Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/make.shared_from_biom.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 |
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26
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1 <tool id="mothur_make_shared_from_biom" name="Make.shared " version="1.25.0" force_history_refresh="True"> |
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2 <description>Make a shared file from a biom file</description> |
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3 <command interpreter="python"> |
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4 mothur_wrapper.py |
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5 #import re, os.path |
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6 --cmd='make.shared' |
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7 --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared$:'$shared |
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8 --outputdir='$logfile.extra_files_path' |
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9 #if $as_datasets.__str__ == "yes": |
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10 --datasetid='$logfile.id' --new_file_path='$__new_file_path__' |
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11 --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' |
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12 #end if |
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13 --biom=$biom |
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14 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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15 --label='$label' |
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16 #end if |
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17 #if $groups.__str__ != "None" and len($groups.__str__) > 0: |
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18 --groups=$groups |
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19 #end if |
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20 </command> |
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21 <inputs> |
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22 <param name="biom" type="data" format="biom" label="biom - The Biological Observation Matrix"/> |
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23 <param name="label" type="text" size="40" label="label - to restrict to these OTU Labels" |
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24 help="multiple labels separated by hyphens, example: unique-0.02-0.04"/> |
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25 <param name="groups" type="text" size="40" label="groups - restrict to these groups" |
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26 help="multiple groups separated by hyphens, example: control-group1-group2"/> |
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27 <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Create a new history dataset for each group rabund"/> |
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28 </inputs> |
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29 <outputs> |
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30 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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31 <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> |
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32 </outputs> |
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33 <requirements> |
27
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34 <requirement type="package" version="1.27">mothur</requirement> |
26
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35 </requirements> |
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36 <tests> |
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37 </tests> |
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38 <help> |
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39 **Mothur Overview** |
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40 |
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41 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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42 in the Department of Microbiology and Immunology at The University of Michigan, |
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43 provides bioinformatics for the microbial ecology community. |
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44 |
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45 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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46 |
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47 **Command Documenation** |
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48 |
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49 The make.shared_ command takes a list_ and a group_ file and outputs a shared_ file, as well as a rabund_ file for each group. |
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50 |
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51 |
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52 .. _list: http://www.mothur.org/wiki/List_file |
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53 .. _group: http://www.mothur.org/wiki/Group_file |
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54 .. _shared: http://www.mothur.org/wiki/Shared_file |
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55 .. _rabund: http://www.mothur.org/wiki/Rabund_file |
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56 .. _make.shared: http://www.mothur.org/wiki/Make.shared |
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57 |
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58 </help> |
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59 </tool> |