diff parse.list.xml @ 0:14062c54b6f6 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/parse.list.xml	Fri May 19 05:46:37 2017 -0400
@@ -0,0 +1,79 @@
+<tool profile="16.07" id="mothur_parse_list" name="Parse.list" version="@WRAPPER_VERSION@.0">
+    <description>Generate a List file for each group</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 "$otu" otu.dat &&
+        ln -s "$group" group.dat &&
+        ln -s "$count" count.dat &&
+
+        echo 'parse.list(
+            list=otu.dat,
+            #if $label:
+                label=${ str($label).replace(",","-") },
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            group=group.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
+        <param name="group" type="data" format="mothur.groups" label="group - Sequences Name reference"/>
+        <param name="label" type="select" optional="true" multiple="true" label="label - To filter: Select OTU Labels to include">
+            <expand macro="labeloptions"/>
+        </param>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="listfiles" type="list" label="${tool.name} on ${on_string}: listfiles per group and label">
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.list" format="mothur.list"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="otu" value="amazon.an.list"/>
+            <param name="group" value="amazon.groups"/>
+            <output_collection name="listfiles" count="72">
+                <element name="pasture.0.21" md5="5c803fd0f0e1de69c51048e02bc02e65" ftype="mothur.list"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+        <test>
+            <param name="otu" value="amazon.an.list"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <param name="label" value="0.03,0.05"/>
+            <output_collection name="listfiles" count="4"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile.
+
+.. _list: https://www.mothur.org/wiki/List_file
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _parse.list: https://www.mothur.org/wiki/Parse.list
+
+v.1.19.0: Updated to mothur 1.33, added count parameter
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>