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

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author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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1 <tool profile="16.07" id="mothur_dist_seqs" name="Dist.seqs" version="@WRAPPER_VERSION@.0">
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2 <description>calculate uncorrected pairwise distances between aligned sequences</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 echo 'dist.seqs(
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10 fasta=$fasta,
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11 #if $calc:
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12 calc=$calc,
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13 #end if
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14 countends=$countends,
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15 #if $cutoff:
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16 cutoff=$cutoff,
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17 #end if
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18 #if $output:
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19 output=$output,
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20 #end if
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21 processors='\${GALAXY_SLOTS:-8}'
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22 )'
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23 | sed 's/ //g' ## mothur trips over whitespace
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24 | mothur &&
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25
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26 ## move output files to correct destination
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27 prefix="$fasta" &&
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28 mv \${prefix%.dat}*.dist "$out_dist" &&
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29 mv mothur.*.logfile "$logfile"
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30 ]]></command>
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31 <inputs>
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32 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
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33 <param name="calc" type="select" label="calc - Calc Method - Gap Penality">
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34 <option value="" selected="true">use default</option>
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35 <option value="onegap">onegap - counts a string of gaps as a single gap</option>
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36 <option value="nogaps">nogaps - ignores gaps</option>
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37 <option value="eachgap ">eachgap - penalize each gap</option>
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38 </param>
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39 <param name="countends" type="boolean" checked="true" truevalue="true" falsevalue="false" label="countends - Penalize terminal gaps"/>
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40 <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"/>
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41 <param name="output" type="select" label="output - Distance Matrix Output Format" help="">
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42 <option value="" selected="true">Default Column-Formatted Matrix</option>
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43 <option value="lt">Phylip formatted Lower Triangle Matrix</option>
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44 <option value="square">Phylip formatted Square Matrix</option>
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45 </param>
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46 </inputs>
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47 <outputs>
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48 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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49 <data name="out_dist" format="mothur.pair.dist" label="${tool.name} on ${on_string}: dist">
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50 <change_format>
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51 <when input="output" value="lt" format="mothur.lower.dist"/>
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52 <when input="output" value="square" format="mothur.square.dist"/>
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53 </change_format>
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54 </data>
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55 </outputs>
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56 <tests>
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57 <test><!-- test with default params -->
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58 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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59 <output name="out_dist" md5="2c4817bb8657b4df2dcb1f2a019f505e" ftype="mothur.pair.dist"/>
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60 <expand macro="logfile-test"/>
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61 </test>
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62 <test><!-- test with all params custom -->
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63 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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64 <param name="calc" value="nogaps"/>
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65 <param name="countends" value="false"/>
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66 <param name="cutoff" value="0.3"/>
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67 <param name="output" value="lt"/>
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68 <output name="out_dist" md5="8a5ccf1ad8f1c344cf4d3e2c97d4cdc6" ftype="mothur.lower.dist"/>
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69 <expand macro="logfile-test"/>
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70 </test>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74
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75 @MOTHUR_OVERVIEW@
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76
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77 **Command Documenation**
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78
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79 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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80
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81 .. _column-formatted_distance_matrix: http://www.mothur.org/wiki/Column-formatted_distance_matrix
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82 .. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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83 .. _dist.seqs: http://www.mothur.org/wiki/Dist.seqs
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84
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85 v.1.20.0: Updated to Mothur 1.33
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86
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87 ]]>
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88 </help>
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89 <expand macro="citations"/>
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90 </tool>