Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/sub.sample.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 5265aa9067e0 |
rev | line source |
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2
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_sub_sample" name="Sub.sample" version="1.19.0"> |
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2 <description>Create a sub sample</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list |
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6 #import re, os.path |
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7 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
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8 --cmd='sub.sample' |
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9 --outputdir='$logfile.extra_files_path' |
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10 #if $input.format == "fasta": |
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11 --fasta=$input.fasta_in |
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12 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.fasta_in.__str__)) + ":'" + $fasta_out.__str__] |
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13 #if $input.name_in.__str__ != "None" and len($input.name_in.__str__) > 0: |
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14 --name=$input.name_in |
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15 ## #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.name_in.__str__)) + ":'" + $names_out.__str__] |
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16 #end if |
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17 #if $input.use_group.to_filter == "yes": |
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18 #if $input.use_group.group_in.__str__ != "None" and len($input.use_group.group_in.__str__) > 0: |
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19 --group=$input.use_group.group_in |
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20 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.use_group.group_in.__str__)) + ":'" + $group_out.__str__] |
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21 #if $input.use_group.groups.__str__ != "None" and len($input.use_group.groups.__str__) > 0: |
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22 --groups=$input.use_group.groups |
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23 #end if |
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24 $input.use_group.persample |
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25 #end if |
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26 #end if |
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27 #elif $input.format == "list": |
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28 --list=$input.otu_in |
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29 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $list_out.__str__] |
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30 #if $input.use_group.to_filter == "yes": |
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31 #if $input.use_group.group_in.__str__ != "None" and len($input.use_group.group_in.__str__) > 0: |
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32 --group=$input.use_group.group_in |
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33 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.use_group.group_in.__str__)) + ":'" + $group_out.__str__] |
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34 #if $input.use_group.groups.__str__ != "None" and len($input.use_group.groups.__str__) > 0: |
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35 --groups=$input.use_group.groups |
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36 #end if |
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37 $input.use_group.persample |
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38 #end if |
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39 #end if |
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40 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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41 --label=$input.label |
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42 #end if |
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43 #elif $input.format == "shared": |
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44 --shared=$input.otu_in |
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45 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $shared_out.__str__] |
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46 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
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47 --groups=$input.groups |
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48 #end if |
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49 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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50 --label=$input.label |
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51 #end if |
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52 #elif $input.format == "sabund": |
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53 --sabund=$input.otu_in |
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54 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $sabund_out.__str__] |
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55 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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56 --label=$input.label |
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57 #end if |
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58 #elif $input.format == "rabund": |
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59 --rabund=$input.otu_in |
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60 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.subsample.\2',$os.path.basename($input.otu_in.__str__)) + ":'" + $rabund_out.__str__] |
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61 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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62 --label=$input.label |
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63 #end if |
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64 #end if |
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65 #if int($size) > 0: |
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66 --size=$size |
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67 #end if |
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68 --result=#echo ','.join($results) |
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69 </command> |
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70 <inputs> |
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71 <conditional name="input"> |
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72 <param name="format" type="select" label="Select type of data to sub sample" > |
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73 <option value="fasta">FASTA</option> |
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74 <option value="list">OTU List</option> |
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75 <option value="shared">OTU Shared</option> |
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76 <option value="sabund">OTU Shared Abundance</option> |
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77 <option value="rabund">OTU Relative Abundance</option> |
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78 </param> |
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79 <when value="fasta"> |
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80 <param name="fasta_in" type="data" format="fasta" label="fasta - "/> |
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81 <param name="name_in" type="data" format="names" optional="true" label="name - Group Names from your history"/> |
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82 <conditional name="use_group"> |
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83 <param name="to_filter" type="select" label="Use groups " > |
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84 <option value="no">No</option> |
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85 <option value="yes">Yes</option> |
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86 </param> |
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87 <when value="no"/> |
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88 <when value="yes"> |
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89 <param name="group_in" type="data" format="groups" label="group - Groups"/> |
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90 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> |
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91 <options from_dataset="group_in"> |
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92 <column name="name" index="1"/> |
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93 <column name="value" index="1"/> |
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94 <filter type="unique_value" name="unq_grp" column="1" /> |
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95 </options> |
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96 </param> |
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97 <param name="persample" type="boolean" truevalue="--persample=true" falsevalue="" checked="false" label="persample - select subsample of the same size from each of the groups"/> |
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98 </when> <!-- yes --> |
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99 </conditional> <!-- use_group --> |
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100 </when> <!-- fasta --> |
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101 <when value="list"> |
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102 <param name="otu_in" type="data" format="list" label="list - OTU List"/> |
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103 <conditional name="use_group"> |
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104 <param name="to_filter" type="select" label="Use groups " > |
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105 <option value="no">No</option> |
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106 <option value="yes">Yes</option> |
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107 </param> |
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108 <when value="no"/> |
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109 <when value="yes"> |
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110 <param name="group_in" type="data" format="groups" label="group - Groups"/> |
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111 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> |
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112 <options from_dataset="group_in"> |
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113 <column name="name" index="1"/> |
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114 <column name="value" index="1"/> |
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115 <filter type="unique_value" name="unq_grp" column="1" /> |
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116 </options> |
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117 </param> |
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118 <param name="persample" type="boolean" truevalue="--persample=true" falsevalue="" checked="false" label="persample - select subsample of the same size from each of the groups"/> |
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119 </when> <!-- yes --> |
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120 </conditional> <!-- use_group --> |
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121 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> |
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122 <options from_dataset="otu_in"> |
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123 <column name="name" index="0"/> |
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124 <column name="value" index="0"/> |
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125 </options> |
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126 </param> |
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127 </when> <!-- list --> |
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128 <when value="shared"> |
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129 <param name="otu_in" type="data" format="shared" label="shared - OTU List"/> |
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130 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> |
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131 <options from_dataset="otu_in"> |
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132 <column name="name" index="1"/> |
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133 <column name="value" index="1"/> |
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134 <filter type="unique_value" name="unq_grp" column="1" /> |
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135 </options> |
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136 </param> |
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137 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> |
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138 <options from_dataset="otu_in"> |
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139 <column name="name" index="0"/> |
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140 <column name="value" index="0"/> |
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141 <filter type="unique_value" name="unq_lbl" column="0" /> |
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142 </options> |
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143 </param> |
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144 </when> <!-- shared --> |
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145 <when value="sabund"> |
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146 <param name="otu_in" type="data" format="sabund" label="sabund - OTU List"/> |
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147 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> |
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148 <options from_dataset="otu_in"> |
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149 <column name="name" index="0"/> |
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150 <column name="value" index="0"/> |
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151 </options> |
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152 </param> |
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153 </when> <!-- sabund --> |
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154 <when value="rabund"> |
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155 <param name="otu_in" type="data" format="rabund" label="rabund - OTU List"/> |
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156 <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> |
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157 <options from_dataset="otu_in"> |
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158 <column name="name" index="0"/> |
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159 <column name="value" index="0"/> |
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160 </options> |
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161 </param> |
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162 </when> <!-- rabund --> |
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163 </conditional> <!-- input --> |
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164 <param name="size" type="integer" value="0" label="size - If greater than 0, the number of samples to pick"/> |
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165 </inputs> |
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166 <outputs> |
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167 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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168 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: subsample.fasta"> |
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169 <filter>input['format'] == 'fasta'</filter> |
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170 </data> |
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171 <data format="list" name="list_out" label="${tool.name} on ${on_string}: subsample.list"> |
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172 <filter>input['format'] == 'list'</filter> |
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173 </data> |
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174 <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: subsample.shared"> |
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175 <filter>input['format'] == 'shared'</filter> |
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176 </data> |
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177 <data format="sabund" name="sabund_out" label="${tool.name} on ${on_string}: subsample.sabund"> |
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178 <filter>input['format'] == 'sabund'</filter> |
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179 </data> |
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180 <data format="rabund" name="rabund_out" label="${tool.name} on ${on_string}: subsample.rabund"> |
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181 <filter>input['format'] == 'rabund'</filter> |
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182 </data> |
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183 <!-- This doesn't appear to be generated even though the documentation says it is |
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184 <data format="names" name="names_out" label="${tool.name} on ${on_string}: subsample.names"> |
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185 <filter>(input['format'] == 'fasta' and input['name_in'] != None)</filter> |
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186 </data> |
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187 --> |
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188 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: subsample.groups"> |
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189 <filter>input['use_group']['group_in'] != None</filter> |
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190 </data> |
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191 </outputs> |
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192 <requirements> |
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193 <requirement type="binary">mothur</requirement> |
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194 </requirements> |
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195 <tests> |
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196 </tests> |
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197 <help> |
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198 **Mothur Overview** |
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199 |
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200 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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201 in the Department of Microbiology and Immunology at The University of Michigan, |
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202 provides bioinformatics for the microbial ecology community. |
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203 |
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204 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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205 |
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206 **Command Documenation** |
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207 |
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208 The sub.sample_ command can be used as a way to normalize your data, or to create a smaller set from your original set. It takes as an input the following file types: fasta, list_, shared_, rabund_ and sabund_ to generate a new file that contains a sampling of your original file. |
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209 |
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210 .. _list: http://www.mothur.org/wiki/List_file |
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211 .. _shared: http://www.mothur.org/wiki/Shared_file |
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212 .. _rabund: http://www.mothur.org/wiki/Rabund_file |
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213 .. _sabund: http://www.mothur.org/wiki/Sabund_file |
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214 .. _sub.sample: http://www.mothur.org/wiki/Sub.sample |
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215 |
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216 |
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217 </help> |
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218 </tool> |