Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/dist.seqs.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 04 Dec 2012 11:05:19 -0600 |
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1 <tool id="mothur_dist_seqs" name="Dist.seqs" version="1.19.0"> |
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2 <description>calculate uncorrected pairwise distances between aligned sequences</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='dist.seqs' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.dist$:'$out_dist |
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7 --outputdir='$logfile.extra_files_path' |
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8 --fasta=$fasta |
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9 #if len($calc.__str__) > 0: |
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10 --calc=$calc |
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11 #end if |
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12 $countends |
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13 #if float($cutoff.__str__) > 0.0: |
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14 --cutoff=$cutoff |
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15 #end if |
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16 #if len($output.__str__) > 0: |
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17 --output=$output |
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18 #end if |
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19 --processors=8 |
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20 </command> |
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21 <inputs> |
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22 <param name="fasta" type="data" format="align" label="fasta - Alignment Fasta"/> |
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23 <param name="calc" type="select" label="calc - Calc Method - Gap Penality" help=""> |
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24 <option value="">use default</option> |
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25 <option value="onegap">onegap - counts a string of gaps as a single gap</option> |
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26 <option value="nogaps">nogaps - ignores gaps</option> |
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27 <option value="eachgap ">eachgap - penalize each gap</option> |
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28 </param> |
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29 <param name="countends" type="boolean" checked="true" truevalue="" falsevalue="--countends=false" label="countends - Penalize terminal gaps"/> |
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30 <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" |
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31 help="Do not save any distances larger than this, a common value would be 0.10"/> |
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32 <param name="output" type="select" label="output - Distance Matrix Output Format" help=""> |
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33 <option value="">Default Column-Formatted Matrix</option> |
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34 <option value="lt">Phylip formatted Lower Triangle Matrix</option> |
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35 <option value="square">Phylip formatted Square Matrix</option> |
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36 </param> |
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37 <!-- |
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38 oldfasta |
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39 column |
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40 --> |
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41 </inputs> |
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42 <outputs> |
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43 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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44 <data format="pair.dist" name="out_dist" label="${tool.name} on ${on_string}: dist"> |
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45 <change_format> |
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46 <when input="output" value="lt" format="lower.dist" /> |
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47 <when input="output" value="square" format="square.dist" /> |
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48 </change_format> |
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49 </data> |
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50 </outputs> |
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51 <requirements> |
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52 <requirement type="package" version="1.27">mothur</requirement> |
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53 </requirements> |
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54 <tests> |
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55 </tests> |
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56 <help> |
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57 **Mothur Overview** |
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58 |
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59 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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60 in the Department of Microbiology and Immunology at The University of Michigan, |
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61 provides bioinformatics for the microbial ecology community. |
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62 |
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63 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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64 |
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65 **Command Documenation** |
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66 |
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67 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. |
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68 |
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69 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix |
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70 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix |
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71 .. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs |
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72 |
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73 |
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74 </help> |
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75 </tool> |