Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.relabund.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | 3202a38e44d9 |
children | e990ac8a0f58 |
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1 <tool id="mothur_get_relabund" name="Get.relabund" version="1.16.0"> |
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2 <description>Calculate the relative abundance of each otu</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='get.relabund' |
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6 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.relabund$:'$relabund |
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7 --outputdir='$logfile.extra_files_path' |
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8 --READ_cmd='read.otu' |
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9 #if $input.source == 'similarity': |
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10 --READ_list=$input.otu |
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11 #if $otu_group.__str__ != "None" and len($otu_group.__str__) > 0: |
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12 --READ_group='$otu_group' |
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13 #end if |
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14 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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15 --READ_label='$input.label' |
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16 #end if |
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17 #elif $input.source == 'shared': |
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18 --READ_shared=$input.otu |
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19 #if $input.label.__str__ != "None" and len($input.label.__str__) > 0: |
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20 --READ_label='$input.label' |
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21 #end if |
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22 #end if |
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23 #if $input.groups.__str__ != "None" and len($input.groups.__str__) > 0: |
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24 --groups=$input.groups |
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25 #end if |
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26 #if $scale.__str__ != "None" and len($scale.__str__) > 0: |
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27 --scale=$scale |
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28 #end if |
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29 </command> |
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30 <inputs> |
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31 <conditional name="input"> |
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32 <param name="source" type="select" label="Get Relative abundance for"> |
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33 <option value="similarity">OTU list</option> |
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34 <option value="shared">OTU Shared</option> |
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35 </param> |
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36 <when value="similarity"> |
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37 <param name="otu" type="data" format="list" label="read.otu(list=) - OTU List"/> |
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38 <param name="otu_group" type="data" format="groups" label="read.otu(group=) - Group file for the OTU List"/> |
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39 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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40 <options from_dataset="otu"> |
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41 <column name="name" index="0"/> |
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42 <column name="value" index="0"/> |
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43 </options> |
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44 </param> |
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45 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
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46 <options from_dataset="otu_group"> |
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47 <column name="name" index="1"/> |
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48 <column name="value" index="1"/> |
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49 <filter type="unique_value" name="unq_grp" column="1" /> |
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50 </options> |
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51 </param> |
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52 </when> |
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53 <when value="shared"> |
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54 <param name="otu" type="data" format="shared" label="read.otu(shared=) - OTU Shared"/> |
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55 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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56 <options from_dataset="otu"> |
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57 <column name="name" index="0"/> |
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58 <column name="value" index="0"/> |
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59 <filter type="unique_value" name="unq_lbl" column="0" /> |
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60 </options> |
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61 </param> |
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62 <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> |
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63 <options from_dataset="otu"> |
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64 <column name="name" index="1"/> |
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65 <column name="value" index="1"/> |
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66 <filter type="unique_value" name="unq_grp" column="1" /> |
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67 </options> |
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68 </param> |
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69 </when> |
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70 </conditional> |
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71 <param name="scale" type="select" label="scale - Scale by"> |
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72 <option value="">Use default</option> |
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73 <option value="totalgroup">Total Groups</option> |
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74 <option value="totalotu">Total OTUs</option> |
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75 <option value="averagegroup">Average Groups</option> |
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76 <option value="averageotu">Average OTUs</option> |
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77 </param> |
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78 </inputs> |
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79 <outputs> |
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80 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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81 <data format="relabund" name="relabund" label="${tool.name} on ${on_string}: relabund" /> |
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82 </outputs> |
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83 <requirements> |
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84 <requirement type="binary">mothur</requirement> |
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85 </requirements> |
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86 <tests> |
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87 </tests> |
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88 <help> |
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89 **Mothur Overview** |
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90 |
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91 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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92 in the Department of Microbiology and Immunology at The University of Michigan, |
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93 provides bioinformatics for the microbial ecology community. |
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94 |
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95 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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96 |
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97 **Command Documenation** |
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98 |
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99 The get.relabund_ command calculates the relative abundance of each otu in a sample. It outputs a .relabund file. |
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100 |
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101 .. _get.relabund: http://www.mothur.org/wiki/Get.relabund |
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102 |
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103 </help> |
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104 </tool> |