Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/split.groups.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 5265aa9067e0 |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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1 <tool id="mothur_split_groups" name="Split.groups" version="1.19.0" force_history_refresh="True"> |
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2 <description>Generates a fasta file for each group</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='split.groups' |
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6 --result='^mothur.\S+\.logfile$:'$logfile |
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7 --outputdir='$logfile.extra_files_path' |
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8 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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9 --new_datasets='^\S+?\.(\S+\.fasta)$:fasta','^\S+?\.(\S+\.names)$:names' |
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10 --fasta=$fasta |
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11 --group=$group |
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12 #if $name.__str__ != "None" and len($name.__str__) > 0: |
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13 --name=$name |
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14 #end if |
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15 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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16 --groups=$groups |
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17 #end if |
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18 </command> |
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19 <inputs> |
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20 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/> |
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21 <param name="name" type="data" format="names" label="name - Names to split by group" optional="true"/> |
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22 <param name="group" type="data" format="groups" label="group - Groups"/> |
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23 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true"> |
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24 <options from_dataset="group"> |
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25 <column name="name" index="1"/> |
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26 <column name="value" index="1"/> |
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27 <filter type="unique_value" name="unq_grp" column="1" /> |
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28 </options> |
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29 </param> |
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30 </inputs> |
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31 <outputs> |
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32 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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33 </outputs> |
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34 <requirements> |
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35 <requirement type="binary">mothur</requirement> |
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36 </requirements> |
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37 <tests> |
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38 </tests> |
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39 <help> |
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40 **Mothur Overview** |
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41 |
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42 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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43 in the Department of Microbiology and Immunology at The University of Michigan, |
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44 provides bioinformatics for the microbial ecology community. |
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45 |
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46 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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47 |
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48 **Command Documenation** |
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49 |
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50 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups. |
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51 |
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52 .. _group: http://www.mothur.org/wiki/Group_file |
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53 .. _name: http://www.mothur.org/wiki/Name_file |
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54 .. _split.groups: http://www.mothur.org/wiki/Split.groups |
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55 |
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56 </help> |
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57 </tool> |