Mercurial > repos > sanbi-uwc > mothur_test
diff tools/mothur/pairwise.seqs.xml @ 0:ee4fee239fe7 draft default tip
planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
| author | sanbi-uwc |
|---|---|
| date | Fri, 03 Jun 2016 09:32:47 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mothur/pairwise.seqs.xml Fri Jun 03 09:32:47 2016 -0400 @@ -0,0 +1,127 @@ +<tool profile="16.07" id="mothur_pairwise_seqs" name="Pairwise.seqs" version="@WRAPPER_VERSION@.0"> + <description>calculate uncorrected pairwise distances between sequences</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="version_command"/> + <command detect_errors="aggressive"><![CDATA[ + echo 'pairwise.seqs( + fasta=$fasta, + align=$align, + #if $calc: + calc=$calc, + #end if + $countends + #if float($cutoff) > 0.0: + cutoff=$cutoff, + #end if + #if $scoring.setby == "user": + match=$scoring.match, + mismatch=$scoring.mismatch, + gapopen=$scoring.gapopen, + gapextend=$scoring.gapextend, + #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="$fasta" && + mv mothur.*.logfile "$logfile" && + mv \${prefix%.dat}*.dist "$out_dist" + ]]></command> + <inputs> + <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> + <param name="align" type="select" label="align - Select a pairwise alignment method" help=""> + <option value="needleman" selected="true">needleman (default)</option> + <option value="gotoh">gotoh</option> + <option value="blast">blast</option> + </param> + <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help=""> + <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="" falsevalue="countends=false," label="countends - Countends" help="Penalize terminal gaps"/> + <param name="cutoff" type="float" value="0.0" min="0" 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"/> + <conditional name="scoring"> + <param name="setby" type="select" label="Scoring match, mismatch, gapopen, and gapextend" help=""> + <option value="default" selecte="true">Use default settings</option> + <option value="user">Manually set scoring values</option> + </param> + <when value="default"/> + <when value="user"> + <param name="match" type="integer" value="1" label="match - Pairwise alignment reward for a match"/> + <param name="mismatch" type="integer" value="-1" label="mismatch - Pairwise alignment penalty for a mismatch"/> + <param name="gapopen" type="integer" value="-2" label="gapopen - Pairwise alignment penalty for opening a gap"/> + <param name="gapextend" type="integer" value="-1" label="gapextend - Pairwise alignment penalty for extending a gap"/> + </when> + </conditional> + <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> + <option value="" selected="true">Column-Formatted Matrix (Default)</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> + <param name="fasta" value="amazon.unique.fasta"/> + <param name="align" value="needleman"/> + <param name="calc" value=""/> + <param name="countends" value=""/> + <param name="cutoff" value="0.0"/> + <param name="setby" value="default"/> + <param name="output" value=""/> + <expand macro="logfile-test"/> + <output name="out_dist" md5="bb2fefcda217604cd0e985f676168379"/> + </test> + <test> + <param name="fasta" value="amazon.unique.fasta"/> + <param name="align" value="gotoh"/> + <param name="calc" value="onegap"/> + <param name="countends" value="countends=false,"/> + <param name="cutoff" value="0.01"/> + <param name="setby" value="user"/> + <param name="match" value="2"/> + <param name="mismatch" value="-1"/> + <param name="gapopen" value="-2"/> + <param name="gapextend" value="-1"/> + <param name="output" value="lt"/> + <expand macro="logfile-test"/> + <output name="out_dist" md5="945c494bee1700c7f9a4ce5d87355190"/> + </test> + </tests> + <help> +<![CDATA[ + +@MOTHUR_OVERVIEW@ + +.. _Mothur: http://www.mothur.org/wiki/Main_Page + +**Command Documenation** + +The pairwise.seqs_ command will calculate uncorrected pairwise distances between sequencesi as a column-formatted_distance_matrix_ or phylip-formatted_distance_matrix_. + +.. _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 +.. _pairwise.seqs: http://www.mothur.org/wiki/Pairwise.seqs + +]]> + </help> + <expand macro="citations"/> +</tool>