Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/remove.groups.xml @ 13:4f797d3eee3a
Change default processor counts to 8, mothur_wrapper.py can overide processors allocated with ENVIRONMENT variable MOTHUR_MAX_PROCESSORS
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 05 Oct 2011 10:34:44 -0500 |
parents | 370b3fc4e7d3 |
children | 09740be2bc9c |
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1 <tool id="mothur_remove_groups" name="Remove.groups" version="1.21.0"> |
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2 <description>Remove groups from groups,fasta,names,list,taxonomy</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 #import re, os.path |
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6 #set results = ["'^mothur.\S+\.logfile$:'" + $logfile.__str__] |
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7 ## adds .pick before the last extension to the input file |
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8 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] |
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9 --cmd='remove.groups' |
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10 --outputdir='$logfile.extra_files_path' |
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11 --group=$group_in |
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12 #if $groupnames.source == 'groups': |
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13 #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: |
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14 --groups=$groupnames.groups |
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15 #end if |
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16 #else |
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17 #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0: |
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18 --accnos=$groupnames.accnos |
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19 #end if |
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20 #end if |
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21 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: |
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22 --fasta=$fasta_in |
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23 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] |
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24 #end if |
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25 #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: |
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26 --name=$name_in |
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27 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] |
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28 #end if |
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29 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: |
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30 --list=$list_in |
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31 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
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32 #end if |
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33 #if $shared_in.__str__ != "None" and len($shared_in.__str__) > 0: |
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34 --shared=$shared_in |
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35 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($shared_in.__str__)) + ":'" + $shared_out.__str__] |
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36 #end if |
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37 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: |
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38 --taxonomy=$taxonomy_in |
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39 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] |
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40 #end if |
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41 --result=#echo ','.join($results) |
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42 </command> |
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43 <inputs> |
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44 <param name="group_in" type="data" format="groups" label="group - Groups"/> |
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45 <conditional name="groupnames"> |
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46 <param name="source" type="select" label="Select Group Names from"> |
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47 <option value="groups">A List of Group Names</option> |
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48 <option value="accnos">A History Group Name Accnos Dataset</option> |
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49 </param> |
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50 <when value="groups"> |
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51 <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true"> |
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52 <options from_dataset="group_in"> |
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53 <column name="name" index="1"/> |
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54 <column name="value" index="1"/> |
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55 <filter type="unique_value" name="unq_grp" column="1" /> |
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56 </options> |
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57 </param> |
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58 </when> |
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59 <when value="accnos"> |
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60 <param name="accnos" type="data" format="accnos" label="accnos - Group Names from your history"/> |
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61 </when> |
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62 </conditional> |
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63 <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/> |
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64 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
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65 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> |
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66 <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/> |
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67 <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> |
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68 </inputs> |
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69 <outputs> |
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70 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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71 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> |
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72 <!-- fix format --> |
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73 <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> |
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74 <filter>fasta_in != None</filter> |
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75 </data> |
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76 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> |
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77 <filter>name_in != None</filter> |
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78 </data> |
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79 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> |
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80 <filter>list_in != None</filter> |
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81 </data> |
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82 <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared"> |
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83 <filter>shared_in != None</filter> |
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84 </data> |
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85 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> |
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86 <filter>taxonomy_in != None</filter> |
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87 </data> |
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88 </outputs> |
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89 <requirements> |
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90 <requirement type="binary">mothur</requirement> |
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91 </requirements> |
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92 <tests> |
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93 </tests> |
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94 <help> |
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95 **Mothur Overview** |
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96 |
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97 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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98 in the Department of Microbiology and Immunology at The University of Michigan, |
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99 provides bioinformatics for the microbial ecology community. |
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100 |
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101 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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102 |
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103 **Command Documenation** |
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104 |
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105 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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106 |
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107 .. _name: http://www.mothur.org/wiki/Name_file |
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108 .. _group: http://www.mothur.org/wiki/Group_file |
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109 .. _list: http://www.mothur.org/wiki/List_file |
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110 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline |
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111 .. _remove.groups: http://www.mothur.org/wiki/Remove.groups |
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112 |
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113 |
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114 </help> |
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115 </tool> |