diff macros.xml @ 0:fc3330ca7c70 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/macros.xml	Fri May 19 05:09:39 2017 -0400
@@ -0,0 +1,98 @@
+<macros>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="1.36.1">mothur</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>mothur "#help()" | sed '7q;d' | cut -d" " -f2 </version_command>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <regex match="\[ERROR\]" source="stdout" level="fatal"/>
+            <exit_code range="1:" level="fatal"/>
+        </stdio>
+    </xml>
+    <token name="@WRAPPER_VERSION@">1.36.1</token>
+    <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
+    <token name="@MOTHUR_OVERVIEW@">
+<![CDATA[
+
+**Mothur Overview**
+
+Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
+in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
+
+.. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
+
+]]>
+    </token>
+    <xml name="labeloptions">
+        <options>
+            <filter type="data_meta" ref="otu" key="labels"/>
+        </options>
+    </xml>
+    <xml name="calc-common">
+        <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first -->
+        <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
+        <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
+        <option value="canberra">canberra - Community Structure Similarity</option>
+        <option value="gower">gower - Community Structure Similarity</option>
+        <option value="hamming">hamming - Community Membership Similarity</option>
+        <option value="hellinger">hellinger - Community Structure Similarity</option>
+        <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
+        <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
+        <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
+        <option value="jsd">jsd</option>
+        <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
+        <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
+        <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
+        <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
+        <option value="manhattan">manhattan - Community Structure Similarity</option>
+        <option value="memchi2">memchi2 - Community Membership Similarity</option>
+        <option value="memchord">memchord - Community Membership Similarity</option>
+        <option value="memeuclidean">memeuclidean - Community Membership Similarity</option>
+        <option value="mempearson">mempearson - Community Membership Similarity</option>
+        <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
+        <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
+        <option value="odum">odum - Community Structure Similarity</option>
+        <option value="rjsd">rjsd</option>
+        <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
+        <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
+        <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
+        <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
+        <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
+        <option value="soergel">soergel - Community Structure Similarity</option>
+        <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
+        <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
+        <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
+        <option value="spearman">spearman - Community Structure Similarity</option>
+        <option value="speciesprofile">speciesprofile - Community Structure Similarity</option>
+        <option value="structchi2">structchi2 - Community Structure Similarity</option>
+        <option value="structchord">structchord - Community Structure Similarity</option>
+        <option value="structeuclidean">structeuclidean - Community Structure Similarity</option>
+        <option value="structkulczynski">structkulczynski - Community Structure Similarity</option>
+        <option value="structpearson">structpearson - Community Structure Similarity</option>
+        <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
+        <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
+        <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
+        <yield/>
+    </xml>
+    <xml name="logfile-output">
+        <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile"/>
+    </xml>
+    <xml name="logfile-test">
+        <output name="logfile" ftype="txt">
+            <assert_contents>
+                <has_text text="mothur"/>
+                <has_text text="@WRAPPER_VERSION@"/>
+            </assert_contents>
+        </output>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1128/AEM.01541-09</citation>
+            <yield/>
+        </citations>
+    </xml>
+</macros>