diff remove.dists.xml @ 0:741303a463c8 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/remove.dists.xml	Fri May 19 04:54:55 2017 -0400
@@ -0,0 +1,70 @@
+<tool profile="16.07" id="mothur_remove_dists" name="Remove.dists" version="@WRAPPER_VERSION@.0">
+    <description>Removes distances from a phylip or column file</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 "$accnos" accnos.dat &&
+        ln -s "$input.dist" input_dist.dat &&
+
+        echo 'remove.dists(
+            accnos=accnos.dat,
+            #if $input.source == "phylip":
+                phylip=input_dist.dat
+            #else
+                column=input_dist.dat
+            #end if
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name="source" type="select" label="Select input format">
+                <option value="column">Pairwise Column Distance Matrix</option>
+                <option value="phylip">Phylip Distance Matrix</option>
+            </param>
+            <when value="column">
+                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
+            </when>
+            <when value="phylip">
+                <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+            </when>
+        </conditional>
+        <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="pick_dist" format_source="dist" from_work_dir="input_dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="source" value="phylip"/>
+            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
+            <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
+            <output name="pick_dist" md5="ec444ddb897d21864a245e8645fcda33" ftype="mothur.square.dist"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file.
+
+.. _remove.dists: https://www.mothur.org/wiki/Remove.dists
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>