Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/bin.seqs.xml @ 7:7bfe1f843858
Support Mothur v1.20
trim.seqs - added name parameter and optional trim.names output
phylo.diversity - group optional, put group and groups in conditional - breaks
get.lineage remove.lineage - allow multiple taxons
dist.shared - added processors
consensus.seqs - add cutoff parameter
trim.seqs,phylo.diversity,get.lineage,remove.lineage,dist.shared,consensus.seqs
new tools - chimera.uchime deunique.tree count.seqs
shared/relabund files - Column headings
refactor lib/galaxy/datatypes/metagenomics.py
add filters to label and group selects in tool configs
mothur_wrapper.py updated with new tools params
author | Jim Johnson <jj@umn.edu> |
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date | Mon, 27 Jun 2011 10:12:25 -0500 |
parents | 5265aa9067e0 |
children | bfbaf823be4c |
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7 | 1 <tool id="mothur_bin_seqs" name="Bin.seqs" version="1.20.0" force_history_refresh="True"> |
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2 <description>Order Sequences by OTU</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 --cmd='bin.seqs' |
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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='$__new_file_path__' |
4 | 9 --new_datasets='^\S+?\.(unique|[0-9.]*)\.fasta$:${fasta.ext}' |
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10 --fasta=$fasta |
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11 --list=$otu |
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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 $label.__str__ != "None" and len($label.__str__) > 0: |
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16 --label='$label' |
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17 #end if |
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18 #if $group.__str__ != "None" and len($group.__str__) > 0: |
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19 --group='$group' |
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20 #end if |
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21 </command> |
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22 <inputs> |
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23 <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin"/> |
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24 <param name="otu" type="data" format="list" label="list - OTU List"/> |
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25 <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> |
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26 <param name="label" type="select" label="label - OTU Labels" multiple="true"> |
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27 <options from_dataset="otu"> |
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28 <column name="name" index="0"/> |
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29 <column name="value" index="0"/> |
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30 </options> |
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31 </param> |
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32 <param name="group" type="data" format="group" optional="true" label="group - Sequences Name reference"/> |
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33 </inputs> |
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34 <outputs> |
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35 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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36 </outputs> |
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37 <requirements> |
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38 <requirement type="binary">mothur</requirement> |
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39 </requirements> |
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40 <tests> |
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41 </tests> |
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42 <help> |
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43 **Mothur Overview** |
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44 |
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45 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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46 in the Department of Microbiology and Immunology at The University of Michigan, |
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47 provides bioinformatics for the microbial ecology community. |
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48 |
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49 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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50 |
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51 **Command Documenation** |
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52 |
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53 The bin.seqs_ command generates fasta-formatted files where sequences are ordered according to the OTU from the list_file_ that they belong to. Such an output may be helpful for generating primers specific to an OTU or for classification of sequences. |
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54 |
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55 .. _list_file: http://www.mothur.org/wiki/List_file |
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56 .. _bin.seqs: http://www.mothur.org/wiki/Bin.seqs |
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57 |
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58 </help> |
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59 </tool> |