diff merge.count.xml @ 0:7ac8c7bfaab2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/merge.count.xml	Tue Mar 20 22:13:46 2018 -0400
@@ -0,0 +1,62 @@
+<tool profile="16.07" id="mothur_merge_count" name="Merge.count" version="@WRAPPER_VERSION@.0">
+    <description>Merge count tables</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.count(
+    count=#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="mothur.count_table" multiple="true" label="input - count tables to merge"/>
+        <expand macro="param-savelog"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="output" format="mothur.count_table" label="${tool.name} on ${on_string}: merged count table"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" value="stool_small.count_table,amazon.count_table"/>
+            <output name="output" ftype="mothur.count_table">
+                <assert_contents>
+                    <expand macro="test-count-format"/>
+                    <has_text text="U68630"/>
+                    <has_text text="F11Fcsw_12747"/>
+                </assert_contents>
+            </output>
+            <param name="savelog" value="true"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+.. _Mothur: https://www.mothur.org/wiki/Main_Page
+
+**Command Documentation**
+
+The merge.count_ command merges count files into a single count table.
+
+.. _merge.count: https://www.mothur.org/wiki/Merge.count
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>