Mercurial > repos > iuc > mothur_clearcut

annotate clearcut.xml @ 4:b46eaad36375 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 283d5933cd945b7815b3da2ce45baa60d73e9746
author iuc
date Fri, 06 Apr 2018 04:11:06 -0400
parents 959bd3b9fa75
children 20e764494303
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f979130469f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_clearcut" name="Clearcut" version="@WRAPPER_VERSION@.0">
f979130469f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Generate a tree using relaxed neighbor joining</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
f979130469f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
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13 ln -s '$input.infile' input.infile.dat &&
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14
3
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15 echo 'clearcut(
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16 #if $input.source == "dna":
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17 fasta=input.infile.dat,
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18 DNA=true,
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19 #elif $input.source == "aa":
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20 fasta=input.infile.dat,
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21 protein=true,
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22 #elif $input.source == "phylip":
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23 phylip=input.infile.dat,
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24 #end if
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25 #if $matrixout == "true":
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26 matrixout=matrixout.dist,
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27 #end if
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28 #if $seed:
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29 seed=$seed,
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30 #end if
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31 ntrees=$ntrees,
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32 norandom=$norandom,
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33 shuffle=$shuffle,
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34 expblen=$expblen,
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35 expdist=$expdist,
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36 neighbor=$neighbor
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
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39 | mothur
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40 | tee mothur.out.log
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41 ]]></command>
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42 <inputs>
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43 <conditional name="input">
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44 <param name="source" type="select" label="Distance Matrix">
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45 <option value="dna">DNA Alignment Fasta</option>
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46 <option value="aa">Protein Alignment Fasta</option>
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47 <option value="phylip">Phylip Distance Matrix</option>
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48 </param>
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49 <when value="dna">
3
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50 <param argument="fasta" name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
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51 </when>
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52 <when value="aa">
3
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53 <param argument="fasta" name="infile" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
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54 </when>
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55 <when value="phylip">
3
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56 <param argument="phylip" name="infile" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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57 </when>
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58 </conditional>
3
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59 <param argument="seed" type="integer" value="" min="0" optional="true" label="seed - Set the PRNG seed to a specific value"/>
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60 <param argument="ntrees" type="integer" value="1" label="ntrees - the number of output trees you want clearcut to generate (default 1)"/>
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61 <param argument="norandom" type="boolean" checked="false" truevalue="true" falsevalue="false" label="norandom - Attempt joins deterministically"/>
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62 <param argument="shuffle" type="boolean" checked="false" truevalue="true" falsevalue="false" label="shuffle - Randomly shuffle the distance matrix"/>
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63 <param argument="neighbor" type="boolean" checked="true" truevalue="true" falsevalue="false" label="neighbor - Use traditional Neighbor-Joining algorithm"/>
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64 <param argument="expblen" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expblen - Use exponential notation for branch lengths"/>
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65 <param argument="expdist" type="boolean" checked="false" truevalue="ON" falsevalue="OFF" label="expdist - Use exponential notation for distance"/>
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66 <param argument="matrixout" type="boolean" checked="false" truevalue="true" falsevalue="false" label="matrixout - Generate a Distance Matrix"/>
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67 <expand macro="param-savelog"/>
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68 </inputs>
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69 <outputs>
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70 <expand macro="logfile-output"/>
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71 <data name="tree" format="mothur.tre" from_work_dir="input.infile.tre" label="${tool.name} on ${on_string}: tree"/>
0
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72 <data name="matrix" format="mothur.lower.dist" from_work_dir="matrixout.dist" label="${tool.name} on ${on_string}: Phylip Distance Matrix">
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73 <filter>matrixout</filter>
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74 </data>
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75 </outputs>
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76 <tests>
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77 <test><!-- test with phylip and default params-->
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78 <param name="source" value="phylip"/>
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79 <param name="infile" value="env.dist"/>
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80 <output name="tree" md5="9c78d54267a985c8ae37dcfbddf6f8d0"/>
3
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81 <param name="savelog" value="true"/>
0
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82 <expand macro="logfile-test"/>
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83 </test>
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84 <test><!-- test with phylip and params set-->
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85 <param name="source" value="phylip"/>
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86 <param name="infile" value="env.dist"/>
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87 <param name="ntrees" value="3"/>
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88 <param name="shuffle" value="true"/>
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89 <param name="norandom" value="true"/>
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90 <param name="neighbor" value="false"/>
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91 <param name="expblen" value="ON"/>
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92 <param name="expdist" value="ON"/>
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93 <param name="matrixout" value="true"/>
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94 <output name="tree" >
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95 <assert_contents>
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96 <has_text text="group"/>
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97 </assert_contents>
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98 </output>
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99 <output name="matrix" md5="ebc0c296d46cbe4b8d50780b9f5f8314" ftype="mothur.lower.dist"/>
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100 <param name="savelog" value="true"/>
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101 <expand macro="logfile-test"/>
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102 </test>
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103 <test><!-- test with fasta (dna) and matrixout-->
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104 <param name="source" value="dna"/>
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105 <param name="infile" value="amazon.align_head"/>
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106 <param name="matrixout" value="true"/>
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107 <output name="tree" md5="54ca5ad8aea6598f8ed03e0616b1b568"/>
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108 <output name="matrix" md5="1c9d7acbd2f1eaba31714cb659c521e8" ftype="mothur.lower.dist"/>
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109 <param name="savelog" value="true"/>
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110 <expand macro="logfile-test"/>
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111 </test>
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112 </tests>
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113 <help><![CDATA[
0
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114
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115 @MOTHUR_OVERVIEW@
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116
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117 **Command Documentation**
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118
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119 The clearcut_ command runs clearcut
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120
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121 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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122
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123 Clearcut is a stand-alone reference implementation of relaxed neighbor joining (RNJ).
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124
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125 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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126
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127 .. _clearcut_program: http://bioinformatics.hungry.com/clearcut/
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128 .. _clearcut: https://www.mothur.org/wiki/Clearcut
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129
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130 v.1.20.0: Trivial upgrade to Mothur 1.33
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131
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132 ]]></help>
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133 <expand macro="citations"/>
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134 </tool>