Mercurial > repos > iuc > mothur_dist_shared

annotate dist.shared.xml @ 9:f25598da7174 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 23:35:25 +0000
parents b7da1494afa1
children 418100660ba3
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1 <tool profile="16.07" id="mothur_dist_shared" name="Dist.shared" version="@WRAPPER_VERSION@.0">
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2 <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</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="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14
2
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15 echo 'dist.shared(
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16 shared=otu.dat,
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17 #if $label:
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18 label=${ str($label).replace(",","-") },
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19 #end if
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20 #if $groups:
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21 groups=${ str($groups).replace(",","-") },
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22 #end if
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23 #if $calc:
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24 calc=${ str($calc).replace(",","-") },
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25 #end if
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26 #if $subsampling.use == "yes":
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27 #if $subsampling.subsample:
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28 subsample=$subsampling.subsample,
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29 #else
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30 subsample=T,
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31 #end if
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32 iters=$subsampling.iters,
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33 #end if
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34 output=$output,
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35 processors='\${GALAXY_SLOTS:-8}'
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36 )'
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37 | sed 's/ //g' ## mothur trips over whitespace
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38 | mothur
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39 | tee mothur.out.log
0
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40 ]]></command>
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41 <inputs>
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42 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
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43 <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true">
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44 <expand macro="labeloptions"/>
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45 </param>
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46 <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
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47 <options>
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48 <filter type="data_meta" ref="otu" key="groups"/>
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49 </options>
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50 </param>
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51 <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
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52 <expand macro="calc-common"/>
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53 <!-- set default option(s) -->
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54 <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
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55 <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
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56 </param>
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57 <conditional name="subsampling">
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58 <param name="use" type="select" label="subsample">
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59 <option value="no" selected="true">no</option>
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60 <option value="yes">yes</option>
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61 </param>
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62 <when value="yes">
2
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63 <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)"
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64 help="Should not exceed the number of sequences in any group"/>
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65 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
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66 </when>
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67 <when value="no"/>
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68 </conditional>
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69 <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair">
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70 <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
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71 <option value="square">Phylip formatted Square Matrix</option>
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72 </param>
2
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73 <expand macro="param-savelog"/>
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74 </inputs>
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75 <outputs>
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76 <expand macro="logfile-output"/>
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77 <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files">
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78 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist"/>
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79 </collection>
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80 </outputs>
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81 <tests>
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82 <test><!-- test with defaults -->
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83 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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84 <output_collection name="distfiles" count="72">
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85 <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/>
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86 </output_collection>
2
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87 <param name="savelog" value="true"/>
0
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88 <expand macro="logfile-test"/>
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89 </test>
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90 <test><!-- test with label,group select and all calculators -->
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91 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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92 <param name="label" value="0.05,0.22"/>
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93 <param name="groups" value="forest,pasture"/>
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94 <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structeuclidean,structpearson,sharednseqs,sharedobserved"/>
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95 <output_collection name="distfiles" count="74">
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96 <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
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97 </output_collection>
2
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98 <param name="savelog" value="true"/>
0
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99 <expand macro="logfile-test"/>
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100 </test>
2
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101 <test><!-- test with subsampling without specifying size -->
0
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102 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
2
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103 <param name="label" value="0.03,0.33"/>
0
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104 <param name="use" value="yes"/>
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105 <param name="calc" value="canberra"/>
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106 <param name="output" value="square"/>
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107 <output_collection name="distfiles" count="6">
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108 <element name="canberra.0.33.square.std" ftype="mothur.dist">
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109 <assert_contents>
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110 <has_text text="forest"/>
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111 <has_text text="pasture"/>
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112 </assert_contents>
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113 </element>
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114 </output_collection>
2
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115 <param name="savelog" value="true"/>
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116 <expand macro="logfile-test"/>
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117 </test>
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118 <test><!-- test with subsampling with specifying size-->
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119 <param name="otu" value="amazon.mothur.shared" ftype="mothur.shared"/>
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120 <param name="use" value="yes"/>
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121 <param name="subsample" value="2"/>
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122 <param name="iters" value="42"/>
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123 <param name="label" value="0.10"/>
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124 <param name="calc" value="canberra"/>
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125 <param name="output" value="square"/>
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126 <output_collection name="distfiles" count="3">
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127 <element name="canberra.0.10.square.std" ftype="mothur.dist">
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128 <assert_contents>
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129 <has_text text="forest"/>
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130 <has_text text="pasture"/>
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131 </assert_contents>
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132 </element>
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133 </output_collection>
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134 <param name="savelog" value="true"/>
0
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135 <expand macro="logfile-test"/>
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136 </test>
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137 </tests>
2
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138 <help><![CDATA[
0
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139
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140 @MOTHUR_OVERVIEW@
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141
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142 **Command Documentation**
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143
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144 The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
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145
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146 .. _phylip-formatted_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
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147 .. _shared: https://www.mothur.org/wiki/Shared_file
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148 .. _dist.shared: https://www.mothur.org/wiki/Dist.shared
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149
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150 v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.
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151
2
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152 ]]></help>
0
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153 <expand macro="citations"/>
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154 </tool>