diff tools/mothur/dist.seqs.xml @ 0:ee4fee239fe7 draft default tip

planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mothur/dist.seqs.xml	Fri Jun 03 09:32:47 2016 -0400
@@ -0,0 +1,90 @@
+<tool profile="16.07" id="mothur_dist_seqs" name="Dist.seqs" version="@WRAPPER_VERSION@.0">
+    <description>calculate uncorrected pairwise distances between aligned sequences</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <expand macro="version_command"/>
+    <command detect_errors="aggressive"><![CDATA[
+        echo 'dist.seqs(
+            fasta=$fasta,
+            #if $calc:
+                calc=$calc,
+            #end if
+            countends=$countends,
+            #if $cutoff:
+                cutoff=$cutoff,
+            #end if
+            #if $output:
+                output=$output,
+            #end if
+            processors='\${GALAXY_SLOTS:-8}'
+        )'
+        | sed 's/ //g'  ## mothur trips over whitespace
+        | mothur &&
+
+        ## move output files to correct destination
+        prefix="$fasta" &&
+        mv \${prefix%.dat}*.dist "$out_dist" &&
+        mv mothur.*.logfile "$logfile"
+    ]]></command>
+    <inputs>
+        <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
+        <param name="calc" type="select" label="calc - Calc Method - Gap Penality">
+            <option value="" selected="true">use default</option>
+            <option value="onegap">onegap - counts a string of gaps as a single gap</option>
+            <option value="nogaps">nogaps - ignores gaps</option>
+            <option value="eachgap ">eachgap - penalize each gap</option>
+        </param>
+        <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/>
+        <param name="cutoff" type="float" value="" min="0.0" optional="true" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Do not save any distances larger than this, a common value would be 0.10"/>
+        <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
+            <option value="" selected="true">Default Column-Formatted Matrix</option>
+            <option value="lt">Phylip formatted Lower Triangle Matrix</option>
+            <option value="square">Phylip formatted Square Matrix</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
+        <data name="out_dist" format="mothur.pair.dist" label="${tool.name} on ${on_string}: dist">
+            <change_format>
+                <when input="output" value="lt" format="mothur.lower.dist"/>
+                <when input="output" value="square" format="mothur.square.dist"/>
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test><!-- test with default params -->
+            <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
+            <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/>
+            <expand macro="logfile-test"/>
+        </test>
+        <test><!-- test with all params custom -->
+            <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
+            <param name="calc" value="nogaps"/>
+            <param name="countends" value="false"/>
+            <param name="cutoff" value="0.3"/>
+            <param name="output" value="lt"/>
+            <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/>
+            <expand macro="logfile-test"/>
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+@MOTHUR_OVERVIEW@
+
+**Command Documenation**
+
+The dist.seqs_ command will calculate uncorrected pairwise distances between aligned sequences.  The command will generate a column-formatted_distance_matrix_ that is compatible with the column option in the read.dist command. The command is also able to generate a phylip-formatted_distance_matrix_. There are several options for how to handle gap comparisons and terminal gaps.
+
+.. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
+.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
+.. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs
+
+v.1.20.0: Updated to Mothur 1.33
+
+]]>
+    </help>
+    <expand macro="citations"/>
+</tool>