Mercurial > repos > iuc > mothur_get_dists

annotate get.dists.xml @ 0:a38b4b058203 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:47:05 -0400
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children bc5112d1d317
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a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_get_dists" name="Get.dists" version="@WRAPPER_VERSION@.0">
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
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13 ln -s "$accnos" accnos.dat &&
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$input.dist" input.dist.dat &&
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15
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16 echo 'get.dists(
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 accnos=accnos.dat,
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18 #if $input.source == "phylip":
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19 phylip=input.dist.dat
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 #else
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21 column=input.dist.dat
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22 #end if
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23 )'
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24 | sed 's/ //g' ## mothur trips over whitespace
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25 | mothur
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26 | tee mothur.out.log
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 ]]></command>
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28 <inputs>
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29 <conditional name="input">
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30 <param name="source" type="select" label="Select input format">
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31 <option value="column">Pairwise Column Distance Matrix</option>
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 <option value="phylip">Phylip Distance Matrix</option>
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33 </param>
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34 <when value="column">
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35 <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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36 </when>
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37 <when value="phylip">
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
a38b4b058203 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 </when>
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40 </conditional>
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41 <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
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42 </inputs>
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43 <outputs>
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44 <expand macro="logfile-output"/>
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45 <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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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="source" value="phylip"/>
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50 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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51 <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
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52 <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/>
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53 <expand macro="logfile-test"/>
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54 </test>
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55 </tests>
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56 <help>
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57 <![CDATA[
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58
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59 @MOTHUR_OVERVIEW@
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60
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61 **Command Documentation**
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62
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63 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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64
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65 .. _get.dists: https://www.mothur.org/wiki/Get.dists
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66
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67 v.1.20.0: Updated to Mothur 1.33
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68 ]]>
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69 </help>
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70 <expand macro="citations"/>
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71 </tool>