Mercurial > repos > iuc > mothur_clearcut

annotate clearcut.xml @ 0:0c5468e0d272 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:39:06 -0400
parents
children eedf2aef456a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_clearcut" name="Clearcut" version="@WRAPPER_VERSION@.0">
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Generate a tree using relaxed neighbor joining</description>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <command detect_errors="aggressive"><![CDATA[
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$input.infile" input.infile.dat &&
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 echo 'clearcut(
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 #if $input.source == "dna":
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 fasta=input.infile.dat,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 DNA=true,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 #elif $input.source == "aa":
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 fasta=input.infile.dat,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 protein=true,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #elif $input.source == "phylip":
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 phylip=input.infile.dat,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #end if
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 #if $matrixout == "true":
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 matrixout=matrixout.dist,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #end if
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #if $seed:
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 seed=$seed,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #end if
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 ntrees=$ntrees,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 norandom=$norandom,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 shuffle=$shuffle,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 expblen=$expblen,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 expdist=$expdist,
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 neighbor=$neighbor
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 )'
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 | sed 's/ //g' ## mothur trips over whitespace
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 | mothur
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 ]]></command>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <inputs>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <conditional name="input">
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <param name="source" type="select" label="Distance Matrix">
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <option value="dna">DNA Alignment Fasta</option>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <option value="aa">Protein Alignment Fasta</option>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <option value="phylip">Phylip Distance Matrix</option>
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44 </param>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <when value="dna">
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
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47 </when>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <when value="aa">
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <param name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
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50 </when>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 <when value="phylip">
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 <param name="infile" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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53 </when>
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54 </conditional>
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55 <param name="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/>
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56 <param name="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (default 1)"/>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <param name="norandom" type="boolean" checked="false" truevalue="true" falsevalue="false" label="norandom - Attempt joins deterministically"/>
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58 <param name="shuffle" type="boolean" checked="false" truevalue="true" falsevalue="false" label="shuffle - Randomly shuffle the distance matrix"/>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <param name="neighbor" type="boolean" checked="true" truevalue="true" falsevalue="false" label="neighbor - Use traditional Neighbor-Joining algorithm"/>
0c5468e0d272 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <param name="expblen" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expblen - Use exponential notation for branch lengths"/>
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61 <param name="expdist" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expdist - Use exponential notation for distance"/>
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62 <param name="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/>
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63 </inputs>
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64 <outputs>
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65 <expand macro="logfile-output"/>
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66 <data name="tree" format="tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/>
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67 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix">
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68 <filter>matrixout</filter>
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69 </data>
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70 </outputs>
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71 <tests>
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72 <test><!-- test with phylip and default params-->
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73 <param name="source" value="phylip"/>
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74 <param name="infile" value="env.dist"/>
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75 <output name="tree" md5="9c78d54267a985c8ae37dcfbddf6f8d0"/>
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76 <expand macro="logfile-test"/>
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77 </test>
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78 <test><!-- test with phylip and params set-->
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79 <param name="source" value="phylip"/>
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80 <param name="infile" value="env.dist"/>
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81 <param name="ntrees" value="3"/>
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82 <param name="shuffle" value="true"/>
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83 <param name="norandom" value="true"/>
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84 <param name="neighbor" value="false"/>
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85 <param name="expblen" value="ON"/>
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86 <param name="expdist" value="ON"/>
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87 <param name="matrixout" value="true"/>
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88 <output name="tree" >
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89 <assert_contents>
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90 <has_text text="group"/>
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91 </assert_contents>
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92 </output>
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93 <output name="matrix" md5="ebc0c296d46cbe4b8d50780b9f5f8314" ftype="mothur.lower.dist"/>
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94 <expand macro="logfile-test"/>
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95 </test>
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96 <test><!-- test with fasta (dna) and matrixout-->
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97 <param name="source" value="dna"/>
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98 <param name="infile" value="amazon.align_head"/>
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99 <param name="matrixout" value="true"/>
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100 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/>
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101 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/>
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102 <expand macro="logfile-test"/>
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103 </test>
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104 </tests>
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105 <help>
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106 <![CDATA[
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107
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108 @MOTHUR_OVERVIEW@
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109
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110 **Command Documenation**
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111
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112 The clearcut_ command runs clearcut
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113
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114 The clearcut command allows mothur users to run the clearcut_program_ from within mothur. The clearcut program written by Initiative for Bioinformatics and Evolutionary Studies (IBEST) at the University of Idaho. For more information about clearcut please refer to http://bioinformatics.hungry.com/clearcut/
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115
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116 Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ).
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117
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118 Clearcut is capable of taking either a distance matrix or a multiple sequence alignment (MSA) as input. If necessary, Clearcut will compute corrected distances based on a configurable distance correction model (Jukes-Cantor or Kimura). Clearcut outputs a phylogenetic tree in Newick format and an optional corrected distance matrix.
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119
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120 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
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121 .. _clearcut: http://www.mothur.org/wiki/Clearcut
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122
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123 v.1.20.0: Trivial upgrade to Mothur 1.33
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124 ]]>
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125 </help>
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126 <expand macro="citations"/>
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127 </tool>