diff split.groups.xml @ 0:dba66f208b1a 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/split.groups.xml	Fri May 19 05:18:43 2017 -0400
@@ -0,0 +1,79 @@
+<tool profile="16.07" id="mothur_split_groups" name="Split.groups" version="@WRAPPER_VERSION@.0">
+    <description>Generates a fasta 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 "$name" name.dat &&
+        ln -s "$count" count.dat &&
+        ln -s "$fasta" fasta.dat &&
+        ln -s "$group" group.dat &&
+
+        echo 'split.groups(
+            #if $name:
+                name=name.dat,
+            #end if
+            #if $groups:
+                groups=${ str($groups).replace(",","-") },
+            #end if
+            #if $count:
+                count=count.dat,
+            #end if
+            fasta=fasta.dat,
+            group=group.dat
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
+        <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
+        <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
+        <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
+            <options>
+                <filter type="data_meta" ref="group" key="groups"/>
+            </options>
+        </param>
+        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <collection name="groupfastas" type="list" label="${tool.name} on ${on_string}: fasta per group">
+            <!-- TODO: format_source on discovered collection elements doesn't seem to work yet, change to format_source="fasta" once it does -->
+            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="amazon.fasta" ftype="fasta"/>
+            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
+            <output_collection name="groupfastas" count="2">
+                <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
+                <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
+            </output_collection>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile.  A name_ file can also be split into groups.
+
+.. _group: https://www.mothur.org/wiki/Group_file
+.. _name: https://www.mothur.org/wiki/Name_file
+.. _split.groups: https://www.mothur.org/wiki/Split.groups
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>