--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alpha_rarefaction.xml	Thu May 18 09:36:01 2017 -0400
@@ -0,0 +1,162 @@
+<tool id="qiime_alpha_rarefaction" name="Perform alpha rarefaction" version="@WRAPPER_VERSION@.0">
+    <description>A workflow script for performing alpha rarefaction</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <version_command>alpha_rarefaction.py --version</version_command>
+    <command detect_errors="aggressive"><![CDATA[
+        ## set matplotlib backend
+        echo "backend:agg" > matplotlibrc &&
+        
+        alpha_rarefaction.py
+            --otu_table_fp '$otu_table_fp'
+            --mapping_fp '$mapping_fp'
+            -o alpha_rarefaction
+            #if $parameter_fp
+                --parameter_fp '$parameter_fp'
+            #end if
+            --num_steps '$num_steps'
+            $parallel
+            -O "\${GALAXY_SLOTS:-4}"
+            #if $tree_fp
+                --tree_fp '$tree_fp'
+            #end if
+            --min_rare_depth '$min_rare_depth'
+            #if $max_rare_depth
+                --max_rare_depth '$max_rare_depth'
+            #end if
+            $retain_intermediate_files
+
+            && mkdir -p $alpha_rarefaction_plots.files_path
+            && cp alpha_rarefaction/alpha_rarefaction_plots/rarefaction_plots.html $alpha_rarefaction_plots
+            && cp -r alpha_rarefaction/alpha_rarefaction_plots/average_plots $alpha_rarefaction_plots.files_path
+    ]]></command>
+    <inputs>
+        <param argument="--otu_table_fp" type="data" format="tabular,txt,tsv,biom" label="OTU table"/>
+        <param argument="--mapping_fp" type="data" format="tabular,txt,tsv" label="Mapping file"/>
+        <param argument="--parameter_fp" type="data" format="txt" optional="true" label="Parameter file" help="It specifies changes to the default behavior"/>
+        <param argument="--num_steps" type="integer" value="10" label="Number of steps (or rarefied OTU table sizes) to make between min and max counts"/>
+        <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="True" label="Run in parallel where available?"/>
+        <param argument="--tree_fp" type="data" format="tabular,txt,tsv" optional="True" label="Tree file (optional)" help="Required for phylogenetic measures"/>
+        <param argument="--min_rare_depth" type="integer" value="10" label="Lower limit of rarefaction depths"/>
+        <param argument="--max_rare_depth" type="integer" label="Upper limit of rarefaction depths" help="By default, median sequence/sample count is used" optional="True"/>
+        <param argument="--retain_intermediate_files" type="boolean" truevalue="--retain_intermediate_files" falsevalue="" checked="True" label="Retain intermediate files?"/>
+    </inputs>
+    <outputs>
+        <data name="alpha_rarefaction_plots" format="html" label="${tool.name} on ${on_string}: Alpha rarefaction plots"/>
+        <collection name="alpha_diversity" type="list" label="${tool.name} on ${on_string}: Alpha diversity information">
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div_collated/"/>
+        </collection>
+        <collection name="rarefaction" type="list" label="${tool.name} on ${on_string}: Rarefied OTU tables">
+            <discover_datasets pattern="rarefaction_(?P&lt;designation&gt;.+)\.biom" directory="alpha_rarefaction/rarefaction/"/>
+            <filter>retain_intermediate_files!=''</filter>
+        </collection>
+        <collection name="alpha_div" type="list" label="${tool.name} on ${on_string}: Alpha diversity results">
+            <discover_datasets pattern="alpha_rarefaction_(?P&lt;designation&gt;.+)\.txt" directory="alpha_rarefaction/alpha_div/"/>
+            <filter>retain_intermediate_files!=''</filter>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu_table_fp" value="alpha_rarefaction/otu_table.biom"/>
+            <param name="mapping_fp" value="alpha_rarefaction/mapping_file.txt"/>
+            <param name="num_steps" value="2"/>
+            <param name="parallel" value=""/>
+            <param name="tree_fp" value="alpha_rarefaction/rep_set.tre"/>
+            <param name="min_rare_depth" value="10"/>
+            <param name="max_rare_depth" value="50"/>
+            <param name="retain_intermediate_files" value="--retain_intermediate_files"/>
+            <output name="alpha_rarefaction_plots">
+                <assert_contents>
+                    <has_text text="Control_mouse_I.D._354" />
+                </assert_contents>
+            </output>
+            <output_collection name="alpha_diversity" type="list" count="3">
+                <element name="chao1">
+                    <assert_contents>
+                        <has_text text="alpha_rarefaction_10_0" />
+                        <has_text text="alpha_rarefaction_30_5" />
+                        <has_text text="alpha_rarefaction_50_9" />
+                    </assert_contents>
+                </element>
+                <element name="observed_otus">
+                    <assert_contents>
+                        <has_text text="alpha_rarefaction_10_0" />
+                        <has_text text="alpha_rarefaction_30_5" />
+                        <has_text text="alpha_rarefaction_50_9" />
+                    </assert_contents>
+                </element>
+                <element name="PD_whole_tree">
+                    <assert_contents>
+                        <has_text text="alpha_rarefaction_10_0" />
+                        <has_text text="alpha_rarefaction_30_5" />
+                        <has_text text="alpha_rarefaction_50_9" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="rarefaction" type="list" count="30">
+                <element name="10_0">
+                    <assert_contents>
+                        <has_text text="PC.636" />
+                        <has_text text="PC.354" />
+                        <has_text text="PC.634" />
+                    </assert_contents>
+                </element>
+                <element name="30_6">
+                    <assert_contents>
+                        <has_text text="PC.636" />
+                        <has_text text="PC.354" />
+                        <has_text text="PC.634" />
+                    </assert_contents>
+                </element>
+                <element name="50_9">
+                    <assert_contents>
+                        <has_text text="PC.636" />
+                        <has_text text="PC.354" />
+                        <has_text text="PC.634" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+            <output_collection name="alpha_div" type="list" count="30">
+                <element name="10_0">
+                    <assert_contents>
+                        <has_text text="PC.636" />
+                        <has_text text="PC.354" />
+                        <has_text text="PC.634" />
+                    </assert_contents>
+                </element>
+                <element name="30_6">
+                    <assert_contents>
+                        <has_text text="PC.636" />
+                        <has_text text="PC.354" />
+                        <has_text text="PC.634" />
+                    </assert_contents>
+                </element>
+                <element name="50_9">
+                    <assert_contents>
+                        <has_text text="PC.636" />
+                        <has_text text="PC.354" />
+                        <has_text text="PC.634" />
+                    </assert_contents>
+                </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+**What it does**
+
+This script performs alpha rarefaction in several steps:
+
+    - Generation of rarefied OTU tables
+    - Computation of alpha diversity metrics for each rarefied OTU table
+    - Concatenation of alpha diversity results
+    - Generation of alpha rarefaction plots
+
+More information about this tool is available on
+`QIIME documentation <http://qiime.org/scripts/alpha_rarefaction.html>`_.
+    ]]></help>
+    <citations>
+        <expand macro="citations"/>
+    </citations>
+</tool>