Mercurial > repos > iuc > mothur_sort_seqs
annotate sort.seqs.xml @ 0:60c599375cad draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
| author | iuc |
|---|---|
| date | Fri, 24 Jun 2016 16:50:30 -0400 |
| parents | |
| children | 9900cd702dcf |
| rev | line source |
|---|---|
|
0
60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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1 <tool profile="16.07" id="mothur_sort_seqs" name="Sort.seqs" version="@WRAPPER_VERSION@.0"> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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2 <description>put sequences in different files in the same order</description> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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3 <macros> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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5 </macros> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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6 <expand macro="requirements"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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7 <expand macro="version_command"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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8 <command detect_errors="aggressive"><![CDATA[ |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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9 ## create symlinks to input datasets |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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10 ln -s "$fasta_in" fasta_in.dat && |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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11 ln -s "$qfile_in" qfile_in.dat && |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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12 ln -s "$flow_in" flow_in.dat && |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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13 ln -s "$name_in" name_in.dat && |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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14 ln -s "$group_in" group_in.dat && |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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15 ln -s "$tax_in" tax_in.dat && |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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16 ln -s "$accnos" accnos.dat && |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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17 ln -s "$count" count.dat && |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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18 |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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19 echo 'sort.seqs( |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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20 #if $fasta_in: |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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21 fasta=fasta_in.dat, |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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22 #end if |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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23 #if $qfile_in: |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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24 qfile=qfile_in.dat, |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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25 #end if |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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26 #if $flow_in: |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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27 flow=flow_in.dat, |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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28 #end if |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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29 #if $name_in: |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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30 name=name_in.dat, |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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31 #end if |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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32 #if $group_in: |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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33 group=group_in.dat, |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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34 #end if |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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35 #if $tax_in: |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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36 taxonomy=tax_in.dat, |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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37 #end if |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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38 #if $accnos: |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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39 accnos=accnos.dat, |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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40 #end if |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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41 #if $count: |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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42 count=count.dat, |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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43 #end if |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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44 large=$large |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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45 )' |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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46 | sed 's/ //g' ## mothur trips over whitespace |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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changeset
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47 | mothur |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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48 ]]></command> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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49 <inputs> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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50 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - sequences" help="format must be fasta"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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51 <param name="qfile_in" type="data" format="qual454" optional="true" label="qfile - sequence quality" help="format must be qual454"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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52 <param name="flow_in" type="data" format="mothur.sff.flow" optional="true" label="flow - sff flowgram" help="format must be mothur.sff.flow"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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53 <param name="group_in" type="data" format="mothur.groups" optional="true" label="groups - sequence groupings" help="format must be mothur.groups"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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54 <param name="name_in" type="data" format="mothur.names" optional="true" label="names - name reference" help="format must be mothur.names"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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55 <param name="tax_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - taxonomy reference" help="format must be mothur.seq.taxonomy"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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56 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - sort" help="format must be mothur.accnos"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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57 <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="format must be mothur.count_table (generated by count.seqs)"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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58 <param name="large" type="boolean" checked="false" truevalue="true" falsevalue="false" label="large - Datasets are large and may not fit in RAM"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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59 </inputs> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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60 <outputs> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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61 <expand macro="logfile-output"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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62 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.fasta"> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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63 <filter>fasta_in</filter> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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64 </data> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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65 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.qfile"> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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66 <filter>qfile_in</filter> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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67 </data> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
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68 <data name="flow_out" format_source="flow_in" from_work_dir="flow_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.flow"> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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69 <filter>flow_in</filter> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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70 </data> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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71 <data name="group_out" format_source="group_in" from_work_dir="group_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.group"> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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72 <filter>group_in</filter> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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73 </data> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
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74 <data name="name_out" format_source="name_in" from_work_dir="name_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.name"> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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75 <filter>name_in</filter> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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76 </data> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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77 <data name="taxonomy_out" format_source="tax_in" from_work_dir="tax_in*.sorted.*" label="${tool.name} on ${on_string}: sorted.taxonomy"> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
changeset
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78 <filter>tax_in</filter> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff
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79 </data> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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80 </outputs> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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81 <tests> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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82 <test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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83 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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84 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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85 <expand macro="logfile-test"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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86 </test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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87 <test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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88 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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89 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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90 <expand macro="logfile-test"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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91 </test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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92 <test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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93 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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94 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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95 <expand macro="logfile-test"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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96 </test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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97 <test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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98 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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99 <param name="count" value="amazon.count_table" ftype="mothur.count_table"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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100 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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101 <expand macro="logfile-test"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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102 </test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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103 <test><!-- test with multiple file types input --> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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104 <param name="fasta_in" value="amazon.fasta" ftype="fasta"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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105 <param name="qfile_in" value="Mock_S280_L001_R1_001_small.trim.contigs.qual" ftype="qual454"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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106 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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107 <output name="fasta_out" md5="0bc9320647234e8367c3b1b654f9302d" ftype="fasta"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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108 <output name="qfile_out" md5="abed9d1811786c810a12fd00a376cee4" ftype="qual454"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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109 <output name="group_out" md5="fb60628ae445e7b06f9833f632b2cd0c" ftype="mothur.groups"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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110 <expand macro="logfile-test"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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111 </test> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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112 </tests> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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113 <help> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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114 <![CDATA[ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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115 |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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116 @MOTHUR_OVERVIEW@ |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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117 |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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118 **Command Documenation** |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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119 |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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120 The sort.seqs_ command puts sequences from a fasta, name, group, quality, flow or taxonomy file in the same order. |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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121 You can provide an accnos file to indicate the order you want, otherwise mothur will use the order of the first file it reads. |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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122 |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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123 .. _sort.seqs: http://www.mothur.org/wiki/Sort.seqs |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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124 |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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125 ]]> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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126 </help> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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127 <expand macro="citations"/> |
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60c599375cad
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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128 </tool> |
