Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/split.groups.xml @ 25:bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 16 May 2012 12:28:44 -0500 |
parents | 7bfe1f843858 |
children | 49058b1f8d3f |
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7 | 1 <tool id="mothur_split_groups" name="Split.groups" version="1.20.0" 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='$__new_file_path__' |
4 | 9 --new_datasets='^\S+?\.(\S+\.fasta)$:${fasta.ext}','^\S+?\.(\S+\.names)$: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=$groups |
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17 #end if |
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18 </command> |
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19 <inputs> |
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20 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/> |
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21 <param name="name" type="data" format="names" label="name - Names to split by group" optional="true"/> |
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22 <param name="group" type="data" format="groups" label="group - Groups"/> |
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23 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true"> |
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bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
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24 <options> |
bfbaf823be4c
Change metagenomics datatypes to include labels and groups metadata. change Mothur tool configs to get label and group select options from a data_meta filter rather than using the options from_dataset attribute. This grealty decreases memory demand for the galaxy server.
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25 <filter type="data_meta" ref="group" key="groups" /> |
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26 </options> |
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27 </param> |
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28 </inputs> |
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29 <outputs> |
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30 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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31 </outputs> |
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32 <requirements> |
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33 <requirement type="binary">mothur</requirement> |
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34 </requirements> |
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35 <tests> |
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36 </tests> |
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37 <help> |
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38 **Mothur Overview** |
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39 |
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40 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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41 in the Department of Microbiology and Immunology at The University of Michigan, |
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42 provides bioinformatics for the microbial ecology community. |
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43 |
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44 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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45 |
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46 **Command Documenation** |
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47 |
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48 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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49 |
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50 .. _group: http://www.mothur.org/wiki/Group_file |
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51 .. _name: http://www.mothur.org/wiki/Name_file |
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52 .. _split.groups: http://www.mothur.org/wiki/Split.groups |
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53 |
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54 </help> |
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55 </tool> |