Mercurial > repos > iuc > mothur_get_dists

annotate get.dists.xml @ 0:c5b0a5fca6d8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:31:17 -0400
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children 9f28030ac5c5
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_get_dists" name="Get.dists" version="@WRAPPER_VERSION@.0">
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2 <description>selects distances from a phylip or column file</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
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10 ln -s "$accnos" accnos.dat &&
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$input.dist" input.dist.dat &&
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12
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13 echo 'get.dists(
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 accnos=accnos.dat,
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 #if $input.source == "phylip":
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 phylip=input.dist.dat
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17 #else
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18 column=input.dist.dat
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19 #end if
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20 )'
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21 | sed 's/ //g' ## mothur trips over whitespace
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 | mothur
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23 ]]></command>
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24 <inputs>
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25 <conditional name="input">
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26 <param name="source" type="select" label="Select input format">
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 <option value="column">Pairwise Column Distance Matrix</option>
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <option value="phylip">Phylip Distance Matrix</option>
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 </param>
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30 <when value="column">
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31 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 </when>
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <when value="phylip">
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34 <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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35 </when>
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36 </conditional>
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37 <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
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38 </inputs>
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39 <outputs>
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40 <expand macro="logfile-output"/>
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <data name="pick_dist" format_source="dist" from_work_dir="input.dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/>
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42 </outputs>
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43 <tests>
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44 <test>
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45 <param name="source" value="phylip"/>
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46 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/>
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49 <expand macro="logfile-test"/>
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50 </test>
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51 </tests>
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52 <help>
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53 <![CDATA[
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54
c5b0a5fca6d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 @MOTHUR_OVERVIEW@
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56
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57 **Command Documenation**
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58
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59 The get.dists_ command selects distances from a phylip or column file related to groups or sequences listed in an accnos file.
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60
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61 .. _get.dists: http://www.mothur.org/wiki/Get.dists
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62
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63 v.1.20.0: Updated to Mothur 1.33
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64 ]]>
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65 </help>
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66 <expand macro="citations"/>
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67 </tool>