Mercurial > repos > iuc > mothur_make_files

diff make.group.xml @ 0:d6b4ae743405 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author: iuc
date: Fri, 24 Jun 2016 16:38:05 -0400
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/make.group.xml	Fri Jun 24 16:38:05 2016 -0400
@@ -0,0 +1,61 @@
+<tool profile="16.07" id="mothur_make_files" name="Make.group" version="@WRAPPER_VERSION@.0">
+    <description>Make a group file</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        ## create symlinks to input datasets
+        ln -s "$fasta" fasta.dat &&
+        #for $i in $inputs:
+            ln -s "$i.fasta" fasta${inputs.index($i)}.dat &&
+        #end for
+
+        echo 'make.group(
+            fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
+            groups=${group}#for $i in $inputs#-${i.group}#end for#
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
+        <param name="group" type="text" label="group - Group name"/>
+        <repeat name="inputs" title="Additional">
+            <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
+            <param name="group" type="text" label="group - Group name"/>
+        </repeat>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="output" format="mothur.groups" from_work_dir="fasta*groups" label="${tool.name} on ${on_string}: group"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+            <param name="group" value="testgroup"/>
+            <repeat name="inputs">
+                <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
+                <param name="group" value="testgroup2"/>
+            </repeat>
+            <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The make.group_ command reads a fasta file or series of fasta files and creates a group_ file.
+
+.. _group: http://www.mothur.org/wiki/Group_file
+.. _make.group: http://www.mothur.org/wiki/Make.group
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>