.label:
+                    label=$input.label,
+                #end if
+                #if $input.groups:
+                    groups=${ str($input.groups).replace(",","-") },
+                #end if
+            #else:
+                metadata=input.metadata.dat,
+            #end if
+            method=$method,
+            axes=$axes,
+            numaxes=$numaxes
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="axes" type="data" format="mothur.axes" label="axes - a pcoa axes dataset"/>
+        <conditional name="input">
+            <param name="source" type="select" label="Generate Collector Curvers for">
+                <option value="shared">OTU Shared or Relabund</option>
+                <option value="metadata">Metadata table</option>
+            </param>
+            <when value="shared">
+                <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
+                <param name="label" type="select" label="label - OTU Labels" multiple="false" optional="true">
+                    <expand macro="labeloptions"/>
+                </param>
+                <param name="groups" type="select" label="groups - Pairwise comparision groups" multiple="true">
+                    <options>
+                        <filter type="data_meta" ref="otu" key="groups"/>
+                    </options>
+                </param>
+            </when>
+            <when value="metadata">
+                <param name="metadata" type="data" format="tabular" label="metadata - Table of floating point values" help="metadata has the same number of rows as the samples, but the column(s) are floats that describe the samples (e.g. temperature, weight, etc.)"/>
+            </when>
+        </conditional>
+        <param name="method" type="select" optional="true" label="method - pearson, spearman, or kendall. Default: pearson">
+                <option value="pearson" selected="true">pearson</option>
+                <option value="spearman">spearman</option>
+                <option value="kendall">kendall</option>
+        </param>
+        <param name="numaxes" type="integer" value="3" min="0" label="numaxes - Number of axes to use (default 3)"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="corr_axes" format="mothur.axes" from_work_dir="input.*.axes" label="${tool.name} on ${on_string}: corr.axes"/>
+    </outputs>
+    <tests>
+        <test><!-- test with shared file -->
+            <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
+            <param name="source" value="shared"/>
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output name="corr_axes" md5="34ff44b9a58780bc558afd1d22d96bb1" ftype="mothur.axes"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with metadata file -->
+            <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
+            <param name="source" value="metadata"/>
+            <param name="metadata" value="amazon.metadata" ftype="tabular"/>
+            <output name="corr_axes" md5="f62a3b7ed2b75312454a03ebbabe1edc" ftype="mothur.axes"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with relabund file and label and group select -->
+            <param name="axes" value="amazon.square.pcoa.axes" ftype="mothur.axes"/>
+            <param name="source" value="shared"/>
+            <param name="label" value="0.05"/>
+            <param name="groups" value="forest,pasture"/>
+            <param name="otu" value="amazon.an.relabund" ftype="mothur.relabund"/>
+            <output name="corr_axes" md5="014f23f191ec6a9abbb82d51b3d5e24c" ftype="mothur.axes"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The corr.axes_ command calculates the correlation of data to axes.
+
+.. _corr.axes: https://www.mothur.org/wiki/Corr.axes
+
+v.1.21.0: Updated to mothur 1.33
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>