Mercurial > repos > iuc > mothur_screen_seqs

annotate screen.seqs.xml @ 0:5a01375eadf0 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 16:49:07 -0400
parents
children d0190913cb6c
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
1 <tool profile="16.07" id="mothur_screen_seqs" name="Screen.seqs" version="@WRAPPER_VERSION@.0">
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
2 <description>Screen sequences</description>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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3 <macros>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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4 <import>macros.xml</import>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
diff changeset
5 </macros>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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6 <expand macro="requirements"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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7 <expand macro="version_command"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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8 <command detect_errors="aggressive"><![CDATA[
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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9 ## create symlinks to input datasets
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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10 ln -s "$fasta_in" fasta_in.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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11 ln -s "$names_in" names_in.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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12 ln -s "$groups_in" groups_in.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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13 ln -s "$qfile_in" qfile_in.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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14 ln -s "$count_in" count_in.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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15 ln -s "$alignreport_in" alignreport_in.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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16 ln -s "$taxonomy_in" taxonomy_in.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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17 ln -s "$summary" summary.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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18 ln -s "$contigsreport" contigsreport.dat &&
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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19
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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20 echo 'screen.seqs(
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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21 fasta=fasta_in.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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22 #if $start > -1:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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23 ,start=$start
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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24 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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25 #if $end > -1:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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26 ,end=$end
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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28 #if $minlength > -1:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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29 ,minlength=$minlength
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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30 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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31 #if $maxlength > -1:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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32 ,maxlength=$maxlength
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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33 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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34 #if $maxambig > -1:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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35 ,maxambig=$maxambig
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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36 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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37 #if $maxhomop > -1:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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38 ,maxhomop=$maxhomop
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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39 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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40 #if $criteria > -1:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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41 ,criteria=$criteria
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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42 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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43 #if $optimize:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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44 ,optimize=$optimize
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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45 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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46 #if $qfile_in:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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47 ,qfile=qfile_in.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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48 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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49 #if $names_in:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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50 ,name=names_in.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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51 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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52 #if $groups_in:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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53 ,group=groups_in.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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54 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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55 #if $alignreport_in:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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56 ,alignreport=alignreport_in.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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57 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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58 #if $taxonomy_in:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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59 ,taxonomy=taxonomy_in.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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60 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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61 #if $count_in:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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62 ,count=count_in.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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63 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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64 #if $summary:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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65 ,summary=summary.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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66 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
parents:
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67 #if $contigsreport:
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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68 ,contigsreport=contigsreport.dat
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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69 #end if
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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70 ,processors='"\${GALAXY_SLOTS:-8}"'
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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71 )'
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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72 | sed 's/ //g' ## mothur trips over whitespace
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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73 | mothur
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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74 ]]></command>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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75 <inputs>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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76 <param name="fasta_in" type="data" format="fasta,mothur.align" label="fasta - Fasta to screen"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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77 <param name="start" type="integer" value="-1" label="start - Remove sequences that start after position (ignored when negative)"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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78 <param name="end" type="integer" value="-1" label="end - Remove sequences that end before position (ignored when negative)"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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79 <param name="minlength" type="integer" value="-1" label="minlength - Remove sequences shorter than (ignored when negative)"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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80 <param name="maxlength" type="integer" value="-1" label="maxlength - Remove sequences longer than (ignored when negative)"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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81 <param name="maxambig" type="integer" value="-1" label="maxambig - Remove sequences with ambiguous bases greater than (ignored when negative)"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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82 <param name="maxhomop" type="integer" value="-1" label="maxhomop - Remove sequences with homopolymers greater than (ignored when negative)"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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83 <param name="criteria" type="integer" value="-1" label="criteria - Percent of sequences that an optimize value must match to be retained(ignored when negative)"/>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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84 <param name="optimize" type="select" multiple="true" display="checkboxes" label="optimize - Optimize selected paramenters">
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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85 <option value="start">start</option>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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86 <option value="end">end</option>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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87 <option value="minlength">minlength</option>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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88 <option value="maxlength">maxlength</option>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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89 <option value="maxambig">maxambig</option>
5a01375eadf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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90 <option value="maxhomop">maxhomop</option>
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91 </param>
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92 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Sequence Quality file to screen"/>
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93 <param name="names_in" type="data" format="mothur.names" optional="true" label="name - Sequence Names to screen"/>
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94 <param name="groups_in" type="data" format="mothur.groups" optional="true" label="group - Groups to screen"/>
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95 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report to screen"/>
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96 <param name="summary" type="data" format="mothur.summary" optional="true" label="summary - allows you to enter the summary file created by summary.seqs to save processing time when screening with parameters in the summary file"/>
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97 <param name="contigsreport" type="data" format="contigs.report" optional="true" label="contigsreport - Contigs Report to screen with" help="this file is created by the make.contigs command. If you provide the contigs report file you can screen your sequences using the following parameters: minoverlap, ostart, oend and mismatches"/>
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98 <param name="taxonomy_in" type="data" format="taxonomy" optional="true" label="taxonomy - Taxonomy to screen"/>
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99 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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100 </inputs>
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101 <outputs>
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102 <expand macro="logfile-output"/>
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103 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.good.dat" label="${tool.name} on ${on_string}: good.${fasta_in.datatype.file_ext}"/>
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104 <data name="bad_accnos" format="mothur.accnos" from_work_dir="fasta_in*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos"/>
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105 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.good.dat" label="${tool.name} on ${on_string}: qfile">
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106 <filter>qfile_in</filter>
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107 </data>
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108 <data name="names_out" format="mothur.names" from_work_dir="names_in*.good.dat" label="${tool.name} on ${on_string}: names">
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109 <filter>names_in</filter>
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110 </data>
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111 <data name="groups_out" format="mothur.groups" from_work_dir="groups_in*.good.dat" label="${tool.name} on ${on_string}: groups">
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112 <filter>groups_in</filter>
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113 </data>
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114 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.good.dat" label="${tool.name} on ${on_string}: align.report">
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115 <filter>alignreport_in</filter>
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116 </data>
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117 <data name="count_out" format="count" from_work_dir="count_in*.good.dat" label="${tool.name} on ${on_string}: count">
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118 <filter>count_in</filter>
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119 </data>
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120 </outputs>
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121 <tests>
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122 <test>
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123 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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124 <param name="maxambig" value="0"/>
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125 <param name="maxlength" value="275"/>
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126 <output name="fasta_out" file="Mock_S280_L001_R1_001_small.trim.contigs.good.fasta"/>
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127 <output name="bad_accnos" file="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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128 <expand macro="logfile-test"/>
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129 </test>
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130 <test>
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131 <param name="fasta_in" value="amazon.fasta"/>
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132 <param name="count_in" value="amazon.count_table"/>
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133 <param name="maxambig" value="0"/>
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134 <param name="maxlength" value="275"/>
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135 <output name="fasta_out" md5="d41d8cd98f00b204e9800998ecf8427e"/>
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136 <output name="count_out" md5="5f4a08bbf3ec12f954edbcc6b2a2feee"/>
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137 <output name="bad_accnos" md5="66acde5349e34fc97be22032ce68eea5"/>
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138 <expand macro="logfile-test"/>
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139 </test>
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140 </tests>
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141 <help>
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142 <![CDATA[
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143
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144 @MOTHUR_OVERVIEW@
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145
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146 **Command Documenation**
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147
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148 The screen.seqs_ command enables you to keep sequences that fulfill certain user defined criteria. Furthermore, it enables you to cull those sequences not meeting the criteria from a name_, group_, or align.report_ file.
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149
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150 .. _name: http://www.mothur.org/wiki/Name_file
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151 .. _group: http://www.mothur.org/wiki/Group_file
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152 .. _align.report: http://www.mothur.org/wiki/Align.seqs
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153 .. _screen.seqs: http://www.mothur.org/wiki/Screen.seqs
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154
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155 ]]>
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156 </help>
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157 <expand macro="citations"/>
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158 </tool>