diff merge.sfffiles.xml @ 0:e7f1da3e0339 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/merge.sfffiles.xml	Fri May 19 05:15:22 2017 -0400
@@ -0,0 +1,60 @@
+<tool profile="16.07" id="mothur_merge_sfffiles" name="Merge.sfffiles" version="@WRAPPER_VERSION@.0">
+    <description>Merge SFF files</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
+        #for $i in $input:
+            ln -s "$i" input${input.index($i)}.dat &&
+        #end for
+
+        echo 'merge.sfffiles(
+            sff=#for $i in $input#input${input.index($i)}.dat-#end for#,
+            output=$output
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | sed 's/-,/,/g'
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="sff" multiple="true" label="input - sff files to merge"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="output" format="sff" label="${tool.name} on ${on_string}: merged sff"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="Fasting_Example1.sff,Fasting_Example2.sff"/>
+            <output name="output" ftype="sff">
+                <assert_contents>
+                    <has_text text="FLP3FBN01ELBSX"/>
+                </assert_contents>
+            </output>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+.. _Mothur: https://www.mothur.org/wiki/Main_Page
+
+**Command Documentation**
+
+The merge.sfffiles_ command merge inputs into a single output.
+
+.. _merge.sfffiles: https://www.mothur.org/wiki/Merge.sfffiles
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>