Mercurial > repos > jjohnson > mothur_toolsuite
annotate mothur/tools/mothur/make.design.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_make_design" name="Make Design" version="1.19.0" > |
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2 <description>Assign groups to Sets</description> |
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3 <command> cat $generated_design > $design |
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4 </command> |
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5 <inputs> |
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6 <param name="source" type="data" format="shared,groups" label="Source containing groups"/> |
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7 <repeat name="groupings" title="Grouping"> |
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8 <param name="name" type="text" label="Name for a new combined grouping"/> |
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9 <param name="groups" type="select" multiple="true" label="Select groups for to include in this grouping"> |
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10 <options from_dataset="source"> |
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11 <column name="name" index="1"/> |
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12 <column name="value" index="1"/> |
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13 <filter type="unique_value" name="unq_grp" column="1" /> |
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14 </options> |
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15 </param> |
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16 </repeat> |
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17 </inputs> |
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18 <configfiles> |
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19 <configfile name="generated_design"> |
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20 #for $grouping in $groupings: |
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21 #set grp_str = $grouping.groups.__str__ |
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22 #if grp_str != None and len(grp_str) > 0: |
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23 #for $grp in grp_str.split(','): |
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24 $grp $grouping.name |
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25 #end for |
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26 #end if |
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27 #end for |
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28 </configfile> |
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29 </configfiles> |
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30 <outputs> |
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31 <data format="design" name="design" label="${tool.name} on ${on_string}: design" /> |
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32 </outputs> |
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33 <requirements> |
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34 <requirement type="binary">mothur</requirement> |
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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 Make Design creates a design file for use in mothur commands: merge.groups_, indicator_, and metastats_. |
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50 A design file looks like the group file. It is a 2 column tab delimited file, where the first column is the group name and the second column is the set the group belongs to. |
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51 |
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52 .. _merge.groups: http://www.mothur.org/wiki/Merge.groups |
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53 .. _indicator: http://www.mothur.org/wiki/Indicator |
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54 .. _metastats: http://www.mothur.org/wiki/Metastats |
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55 |
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56 </help> |
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57 </tool> |