Mercurial > repos > iuc > mothur_remove_rare

annotate remove.rare.xml @ 0:e3e42e0b45a3 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 16:48:11 -0400
parents
children 6352c9aa5116
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0
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_remove_rare" name="Remove.rare" version="@WRAPPER_VERSION@.0">
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Remove rare OTUs</description>
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$input.otu" input_otu.dat &&
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 #if $input.source == 'list':
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$input.group" input.group.dat &&
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$input.count" input.count.dat &&
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #end if
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15
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 echo 'remove.rare(
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #if $input.otu.is_of_type("mothur.rabund"):
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 rabund=input_otu.dat,
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 #elif $input.otu.is_of_type("mothur.sabund"):
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20 sabund=input_otu.dat,
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #elif $input.otu.is_of_type("mothur.list"):
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22 list=input_otu.dat,
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #if $input.group:
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24 group=input.group.dat,
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #end if
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #if $input.groups:
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27 groups=${ str($input.groups).replace(",","-") },
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 #end if
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29 #if $input.count:
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 count=input.count.dat,
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31 #end if
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 #elif $input.otu.is_of_type("mothur.shared"):
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 shared=input_otu.dat,
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 bygroup=$input.bygroup,
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35 #if $input.groups:
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 groups=${ str($input.groups).replace(",","-") },
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 #end if
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38 #end if
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39 #if $input.label:
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40 label=${ str($input.label).replace(",","-") },
e3e42e0b45a3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 #end if
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42 nseqs=$nseqs
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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 ]]></command>
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47 <inputs>
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48 <conditional name="input">
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49 <param name="source" type="select" label="Select Input Format">
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50 <option value="shared">shared</option>
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51 <option value="list">list</option>
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52 <option value="default">rabund or sabund</option>
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53 </param>
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54 <when value="shared">
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55 <param name="otu" type="data" format="mothur.shared" label="shared - Otu dataset"/>
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56 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
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57 <options>
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58 <filter type="data_meta" ref="otu" key="groups"/>
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59 </options>
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60 </param>
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61 <param name="bygroup" type="boolean" truevalue="true" falsevalue="false" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/>
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62 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels">
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63 <expand macro="labeloptions"/>
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64 </param>
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65 </when>
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66 <when value="list">
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67 <param name="otu" type="data" format="mothur.list" label="list - Otu dataset"/>
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68 <param name="group" type="data" optional="true" format="mothur.groups" label="group - Groups"/>
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69 <param name="count" type="data" format="count_table" optional="true" label="count - Count Table" help="If you clustered with a count file, can only supply one of group or count table, not both"/>
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70 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
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71 <options>
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72 <filter type="data_meta" ref="group" key="groups"/>
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73 </options>
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74 </param>
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75 <param name="label" type="select" multiple="false" optional="true" label="label - OTU Labels">
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76 <expand macro="labeloptions"/>
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77 </param>
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78 </when>
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79 <when value="default">
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80 <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund" label="list,rabund,sabund - Otu dataset"/>
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81 <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels">
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82 <expand macro="labeloptions"/>
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83 </param>
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84 </when>
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85 </conditional>
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86 <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/>
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87 </inputs>
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88 <outputs>
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89 <expand macro="logfile-output"/>
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90 <data name="pick_otu" format_source="otu" from_work_dir="input_otu*.pick.*" label="${tool.name} on ${on_string}: pick.${input.otu.ext}">
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91 <filter>input['source'] != 'shared'</filter>
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92 </data>
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93 <collection name="pick_shared" type="list" label="${tool.name} on ${on_string}: pick.shared per label">
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94 <filter>input['source'] == 'shared'</filter>
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95 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
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96 </collection>
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97 <data name="pick_group" format="mothur.groups" from_work_dir="input.group*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
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98 <filter>input['source'] == 'list'</filter>
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99 </data>
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100 </outputs>
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101 <tests>
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102 <test><!-- test with list -->
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103 <param name="source" value="list"/>
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104 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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105 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
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106 <expand macro="logfile-test"/>
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107 </test>
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108 <test><!-- test with list and group file -->
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109 <param name="source" value="list"/>
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110 <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
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111 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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112 <param name="groups" value="forest,pasture"/>
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113 <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
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114 <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/>
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115 <expand macro="logfile-test"/>
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116 </test>
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117 <test><!-- test with shared file -->
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118 <param name="source" value="shared"/>
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119 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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120 <output_collection name="pick_shared" count="36">
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121 <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/>
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122 </output_collection>
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123 <expand macro="logfile-test"/>
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124 </test>
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125 <test><!-- test with shared file and label/group select -->
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126 <param name="source" value="shared"/>
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127 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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128 <param name="bygroup" value="true"/>
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129 <param name="label" value="0.05,0.22,0.41"/>
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130 <param name="groups" value="forest,pasture"/>
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131 <output_collection name="pick_shared" count="3">
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132 <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/>
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133 </output_collection>
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134 <expand macro="logfile-test"/>
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135 </test>
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136 <test><!-- test with rabund/sabund file -->
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137 <param name="source" value="default"/>
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138 <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
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139 <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/>
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140 <expand macro="logfile-test"/>
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141 </test>
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142 </tests>
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143 <help>
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144 <![CDATA[
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145
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146 @MOTHUR_OVERVIEW@
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147
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148 **Command Documenation**
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149
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150 The remove.rare_ command reads one of the following file types: list_, rabund_, sabund_ or shared_ file. It outputs a new file after removing the rare otus.
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151
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152 .. _list: http://www.mothur.org/wiki/List_file
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153 .. _sabund: http://www.mothur.org/wiki/Sabund_file
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154 .. _rabund: http://www.mothur.org/wiki/Rabund_file
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155 .. _shared: http://www.mothur.org/wiki/Shared_file
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156 .. _remove.rare: http://www.mothur.org/wiki/Remove.rare
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157
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158 ]]>
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159 </help>
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160 <expand macro="citations"/>
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161 </tool>