diff get.coremicrobiome.xml @ 0:fb34c63ab676 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/get.coremicrobiome.xml	Fri May 19 05:55:47 2017 -0400
@@ -0,0 +1,103 @@
+<tool profile="16.07" id="mothur_get_coremicrobiome" name="Get.coremicrobiome" version="@WRAPPER_VERSION@.0">
+    <description>fraction of OTUs for samples or abundances</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 &&
+
+        echo 'get.coremicrobiome(
+            #if $otu.is_of_type("mothur.relabund"):
+                relabund=otu.dat
+            #elif $otu.is_of_type("mothur.shared"):
+                shared=otu.dat
+            #end if
+            #if $label:
+                ,label=${ str($label).replace(",","-") }
+            #end if
+            #if $groups:
+                ,groups=${ str($groups).replace(",","-") }
+            #end if
+            #if $abundance:
+                ,abundance=$abundance
+            #end if
+            #if $samples:
+                ,samples=$samples
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
+        <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="groups" type="select" optional="true" label="groups - Pairwise comparision groups" multiple="true">
+            <options>
+                <filter type="data_meta" ref="otu" key="groups"/>
+            </options>
+        </param>
+        <param name="abundance" type="integer" optional="true" value="" min="0" max="100" label="abundance - list OTU names at this abundance"/>
+        <param name="samples" type="integer" optional="true" value="" min="1" label="samples - minimum number of samples requied to list OTU names"/>
+        <param name="output" type="select" label="output - fraction or count">
+            <option value="fraction" selected="true">fraction</option>
+            <option value="count">count</option>
+        </param>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="core_microbiome" type="list" label="${tool.name} on ${on_string}: core.microbiome files">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiome$" format="tabular"/>
+        </collection>
+        <collection name="core_microbiome_list" type="list" label="${tool.name} on ${on_string}: core.microbiome list files">
+            <filter>abundance or samples </filter>
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiomelist" format="tabular"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test><!-- test with default params -->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <output_collection name="core_microbiome" count="36">
+                <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with list output and label and group select-->
+            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
+            <param name="abundance" value="30"/>
+            <param name="label" value="0.05,0.22,0.45"/>
+            <param name="group" value="forest,pasture"/>
+            <output_collection name="core_microbiome" count="3">
+                <element name="0.05" md5="72bb437ab5f3a66965029a616fbaf317" ftype="tabular"/>
+            </output_collection>
+            <output_collection name="core_microbiome_list" count="3">
+                <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.
+
+.. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome
+
+v1.27.0: Updated to Mothur 1.33
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>