Mercurial > repos > iuc > mothur_dist_seqs
diff dist.seqs.xml @ 0:d103727775eb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author | iuc |
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date | Fri, 19 May 2017 04:59:45 -0400 |
parents | |
children | 189b742d2434 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dist.seqs.xml Fri May 19 04:59:45 2017 -0400 @@ -0,0 +1,92 @@ +<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="stdio"/> + <expand macro="version_command"/> + <command><![CDATA[ + @SHELL_OPTIONS@ + + ## create symlinks to input datasets + ln -s "$fasta" fasta.dat && + + echo 'dist.seqs( + fasta=fasta.dat, + #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 + | tee mothur.out.log + ]]></command> + <inputs> + <param name="fasta" type="data" format="mothur.align,fasta" 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> + <expand macro="logfile-output"/> + <data name="out_dist" format="mothur.pair.dist" from_work_dir="fasta*.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 Documentation** + +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: https://www.mothur.org/wiki/Column-formatted_distance_matrix +.. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix +.. _dist.seqs: https://www.mothur.org/wiki/Dist.seqs + +v.1.20.0: Updated to Mothur 1.33 + +]]> + </help> + <expand macro="citations"/> +</tool>