Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/get.otulist.xml @ 32:ec8df51e841a
Fixes courtesy of Peter Briggs:
metagenomics.py:
- Groups class: Fix for when second column not present
- Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular
data uploads being sniffed as this type
mothur_wrapper.py:
- update cmd_dict['chimera.perseus'], to use correct inputs
- add --beta option (needed for chimera.perseus tool)
- add function for converting input floats from scientific notation (e.g. 1e-6,
which mothur can't handle) to decimal format (e.g. 0.00001, which it can)
chimera.perseus.xml:
- add output data item for the "accnos" file (not previous captured in the
history)
trim.flows.xml:
- cosmetic change: base name for additional output data items is now "trim.flows",
rather than "logfile" (clarifies history items)
shhh.flows.xml:
- cosmetic change: update default value specified in help for mindiff to be
consistent with that given in the mothur documentation
author | Jim Johnson <jj@umn.edu> |
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date | Wed, 04 Sep 2013 10:51:34 -0500 |
parents | 49058b1f8d3f |
children | 95d75b35e4d2 |
rev | line source |
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1 <tool id="mothur_get_otulist" name="Get.otulist" force_history_refresh="True" version="1.19.0"> |
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2 <description>Get otus for each distance in a otu list</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 ## output {group_file_name}.pick.{label}.groups {list_file_name}.pick.{label}.list |
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6 #import re, os.path |
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7 --cmd='get.otulist' |
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8 --result='^mothur.\S+\.logfile$:'$logfile |
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9 --outputdir='$logfile.extra_files_path' |
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10 #if $as_datasets.__str__ == "yes": |
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11 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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12 --new_datasets='^\S+?\.((unique|[0-9.]*)\.otu)$:tabular' |
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13 #end if |
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14 --list=$list_in |
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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 $sort.__str__ != "None" and len($sort.__str__) > 0: |
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19 --sort=$sort |
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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="list_in" type="data" format="list" label="list - OTU List"/> |
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24 <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="By default, uses all if none are selected."> |
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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 <options> |
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26 <filter type="data_meta" ref="list_in" key="labels" /> |
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27 </options> |
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28 </param> |
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29 <param name="sort" type="select" label="sort - select the output format"> |
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30 <help>If otu is selected the output will be otu number followed by the list of names in that otu. |
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31 If name is selected the output will be a sequence name followed by its otu number.</help> |
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32 <option value="otu" selected="true">otu</option> |
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33 <option value="name">name</option> |
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34 </param> |
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35 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Create a new history dataset for each label list"/> |
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36 </inputs> |
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37 <outputs> |
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38 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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39 </outputs> |
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40 <requirements> |
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41 <requirement type="package" version="1.27">mothur</requirement> |
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42 </requirements> |
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43 <tests> |
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44 </tests> |
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45 <help> |
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46 **Mothur Overview** |
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47 |
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48 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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49 in the Department of Microbiology and Immunology at The University of Michigan, |
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50 provides bioinformatics for the microbial ecology community. |
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51 |
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52 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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53 |
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54 **Command Documenation** |
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55 |
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56 The get.otulist_ command parses a list file and creates an .otu file for each distance containing 2 columns. The first column is the OTU number the second column is a list of sequences in that OTU. |
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57 |
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58 .. _get.otulist: http://www.mothur.org/wiki/Get.otulist |
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59 |
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60 |
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61 </help> |
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62 </tool> |