Mercurial > repos > iuc > mothur_remove_dists

annotate remove.dists.xml @ 5:9067f78ae9bd draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:30:19 -0500
parents 27ab74145f55
children 6a4feed29ebc
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1c601f47dd3d 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_remove_dists" name="Remove.dists" version="@WRAPPER_VERSION@.0">
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2 <description>Removes 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 '$accnos' accnos.dat &&
9067f78ae9bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$input.dist' input_dist.dat &&
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15
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16 echo 'remove.dists(
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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
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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
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27 ]]></command>
1c601f47dd3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <inputs>
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29 <conditional name="input">
1c601f47dd3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <param name="source" type="select" label="Select input format">
1c601f47dd3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 <option value="column">Pairwise Column Distance Matrix</option>
1c601f47dd3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <option value="phylip">Phylip Distance Matrix</option>
1c601f47dd3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 </param>
1c601f47dd3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <when value="column">
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35 <param name="dist" argument="column" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
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36 </when>
1c601f47dd3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <when value="phylip">
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38 <param name="dist" argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
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39 </when>
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40 </conditional>
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41 <param argument="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 ${on_string}: pick.dist"/>
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="source" value="phylip"/>
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50 <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
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51 <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
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52 <output name="pick_dist" ftype="mothur.square.dist">
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53 <assert_contents>
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54 <expand macro="test-dist-format"/>
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55 <has_text text="U68589"/>
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56 <has_line_matching expression="^90$"/>
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57 </assert_contents>
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58 </output>
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59 <expand macro="logfile-test"/>
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60 </test>
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61 </tests>
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62 <help><![CDATA[
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63
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64 @MOTHUR_OVERVIEW@
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65
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66 **Command Documentation**
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67
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68 The remove.dists_ removes distances from a phylip or column file related to groups or sequences listed in an accnos file.
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69
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70 .. _remove.dists: https://www.mothur.org/wiki/Remove.dists
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71
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72 ]]></help>
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73 <expand macro="citations"/>
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74 </tool>