Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.lineage.xml @ 33:d53b9eb16c2d
mothur_wrapper.py - convert_value needs to return a String
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 11 Sep 2013 16:56:31 -0500 |
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7 | 1 <tool id="mothur_get_lineage" name="Get.lineage" version="1.20.0"> |
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2 <description>Picks by taxon</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($taxonomy.__str__)) + ":'" + $taxonomy_out.__str__] |
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9 --cmd='get.lineage' |
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10 --outputdir='$logfile.extra_files_path' |
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11 --taxonomy=$taxonomy |
7 | 12 --taxon="'$re.sub('(\s|,)+',',',$re.sub('\(\d+\)','',$taxon.value.__str__))'" |
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13 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: |
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14 --fasta=$fasta_in |
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15 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] |
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16 #end if |
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17 #if $group_in.__str__ != "None" and len($group_in.__str__) > 0: |
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18 --group=$group_in |
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19 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($group_in.__str__)) + ":'" + $group_out.__str__] |
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20 #end if |
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21 #if $alignreport_in.__str__ != "None" and len($alignreport_in.__str__) > 0: |
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22 --alignreport=$alignreport_in |
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23 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)$',r'\1.pick.align.report',$os.path.basename($alignreport_in.__str__)) + ":'" + $alignreport_out.__str__] |
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24 #end if |
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25 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: |
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26 --list=$list_in |
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27 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
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28 #end if |
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29 #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: |
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30 --name=$name_in |
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31 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] |
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32 $dups |
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33 #end if |
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34 --result=#echo ','.join($results) |
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35 </command> |
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36 <inputs> |
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37 <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/> |
7 | 38 <!-- |
39 <param name="taxons" type="select" size="120" multiple="true" label="Browse Taxons from Taxonomy"> | |
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40 <options from_dataset="taxonomy"> |
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41 <column name="name" index="1"/> |
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42 <column name="value" index="1"/> |
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43 <filter type="unique_value" name="unique_taxon" column="1" /> |
7 | 44 <filter type="sort_by" name="sorted_taxon" column="1" /> |
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45 </options> |
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46 </param> |
7 | 47 --> |
48 <param name="taxon" type="text" area="True" size="5x120" label="taxon - Select Taxons for filtering" help="Enter 1 or more taxons separated by whitespace or commas"/> | |
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49 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> |
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50 <param name="group_in" type="data" format="groups" optional="true" label="group - Groups"/> |
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51 <param name="alignreport_in" type="data" format="align.report" optional="true" label="alignreport - Align Report"/> |
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52 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> |
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53 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
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54 <param name="dups" type="boolean" truevalue="" falsevalue="--dups=false" checked="true" label="dups - Apply to duplicate names"/> |
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55 </inputs> |
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56 <outputs> |
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57 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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58 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"/> |
4 | 59 <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> |
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60 <filter>fasta_in != None</filter> |
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61 </data> |
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62 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.group"> |
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63 <filter>group_in != None</filter> |
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64 </data> |
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65 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> |
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66 <filter>list_in != None</filter> |
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67 </data> |
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68 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> |
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69 <filter>name_in != None</filter> |
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70 </data> |
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71 <data format="align.report" name="alignreport_out" label="${tool.name} on ${on_string}: pick.align.report"> |
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72 <filter>alignreport_in != None</filter> |
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73 </data> |
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74 </outputs> |
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75 <requirements> |
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76 <requirement type="package" version="1.27">mothur</requirement> |
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77 </requirements> |
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78 <tests> |
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79 </tests> |
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80 <help> |
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81 **Mothur Overview** |
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82 |
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83 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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84 in the Department of Microbiology and Immunology at The University of Michigan, |
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85 provides bioinformatics for the microbial ecology community. |
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86 |
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87 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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88 |
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89 **Command Documenation** |
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90 |
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91 The get.lineage_ command reads a taxonomy_ file and a taxon and generates a new file that contains only the sequences in the that are from that taxon. You may also include either a fasta, name_, group_, list_, or align.report_ file to this command and mothur will generate new files for each of those containing only the selected sequences. |
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92 |
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93 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline |
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94 .. _name: http://www.mothur.org/wiki/Name_file |
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95 .. _group: http://www.mothur.org/wiki/Group_file |
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96 .. _list: http://www.mothur.org/wiki/List_file |
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97 .. _align.report: http://www.mothur.org/wiki/Align.seqs |
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98 .. _get.lineage: http://www.mothur.org/wiki/Get.lineage |
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99 |
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100 |
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101 </help> |
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102 </tool> |