Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.groups.xml @ 36:040410b8167e default tip
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author | galaxyuser <galaxy_user@agr.g.ca> |
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date | Mon, 10 Nov 2014 15:40:02 -0500 |
parents | 95d75b35e4d2 |
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24
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1 <tool id="mothur_get_groups" name="Get.groups" version="1.24.0"> |
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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 #if isinstance($group_in.datatype, $__app__.datatypes_registry.get_datatype_by_extension('groups').__class__): |
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12 --group=$group_in |
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13 #else |
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14 --count=$group_in |
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15 #end if |
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16 #if $groupnames.source == 'groups': |
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17 #if $groupnames.groups.__str__ != "None" and len($groupnames.groups.__str__) > 0: |
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18 --groups=$groupnames.groups |
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19 #end if |
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20 #else |
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21 #if $groupnames.accnos.__str__ != "None" and len($groupnames.accnos.__str__) > 0: |
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22 --accnos=$groupnames.accnos |
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23 #end if |
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24 #end if |
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25 #if $fasta_in.__str__ != "None" and len($fasta_in.__str__) > 0: |
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26 --fasta=$fasta_in |
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27 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($fasta_in.__str__)) + ":'" + $fasta_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 #end if |
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33 #if $list_in.__str__ != "None" and len($list_in.__str__) > 0: |
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34 --list=$list_in |
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35 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($list_in.__str__)) + ":'" + $list_out.__str__] |
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36 #end if |
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37 #if $shared_in.__str__ != "None" and len($shared_in.__str__) > 0: |
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38 --shared=$shared_in |
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39 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($shared_in.__str__)) + ":'" + $shared_out.__str__] |
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40 #end if |
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41 #if $taxonomy_in.__str__ != "None" and len($taxonomy_in.__str__) > 0: |
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42 --taxonomy=$taxonomy_in |
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43 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1\\.pick\\.\2',$os.path.basename($taxonomy_in.__str__)) + ":'" + $taxonomy_out.__str__] |
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44 #end if |
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45 #if $design_in.__str__ != "None" and len($design_in.__str__) > 0: |
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46 --design=$design_in |
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47 #set results = $results + ["'" + $re.sub(r'(^.*)\.(.*?)',r'\1.*\\.pick\\.\2',$os.path.basename($design_in.__str__)) + ":'" + $design_out.__str__] |
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48 #end if |
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49 --result=#echo ','.join($results) |
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50 </command> |
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51 <inputs> |
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52 <param name="group_in" type="data" format="groups,count_table" label="group or count_table file"/> |
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53 <conditional name="groupnames"> |
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54 <param name="source" type="select" label="Select Group Names from"> |
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55 <option value="groups">A List of Group Names</option> |
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56 <option value="accnos">A History Group Name Accnos Dataset</option> |
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57 </param> |
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58 <when value="groups"> |
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59 <param name="groups" type="select" label="groups - Pick groups to include" multiple="true"> |
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60 <options> |
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61 <filter type="data_meta" ref="group_in" key="groups" /> |
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62 </options> |
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63 </param> |
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64 </when> |
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65 <when value="accnos"> |
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66 <param name="accnos" type="data" format="accnos" label="accnos - Group Names from your history"/> |
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67 </when> |
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68 </conditional> |
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69 <param name="fasta_in" type="data" format="fasta,align" optional="true" label="fasta - Fasta Sequences"/> |
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70 <param name="name_in" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
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71 <param name="list_in" type="data" format="list" optional="true" label="list - OTU List"/> |
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72 <param name="shared_in" type="data" format="shared" optional="true" label="shared - OTU Shared"/> |
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73 <param name="taxonomy_in" type="data" format="seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/> |
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74 <param name="design_in" type="data" format="tabular" optional="true" label="design - assign groups to new grouping" |
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75 help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/> |
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76 </inputs> |
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77 <outputs> |
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78 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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79 <data format="groups" name="group_out" label="${tool.name} on ${on_string}: pick.groups"/> |
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80 <!-- fix format --> |
4 | 81 <data format_source="fasta_in" name="fasta_out" label="${tool.name} on ${on_string}: pick.fasta"> |
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82 <filter>fasta_in != None</filter> |
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83 </data> |
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84 <data format="names" name="name_out" label="${tool.name} on ${on_string}: pick.name"> |
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85 <filter>name_in != None</filter> |
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86 </data> |
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87 <data format="list" name="list_out" label="${tool.name} on ${on_string}: pick.list"> |
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88 <filter>list_in != None</filter> |
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89 </data> |
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90 <data format="shared" name="shared_out" label="${tool.name} on ${on_string}: pick.shared"> |
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91 <filter>shared_in != None</filter> |
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92 </data> |
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93 <data format="seq.taxonomy" name="taxonomy_out" label="${tool.name} on ${on_string}: pick.taxonomy"> |
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94 <filter>taxonomy_in != None</filter> |
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95 </data> |
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96 <data format="design" name="design_out" label="${tool.name} on ${on_string}: pick.design"> |
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97 <filter>design_in != None</filter> |
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98 </data> |
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99 </outputs> |
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100 <requirements> |
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101 <requirement type="package" version="1.33">mothur</requirement> |
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102 </requirements> |
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103 <tests> |
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104 </tests> |
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105 <help> |
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106 **Mothur Overview** |
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107 |
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108 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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109 in the Department of Microbiology and Immunology at The University of Michigan, |
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110 provides bioinformatics for the microbial ecology community. |
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111 |
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112 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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113 |
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114 **Command Documenation** |
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115 |
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116 The get.groups_ command selects sequences from a specific group or set of groups from the following file types: fasta, fasta, name_, group_, list_, taxonomy_. |
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117 |
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118 .. _name: http://www.mothur.org/wiki/Name_file |
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119 .. _group: http://www.mothur.org/wiki/Group_file |
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120 .. _list: http://www.mothur.org/wiki/List_file |
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121 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline |
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122 .. _get.groups: http://www.mothur.org/wiki/Get.groups |
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123 |
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124 |
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125 </help> |
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126 </tool> |