diff clearcut.xml @ 0:f979130469f4 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/clearcut.xml	Fri May 19 05:48:09 2017 -0400
@@ -0,0 +1,131 @@
+<tool profile="16.07" id="mothur_clearcut" name="Clearcut" version="@WRAPPER_VERSION@.0">
+    <description>Generate a tree using relaxed neighbor joining</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 "$input.infile" input.infile.dat &&
+
+        echo 'clearcut(
+            #if $input.source == "dna":
+                fasta=input.infile.dat,
+                DNA=true,
+            #elif $input.source == "aa":
+                fasta=input.infile.dat,
+                protein=true,
+            #elif $input.source == "phylip":
+                phylip=input.infile.dat,
+            #end if
+            #if $matrixout == "true":
+                matrixout=matrixout.dist,
+            #end if
+            #if $seed:
+                seed=$seed,
+            #end if
+            ntrees=$ntrees,
+            norandom=$norandom,
+            shuffle=$shuffle,
+            expblen=$expblen,
+            expdist=$expdist,
+            neighbor=$neighbor
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur
+        | tee mothur.out.log
+    ]]></command>
+    <inputs>
+        <conditional name="input">
+            <param name="source" type="select" label="Distance Matrix">
+                <option value="dna">DNA Alignment Fasta</option>
+                <option value="aa">Protein Alignment Fasta</option>
+                <option value="phylip">Phylip Distance Matrix</option>
+            </param>
+            <when value="dna">
+                <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
+            </when>
+            <when value="aa">
+                <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
+            </when>
+            <when value="phylip">
+                <param name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
+            </when>
+        </conditional>
+        <param name="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/>
+        <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (default 1)"/>
+        <param name="norandom" type="boolean" checked="false" truevalue="true" falsevalue="false" label="norandom - Attempt joins deterministically"/>
+        <param name="shuffle" type="boolean" checked="false" truevalue="true" falsevalue="false" label="shuffle - Randomly shuffle the distance matrix"/>
+        <param name="neighbor" type="boolean" checked="true" truevalue="true" falsevalue="false" label="neighbor - Use traditional Neighbor-Joining algorithm"/>
+        <param name="expblen" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expblen - Use exponential notation for branch lengths"/>
+        <param name="expdist" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expdist - Use exponential notation for distance"/>
+        <param name="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/>
+    </inputs>
+    <outputs>
+        <expand macro="logfile-output"/>
+        <data name="tree" format="tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/>
+        <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix">
+            <filter>matrixout</filter>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test with phylip and default params-->
+            <param name="source" value="phylip"/>
+            <param name="infile" value="env.dist"/>
+            <output name="tree" md5="9c78d54267a985c8ae37dcfbddf6f8d0"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with phylip and params set-->
+            <param name="source" value="phylip"/>
+            <param name="infile" value="env.dist"/>
+            <param name="ntrees" value="3"/>
+            <param name="shuffle" value="true"/>
+            <param name="norandom" value="true"/>
+            <param name="neighbor" value="false"/>
+            <param name="expblen" value="ON"/>
+            <param name="expdist" value="ON"/>
+            <param name="matrixout" value="true"/>
+            <output name="tree" >
+                <assert_contents>
+                    <has_text text="group"/>
+                </assert_contents>
+            </output>
+            <output name="matrix" md5="ebc0c296d46cbe4b8d50780b9f5f8314" ftype="mothur.lower.dist"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with fasta (dna) and matrixout-->
+            <param name="source" value="dna"/>
+            <param name="infile" value="amazon.align_head"/>
+            <param name="matrixout" value="true"/>
+            <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/>
+            <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documentation**
+
+The clearcut_ command runs clearcut
+
+The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/
+
+Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ).
+
+Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input.  If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura).  Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix.
+
+.. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
+.. _clearcut: https://www.mothur.org/wiki/Clearcut
+
+v.1.20.0: Trivial upgrade to Mothur 1.33
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>