Mercurial > repos > sanbi-uwc > mothur_test

annotate tools/mothur/remove.groups.xml @ 0:ee4fee239fe7 draft default tip

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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 <tool profile="16.07" id="mothur_remove_groups" name="Remove.groups" version="@WRAPPER_VERSION@.0">
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2 <description>Remove groups from groups,fasta,names,list,taxonomy</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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 echo 'remove.groups(
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10 #if $groupnames.source == "other":
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11 #if $group_in.is_of_type("mothur.groups"):
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12 group=$groupnames.group_in
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13 #else
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14 count=$groupnames.group_in
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15 #end if
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16 #if $groupnames.fasta_in:
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17 ,fasta=$groupnames.fasta_in
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18 #end if
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19 #if $groupnames.name_in:
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20 ,name=$groupnames.name_in
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21 #end if
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22 #if $groupnames.list_in:
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23 ,list=$groupnames.list_in
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24 #end if
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25 #if $groupnames.taxonomy_in:
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26 ,taxonomy=$groupnames.taxonomy_in
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27 #end if
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28 #else
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29 shared=$groupnames.shared_in
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30 #end if
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31 ,groups=${ str($groupnames.groups).replace(",","-") }
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32 )'
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33 | sed 's/ //g' ## mothur trips over whitespace
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34 | mothur &&
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35
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36 ## move output files to correct destination
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37 #if $groupnames.source == "shared":
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38 prefix="$groupnames.shared_in" &&
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39 mv \${prefix%.dat}*.pick.* . &&
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40 #else
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41 prefix="$groupnames.group_in" &&
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42 mv \${prefix%.dat}*.pick.* "$group_out" &&
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43 #if $groupnames.fasta_in:
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44 prefix="$groupnames.fasta_in" &&
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45 mv \${prefix%.dat}*.pick.* "$fasta_out" &&
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46 #end if
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47 #if $groupnames.name_in:
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48 prefix="$groupnames.name_in" &&
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49 mv \${prefix%.dat}*.pick.* "$name_out" &&
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50 #end if
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51 #if $groupnames.taxonomy_in:
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52 prefix="$groupnames.taxonomy_in" &&
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53 mv \${prefix%.dat}*.pick.* "$taxonomy_out" &&
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54 #end if
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55 #if $groupnames.list_in:
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56 prefix="$groupnames.list_in" &&
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57 mv \${prefix%.dat}*.pick.* . &&
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58 #end if
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59 #end if
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60 mv mothur.*.logfile "$logfile"
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61 ]]></command>
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62 <inputs>
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63 <conditional name="groupnames">
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64 <param name="source" type="select" label="Select Input Type">
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65 <option value="shared">shared file</option>
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66 <option value="other">fasta, name, taxonomy, or list with a group file or count table</option>
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67 </param>
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68 <when value="other">
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69 <param name="group_in" type="data" format="mothur.groups,mothur.count_table" label="group or count table - Groups"/>
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70 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
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71 <options>
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72 <filter type="data_meta" ref="group_in" key="groups"/>
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73 </options>
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74 </param>
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75 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
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76 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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77 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
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78 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
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79 </when>
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80 <when value="shared">
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81 <param name="shared_in" type="data" format="mothur.shared" optional="true" label="shared - OTU Shared"/>
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82 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" optional="false">
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83 <options>
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84 <filter type="data_meta" ref="shared_in" key="groups"/>
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85 </options>
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86 </param>
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87 </when>
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88 </conditional>
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89 </inputs>
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90 <outputs>
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91 <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
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92 <data name="fasta_out" format_source="fasta_in" label="${tool.name} on ${on_string}: pick.fasta">
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93 <filter>groupname['source'] == 'other' and fasta_in</filter>
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94 </data>
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95 <data name="group_out" format="mothur.groups" label="${tool.name} on ${on_string}: pick.groups">
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96 <filter>groupname['source'] == 'other' and group_in</filter>
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97 </data>
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98 <data name="name_out" format="mothur.names" label="${tool.name} on ${on_string}: pick.names">
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99 <filter>groupname['source'] == 'other' and name_in</filter>
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100 </data>
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101 <data name="taxonomy_out" format="mothur.seq.taxonomy" label="${tool.name} on ${on_string}: pick.taxonomy">
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102 <filter>groupname['source'] == 'other' and taxonomy_in</filter>
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103 </data>
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104 <collection name="list_out" type="list" label="${tool.name} on ${on_string}: pick.list">
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105 <filter>groupname['source'] == 'other' and list_in</filter>
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106 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.list"/>
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107 </collection>
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108 <collection name="shared_out" type="list" label="${tool.name} on ${on_string}: pick.shared">
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109 <filter>groupname['source'] == 'shared'</filter>
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110 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
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111 </collection>
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112 </outputs>
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113 <tests>
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114 <test><!-- test with shared file -->
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115 <param name="source" value="shared"/>
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116 <param name="shared_in" value="amazon.an.shared"/>
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117 <param name="groups" value="pasture"/>
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118 <output_collection name="shared_out" count="36">
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119 <element name="0.26" md5="c5043237225f0292ce1bfbd2766b96ea" ftype="mothur.shared"/>
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120 </output_collection>
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121 <expand macro="logfile-test"/>
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122 </test>
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123 <test><!-- test with group file and fasta/names/list/taxonomy files -->
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124 <param name="source" value="other"/>
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125 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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126 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/>
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127 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
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128 <param name="list_in" value="amazon.an.list" ftype="mothur.list"/>
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129 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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130 <param name="groups" value="pasture"/>
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131 <output name="fasta_out" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
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132 <output name="taxonomy_out" md5="8fcaadcb5ad40873e270ad7e2cebe7fa" ftype="mothur.seq.taxonomy"/>
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133 <output name="group_out" md5="6d689ead98f3eb1af41f1a78386d0b50" ftype="mothur.groups"/>
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134 <output name="name_out" md5="55dbcadbb414d95bae8a282a93c10e63" ftype="mothur.names"/>
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135 <output_collection name="list_out" count="36">
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136 <element name="0.26" md5="71282909924de5f43452f1a5dbf623e8" ftype="mothur.list"/>
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137 </output_collection>
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138 <expand macro="logfile-test"/>
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139 </test>
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140 </tests>
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141 <help><![CDATA[
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142
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143 @MOTHUR_OVERVIEW@
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144
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145 **Command Documenation**
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146
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147 The remove.groups_ command removes sequences from a specific group or set of groups from the following file types: fasta, name_, group_, list_, taxonomy_.
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148
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149 .. _name: http://www.mothur.org/wiki/Name_file
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150 .. _group: http://www.mothur.org/wiki/Group_file
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151 .. _list: http://www.mothur.org/wiki/List_file
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152 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
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153 .. _remove.groups: http://www.mothur.org/wiki/Remove.groups
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154
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155 ]]>
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156 </help>
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157 <expand macro="citations"/>
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158 </tool>