Mercurial > repos > iuc > mothur_sens_spec

annotate sens.spec.xml @ 10:03dd3c928d65 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 12:55:22 +0000
parents ddda05cfccb4
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78776d48bbad 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_sens_spec" name="Sens.spec" version="@WRAPPER_VERSION@.0">
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2 <description>Determine the quality of OTU assignment</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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03dd3c928d65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <expand macro="version_command"/>
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10 <command><![CDATA[
2
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11 @SHELL_OPTIONS@
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12
2
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13 ## create symlinks to input datasets
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14 ln -s '$otu' otu.dat &&
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15 ln -s '$matrix.dist' matrix.dist.dat &&
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16 #if str($matrix.method_name.method) == "count" :
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17 ln -s '$matrix.method_name.count' matrix.method_name.count.dat &&
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18 #else
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19 ln -s '$matrix.method_name.names' matrix.method_name.names.dat &&
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20 #end if
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21
0
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22
2
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23 echo 'sens.spec(
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24 list=otu.dat,
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25 #if str($matrix.format) == "phylip":
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26 phylip=matrix.dist.dat,
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27 #else
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28 column=matrix.dist.dat,
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29 #end if
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30 #if str($matrix.method_name.method) == "count" :
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31 count=matrix.method_name.count.dat,
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32 #else
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33 names=matrix.method_name.names.dat,
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34 #end if
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35 #if $label:
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36 label=${ str($label).replace(",","-") },
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37 #end if
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38 #if $label:
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39 label=${ str($label).replace(",","-") },
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40 #end if
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41 precision=$precision,
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42 cutoff=$cutoff
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43 )'
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44 | sed 's/ //g' ## mothur trips over whitespace
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45 | mothur
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46 | tee mothur.out.log
0
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47 ]]></command>
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48 <inputs>
2
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49 <conditional name="matrix">
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50 <param name="format" type="select" label="Select a Distance Matrix Format" help="">
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51 <option value="column">Pairwise Column Matrix </option>
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52 <option value="phylip">Phylip Distance Matrix</option>
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53 </param>
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54 <when value="column">
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55 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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56 <conditional name="method_name">
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57 <param name="method" type="select" label="Select a Method" help="">
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58 <option value="count">count file associated with your distance matrix.</option>
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59 <option value="name">name file associated with your distance matrix. </option>
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60 </param>
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61 <when value="count">
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62 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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63 </when>
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64 <when value="name">
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65 <param name="names" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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66 </when>
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67
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68 </conditional>
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69 </when>
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70 <when value="phylip">
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71 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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72 </when>
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73 </conditional>
0
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74 <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
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75 <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/>
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76 <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
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77 <options>
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78 <filter type="data_meta" ref="otu" key="labels"/>
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79 </options>
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80 </param>
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81 <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/>
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82 <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
2
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83 <expand macro="param-savelog"/>
0
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84 </inputs>
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85 <outputs>
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86 <expand macro="logfile-output"/>
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87 <data name="sensspec" format="tabular" from_work_dir="otu*.sensspec" label="${tool.name} on ${on_string}: sensspec"/>
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88 </outputs>
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89 <tests>
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90 <test>
2
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91 <param name="count" value="amazon.count_table"/>
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92 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
0
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93 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
2
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94 <output name="sensspec" md5="720789a7ef4da26928a61161279d7344" ftype="tabular"/>
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95 <param name="savelog" value="true"/>
0
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96 <expand macro="logfile-test"/>
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97 </test>
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98 <test>
2
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99 <param name="count" value="amazon.count_table"/>
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100 <param name="names" value="amazon.names"/>
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101 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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102 <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
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103 <param name="cutoff" value="0.10"/>
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104 <param name="label" value="0.03,0.05,0.22"/>
2
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105 <output name="sensspec" md5="3992dec1d799ec3a061b3ef713a58382" ftype="tabular"/>
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106 <param name="savelog" value="true"/>
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107 <expand macro="logfile-test"/>
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108 </test>
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109 </tests>
2
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110 <help><![CDATA[
0
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111
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112 @MOTHUR_OVERVIEW@
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113
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114 **Command Documentation**
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115
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116 The sens.spec_ command takes a list_ and either a column_ or phylip_ distance matrix to determine the quality of OTU assignment.
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117
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118
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119 .. _list: https://www.mothur.org/wiki/List_file
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120 .. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
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121 .. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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122 .. _sens.spec: https://www.mothur.org/wiki/Sens.spec
2
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123
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124 ]]></help>
5
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125 <expand macro="citations">
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126 <citation type="doi">10.1128/AEM.02810-10</citation>
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127 </expand>
0
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128 </tool>