Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.groups.xml @ 0:3202a38e44d9
Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:32:23 -0400 |
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children | fcc0778f6987 |
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Migrated tool version 1.15.1 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_get_groups" name="Get.groups" version="1.15.0"> |
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2 <description>Select groups</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__)) + ":'" + $group_out.__str__] |
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9 --cmd='get.groups' |
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10 --outputdir='$logfile.extra_files_path' |
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11 --group=$group_in |
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12 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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13 --groups=$groups |
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14 #end if |
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15 #if $accnos.__str__ != "None" and len($accnos.__str__) > 0: |
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16 --accnos=$accnos |
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17 #end if |
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18 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: |
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19 --fasta=$fasta_in |
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20 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_out.__str__] |
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21 #end if |
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22 #if $name_in.__str__ != "None" and len($name_in.__str__) > 0: |
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23 --name=$name_in |
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24 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($name_in.__str__)) + ":'" + $name_out.__str__] |
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25 #end if |
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26 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: |
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27 --list=$list_in |
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28 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
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29 #end if |
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30 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: |
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31 --taxonomy=$taxonomy_in |
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32 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.pick.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] |
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33 #end if |
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34 --result=#echo ','.join($results) |
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35 </command> |
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36 <inputs> |
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37 <param name="group_in" type="data" format="groups" label="group - Groups"/> |
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38 <param name="groups" type="select" optional="true" label="groups - Pick groups to include" multiple="true"> |
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39 <options from_dataset="group_in"> |
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40 <column name="name" index="1"/> |
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41 <column name="value" index="1"/> |
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42 <filter type="unique_value" name="unq_grp" column="1" /> |
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43 </options> |
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44 </param> |
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45 <param name="accnos" type="data" format="accnos" optional="true" label="accnos - Accession Names"/> |
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46 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/> |
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47 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
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48 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> |
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49 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy"/> |
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50 </inputs> |
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51 <outputs> |
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52 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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53 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> |
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54 <!-- fix format --> |
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55 <data format="fasta" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> |
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56 <filter>fasta_in != None</filter> |
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57 </data> |
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58 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> |
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59 <filter>name_in != None</filter> |
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60 </data> |
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61 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> |
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62 <filter>list_in != None</filter> |
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63 </data> |
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64 <data format="taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> |
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65 <filter>taxonomy_in != None</filter> |
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66 </data> |
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67 </outputs> |
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68 <requirements> |
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69 <requirement type="binary">mothur</requirement> |
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70 </requirements> |
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71 <tests> |
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72 </tests> |
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73 <help> |
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74 **Mothur Overview** |
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75 |
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76 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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77 in the Department of Microbiology and Immunology at The University of Michigan, |
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78 provides bioinformatics for the microbial ecology community. |
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79 |
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80 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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81 |
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82 **Command Documenation** |
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83 |
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84 The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, name, group, list, taxonomy. |
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85 |
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86 .. _get.groups: http://www.mothur.org/wiki/Get.groups |
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87 |
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88 |
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89 </help> |
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90 </tool> |