Mercurial > repos > iuc > mothur_phylo_diversity

annotate macros.xml @ 7:c7d41770f4ce draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author iuc
date Mon, 02 Dec 2019 05:22:45 -0500
parents 3868f54b097e
children ef55ccbfb725
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917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <macros>
2
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2 <token name="@WRAPPER_VERSION@">1.39.5</token>
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3 <xml name="requirements">
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <requirements>
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5 <requirement type="package" version="@WRAPPER_VERSION@">mothur</requirement>
292c7c4d2789 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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6 <yield/>
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7 </requirements>
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 </xml>
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9 <xml name="version_command">
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10 <version_command><![CDATA[ mothur "#help()" | sed '7q;d' | cut -d" " -f2 ]]></version_command>
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11 </xml>
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 <xml name="stdio">
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13 <stdio>
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 <regex match="\[ERROR\]" source="stdout" level="fatal"/>
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 <exit_code range="1:" level="fatal"/>
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 </stdio>
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17 </xml>
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18 <token name="@SHELL_OPTIONS@">set -o pipefail;</token>
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19
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20
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21 <!-- Input parameters -->
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22 <xml name="labeloptions">
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23 <options>
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24 <filter type="data_meta" ref="otu" key="labels"/>
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25 </options>
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26 </xml>
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27 <xml name="calc-common">
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28 <!-- you can set defaults in tool xml by repeating those options again after macro expand, overriding first -->
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29 <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 <option value="canberra">canberra - Community Structure Similarity</option>
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32 <option value="gower">gower - Community Structure Similarity</option>
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33 <option value="hamming">hamming - Community Membership Similarity</option>
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34 <option value="hellinger">hellinger - Community Structure Similarity</option>
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35 <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
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36 <option value="jclass">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
917aa3b39ccd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
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38 <option value="jsd">jsd</option>
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39 <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
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40 <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
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41 <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
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42 <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
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43 <option value="manhattan">manhattan - Community Structure Similarity</option>
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44 <option value="memchi2">memchi2 - Community Membership Similarity</option>
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45 <option value="memchord">memchord - Community Membership Similarity</option>
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46 <option value="memeuclidean">memeuclidean - Community Membership Similarity</option>
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47 <option value="mempearson">mempearson - Community Membership Similarity</option>
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48 <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
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49 <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
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50 <option value="odum">odum - Community Structure Similarity</option>
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51 <option value="rjsd">rjsd</option>
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52 <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
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53 <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
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54 <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
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55 <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
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56 <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
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57 <option value="soergel">soergel - Community Structure Similarity</option>
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58 <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
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59 <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
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60 <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
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61 <option value="spearman">spearman - Community Structure Similarity</option>
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62 <option value="speciesprofile">speciesprofile - Community Structure Similarity</option>
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63 <option value="structchi2">structchi2 - Community Structure Similarity</option>
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64 <option value="structchord">structchord - Community Structure Similarity</option>
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65 <option value="structeuclidean">structeuclidean - Community Structure Similarity</option>
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66 <option value="structkulczynski">structkulczynski - Community Structure Similarity</option>
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67 <option value="structpearson">structpearson - Community Structure Similarity</option>
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68 <option value="thetan">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
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69 <option value="thetayc">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
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70 <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
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71 <yield/>
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72 </xml>
2
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73
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74 <!-- CLUSTERING -->
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75 <xml name="param-clustermethods">
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76 <param argument="method" type="select" label="Clustering Method">
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77 <option value="opti" selected="true">Opticlust method</option>
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78 <option value="furthest">Furthest neighbor</option>
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79 <option value="nearest">Nearest neighbor</option>
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80 <option value="average">Average neighbor</option>
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81 <yield/>
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82 </param>
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83 </xml>
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84 <xml name="option-vsearch-clustermethods">
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85 <option value="agc">Abundance-based greedy clustering (agc)(VSEARCH)</option>
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86 <option value="dgc">Distance-based greedy clustering (dgc)(VSEARCH)</option>
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87 </xml>
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88 <xml name="params-opticlust">
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89 <param argument="metric" type="select" label="metric - select the metric in the opticluster method"
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90 help="Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn),
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91 false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score),
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92 accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). Default=mcc.">
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93 <option value="mcc" selected="true">Matthews correlation coefficient (mcc)</option>
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94 <option value="sens">Sensitivity</option>
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95 <option value="spec">specificity</option>
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96 <option value="tptn">true positives + true negatives</option>
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97 <option value="fpfn">false positives + false negatives</option>
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98 <option value="tp">true positives</option>
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99 <option value="tn">true negative</option>
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100 <option value="fp">false positive</option>
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101 <option value="fn">false negative</option>
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102 <option value="f1score">f1score</option>
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103 <option value="accuracy">accuracy</option>
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104 <option value="ppv">positive predictive value</option>
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105 <option value="npv">negative predictive value</option>
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106 <option value="fdr">false discovery rate</option>
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107 </param>
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108 <param argument="initialize" type="select" label="Initial randomization"
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109 help="singleton: each sequence is randomly assigned to its own OTU; oneotu: all sequences are assigned to one otu">
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110 <option value="singleton" selected="true">Singleton</option>
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111 <option value="oneotu">Oneotu</option>
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112 </param>
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113 <param argument="delta" type="float" value="0.0001" label="set the stable value for the metric in the opticluster method"
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114 help="The delta parameter allows to set the stable value for the metric in the opticluster method. To reach a full convergence, set delta=0."/>
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115 <param argument="iters" type="integer" value="100" label="Maximum number of iterations"/>
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116 </xml>
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117 <xml name="param-output">
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118 <param argument="output" type="select" label="Tax summary output type"
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119 help="The detail format outputs the totals at each level, where as the simple format outputs the highest level">
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120 <option value="simple" selected="true">simple</option>
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121 <option value="detail">detail</option>
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122 </param>
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123 </xml>
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124 <xml name="param-printlevel">
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125 <param argument="printlevel" type="integer" value="-1" min="-1" label="Print level" help="specify taxlevel of your *tax.summary file to print to. Options are 1 to the maz level in the file. The default is -1, meaning max level" />
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126 </xml>
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127 <xml name="param-savelog">
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128 <param name="savelog" type="boolean" checked="false" label="Output logfile?"/>
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129 </xml>
0
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130 <xml name="logfile-output">
2
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131 <data name="logfile" format="txt" from_work_dir="mothur.out.log" label="${tool.name} on ${on_string}: logfile">
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132 <filter>savelog</filter>
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133 </data>
0
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134 </xml>
2
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135
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136 <!-- Output file tests -->
0
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137 <xml name="logfile-test">
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138 <output name="logfile" ftype="txt">
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139 <assert_contents>
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140 <has_text text="mothur"/>
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141 <has_text text="@WRAPPER_VERSION@"/>
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142 </assert_contents>
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143 </output>
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144 </xml>
2
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145
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146 <xml name="test-accnos-format">
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147 <!-- one or two columns -->
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148 <has_line_matching expression="^[\w\d\-]+(\t[^\t]+)?$"/>
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149 </xml>
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150 <xml name="test-align-format">
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151 <has_line_matching expression="^>.+$"/>
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152 <has_line_matching expression="^[ACTG\-\.]+$"/>
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153 </xml>
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154 <xml name="test-aligncheck-format">
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155 <has_n_columns n="9"/>
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156 <has_line_matching expression="^name\tpound\tdash\tplus\tequal\tloop\ttilde\ttotal\tnumseqs$"/>
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157 </xml>
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158 <xml name="test-alignreport-format">
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159 <has_line_matching expression="^QueryName\tQueryLength\tTemplateName\tTemplateLength\tSearchMethod\tSearchScore\tAlignmentMethod\tQueryStart\tQueryEnd\tTemplateStart\tTemplateEnd\tPairwiseAlignmentLength\tGapsInQuery\tGapsInTemplate\tLongestInsert\tSimBtwnQuery&amp;Template$"/>
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160 </xml>
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161 <xml name="test-axes-format">
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162 <has_line_matching expression="^group(\taxis\d+)+$"/>
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163 </xml>
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164 <xml name="test-chimera-format">
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165 <has_line_matching expression="Score\tQuery\tParentA\tParentB\tIdQM\tIdQA\tIdQB\tIdAB\tIdQT\tLY\tLN\tLA\tRY\tRN\tRA\tDiv\tYN"/>
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166 </xml>
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167 <xml name="test-column-format">
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168 <has_n_columns n="3"/>
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169 <has_line_matching expression="^[\w\d\-]+\t[\w\d\-]+\t[\d\.]+$"/>
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170 </xml>
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171 <xml name="test-contigsreport-format">
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172 <has_n_columns n="7"/>
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173 <has_line_matching expression="^Name\tLength\tOverlap_Length\tOverlap_Start\tOverlap_End\tMisMatches\tNum_Ns$"/>
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174 </xml>
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175 <xml name="test-count-format">
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176 <has_line_matching expression="^Representative_Sequence\ttotal(\t\w+)*$"/>
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177 <has_line_matching expression="^\w+(\t\d+)+(\s)*$"/>
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178 </xml>
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179 <xml name="test-dist-format">
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180 <has_line_matching expression="^[ \t]*\d+$"/>
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181 <has_line_matching expression="^[\w\d\-]+(\t[\d\.]+)+\s?$"/>
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182 </xml>
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183 <xml name="test-fasta-format">
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184 <has_line_matching expression="^>.+$"/>
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185 <has_line_matching expression="^[ACTGN-]+$"/>
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186 </xml>
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187 <xml name="test-fastq-format">
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188 <has_line_matching expression="^@.+$"/>
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189 <has_line_matching expression="^[ACTGN]+$"/>
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190 <has_line_matching expression="^\+$"/>
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191 </xml>
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192 <xml name="test-group-format">
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193 <has_line_matching expression="^Representative_Sequence\ttotal(\t[\w\d\-]+)+$"/>
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194 <has_line_matching expression="^[\w\d\-]+(\t\d+)+$"/>
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195 </xml>
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196 <xml name="test-list-format">
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197 <has_line_matching expression="^label\tnumOtus(\tOtu\d+)+$"/>
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198 <has_line_matching expression="^(unique|0\.\d+)\t\d+(\t[\w\d\-,]+)+$"/>
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199 </xml>
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200 <xml name="test-names-format">
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201 <has_line_matching expression="^[a-zA-Z0-9]+\t[a-zA-Z0-9]+$"/>
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202 </xml>
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203 <xml name="test-qfile-format">
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204 <has_line_matching expression="^(\d+ )+$"/>
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205 <has_line_matching expression="^>.+$"/>
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206 </xml>
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207 <xml name="test-rabund-format">
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208 <has_line_matching expression="^(unique|0\.\d+)(\t\d+\.?\d*)+$"/>
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209 </xml>
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210 <xml name="test-sabund-format">
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211 <has_line_matching expression="^(unique|0\.\d+)(\t\d+)+$"/>
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212 </xml>
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213 <xml name="test-sensspec-format">
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214 <has_n_columns n="14"/>
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215 <has_line_matching expression="^label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\t\w+\tf1score$"/>
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216 </xml>
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217 <xml name="test-shared-format">
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218 <has_line_matching expression="^label\tGroup\tnumOtus(\t(Otu|rareOTUs|.*OTU.*)\d+)+$"/>
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219 </xml>
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220 <xml name="test-taxonomy-format">
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221 <has_n_columns n="3"/>
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222 <has_line_matching expression="^OTU\tSize\tTaxonomy$"/>
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223 </xml>
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224 <xml name="test-taxsummary-format">
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225 <has_line_matching expression="^((taxlevel\trankID\ttaxon\tdaughterlevels\ttotal(\t[\w\d\-]+)*)|(taxonomy\ttotal(\t[\w\d]+)*))$"/>
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226 </xml>
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227 <!-- backmatter -->
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228 <token name="@MOTHUR_OVERVIEW@">
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229 <![CDATA[
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230
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231 **Mothur Overview**
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232
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233 Mothur is a comprehensive suite of tools for microbial ecology community. It is initiated by Dr. Patrick Schloss and his software development team
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234 in the Department of Microbiology and Immunology at The University of Michigan. For more information, see Mothur-Wiki_.
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235
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236 .. _Mothur-Wiki: https://www.mothur.org/wiki/Main_Page
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237
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238 ]]>
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239 </token>
0
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240 <xml name="citations">
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241 <citations>
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242 <citation type="doi">10.1128/AEM.01541-09</citation>
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243 <yield/>
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244 </citations>
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245 </xml>
6
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246 <xml name="citations-ecology">
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247 <citation type="bibtex">
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248 @book{mccune2002analysis,
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249 title={Analysis of ecological communities},
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250 author={McCune, Bruce and Grace, James B and Urban, Dean L},
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251 volume={28},
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252 year={2002},
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253 publisher={MjM software design Gleneden Beach, OR}
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254 }
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255 </citation>
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256 <citation type="bibtex">
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257 @misc{legendre1998numerical,
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258 title={Numerical Ecology, Volume 24, (Developments in Environmental Modelling)},
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259 author={Legendre, Pierre and Legendre, Louis},
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260 year={1998},
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261 publisher={Elsevier Science Amsterdam, The Netherlands}
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262 }
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263 </citation>
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264 </xml>
0
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265 </macros>