Mercurial > repos > iuc > mothur_split_groups

annotate split.groups.xml @ 1:addf3c859349 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 17:02:15 -0400
parents dba66f208b1a
children 5f34cf40f36d
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dba66f208b1a 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_split_groups" name="Split.groups" version="@WRAPPER_VERSION@.0">
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Generates a fasta file for each group</description>
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$name" name.dat &&
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$count" count.dat &&
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$fasta" fasta.dat &&
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 ln -s "$group" group.dat &&
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17
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18 echo 'split.groups(
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 #if $name:
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20 name=name.dat,
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 #end if
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22 #if $groups:
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23 groups=${ str($groups).replace(",","-") },
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #end if
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25 #if $count:
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 count=count.dat,
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 #end if
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28 fasta=fasta.dat,
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 group=group.dat
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 )'
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31 | sed 's/ //g' ## mothur trips over whitespace
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 | mothur
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33 | tee mothur.out.log
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34 ]]></command>
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35 <inputs>
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36 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to split by group"/>
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 <param name="name" type="data" format="mothur.names" label="name - Names to split by group" optional="true"/>
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <param name="group" type="data" format="mothur.groups" label="group - Groups"/>
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 <options>
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41 <filter type="data_meta" ref="group" key="groups"/>
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42 </options>
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43 </param>
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44 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
dba66f208b1a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 </inputs>
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46 <outputs>
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47 <expand macro="logfile-output"/>
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48 <collection name="groupfastas" type="list" label="${tool.name} on ${on_string}: fasta per group">
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49 <!-- TODO: format_source on discovered collection elements doesn't seem to work yet, change to format_source="fasta" once it does -->
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50 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.fasta" format="fasta"/>
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51 </collection>
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52 </outputs>
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53 <tests>
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54 <test>
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55 <param name="fasta" value="amazon.fasta" ftype="fasta"/>
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56 <param name="group" value="amazon.groups" ftype="mothur.groups"/>
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57 <output_collection name="groupfastas" count="2">
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58 <element name="pasture" md5="3844bc02ec09acbbf31845ea6ac6632d" ftype="fasta"/>
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59 <element name="forest" md5="f0e662d1d82e96b4977864925493dbf5" ftype="fasta"/>
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60 </output_collection>
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61 <expand macro="logfile-test"/>
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62 </test>
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63 </tests>
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64 <help>
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65 <![CDATA[
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66
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67 @MOTHUR_OVERVIEW@
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68
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69 **Command Documentation**
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70
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71 The split.groups_ command reads a fasta file and group_ file and generates a fasta file for each group in the groupfile. A name_ file can also be split into groups.
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72
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73 .. _group: https://www.mothur.org/wiki/Group_file
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74 .. _name: https://www.mothur.org/wiki/Name_file
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75 .. _split.groups: https://www.mothur.org/wiki/Split.groups
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76 ]]>
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77 </help>
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78 <expand macro="citations"/>
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79 </tool>