Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/parse.list.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 | bfbaf823be4c |
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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_parse_list" name="Parse.list" version="1.19.0" force_history_refresh="True"> |
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2 <description>Generate a List 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='parse.list' |
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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='$__new_file_path__' |
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9 --new_datasets='^\S+?\.(\S+\.list)$:list' |
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10 --list=$otu |
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11 --group=$group |
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12 #if $label.__str__ != "None" and len($label.__str__) > 0: |
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13 --label='$label' |
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14 #end if |
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15 </command> |
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16 <inputs> |
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17 <param name="otu" type="data" format="list" label="list - OTU List"/> |
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18 <param name="group" type="data" format="groups" label="group - Sequences Name reference"/> |
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19 <param name="label" type="select" optional="true" label="label - To filter: Select OTU Labels to include" multiple="true"> |
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20 <help>All labels are included if none are selected</help> |
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21 <options from_dataset="otu"> |
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22 <column name="name" index="0"/> |
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23 <column name="value" index="0"/> |
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24 </options> |
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25 </param> |
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26 </inputs> |
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27 <outputs> |
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28 <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> |
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29 </outputs> |
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30 <requirements> |
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31 <requirement type="binary">mothur</requirement> |
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32 </requirements> |
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33 <tests> |
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34 </tests> |
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35 <help> |
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36 **Mothur Overview** |
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37 |
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38 Mothur_, initiated by Dr. Patrick Schloss and his software development team |
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39 in the Department of Microbiology and Immunology at The University of Michigan, |
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40 provides bioinformatics for the microbial ecology community. |
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41 |
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42 .. _Mothur: http://www.mothur.org/wiki/Main_Page |
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43 |
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44 **Command Documenation** |
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45 |
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Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
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46 The parse.list_ command reads a list_ file and group_ file and generates a list_ file for each group_ in the groupfile. |
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47 |
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48 .. _list: http://www.mothur.org/wiki/List_file |
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49 .. _group: http://www.mothur.org/wiki/Group_file |
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50 .. _parse.list: http://www.mothur.org/wiki/Parse.list |
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51 |
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52 </help> |
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53 </tool> |