Mercurial > repos > iuc > mothur_pcr_seqs

annotate pcr.seqs.xml @ 0:3a534aab3952 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 16:44:52 -0400
parents
children 0ef1f460a44f
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3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_pcr_seqs" name="Pcr.seqs" version="@WRAPPER_VERSION@.0">
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Trim sequences</description>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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4 <import>macros.xml</import>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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6 <expand macro="requirements"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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7 <expand macro="version_command"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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8 <command detect_errors="aggressive"><![CDATA[
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ln -s "$fasta" fasta.dat &&
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$name_in" name_in.dat &&
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$group_in" group_in.dat &&
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$taxonomy_in" taxonomy_in.dat &&
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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14 #if $trim.method == "oligos":
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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15 ln -s "$trim.oligos" trim.oligos.dat &&
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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16 #elif $trim.method == "reference":
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 ln -s "$trim.ecoli" trim.ecoli.dat &&
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 #end if
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 echo 'pcr.seqs(
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 fasta=fasta.dat,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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22 #if $name_in
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 name=name_in.dat,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #end if
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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25 #if $group_in:
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 group=group_in.dat,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #end if
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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28 #if $taxonomy_in:
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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29 taxonomy=taxonomy_in.dat,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 #end if
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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31 #if $trim.method == "oligos":
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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32 oligos=trim.oligos.dat,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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33 nomatch=$trim.nomatch,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 $trim.keepprimer
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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35 #elif $trim.method == "reference":
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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36 ecoli=trim.ecoli.dat,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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37 #elif $trim.method == "position":
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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38 start=$trim.start,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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39 #if $trim.end and int($trim.end) > 0:
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 end=$trim.end,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 #end if
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 #end if
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 #if $pdiffs:
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 pdiffs=$pdiffs,
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 #end if
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 $keepdots
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 processors='\${GALAXY_SLOTS:-8}'
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 )'
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 | sed 's/ //g' ## mothur trips over whitespace
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 | mothur
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 ]]></command>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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52 <inputs>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <param name="fasta" type="data" format="mothur.align" label="fasta - Candiate Sequences" help="sequences must be aligned"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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54 <conditional name="trim">
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 <param name="method" type="select" label="Trim with an oligos file?" help="">
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56 <option value="oligos">oligos</option>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <option value="reference">reference sequence</option>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <option value="position">start and end positions</option>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 </param>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <when value="oligos">
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 <param name="oligos" type="data" format="mothur.oligos" optional="true" label="oligos - barcodes and primers" help="a file that can contain the sequences of the forward and reverse primers and barcodes and their sample identifier. Each line of the oligos file can start with the key words &quot;forward&quot;, &quot;reverse&quot;, and &quot;barcode&quot; or it can start with a &quot;#&quot; to tell mothur to ignore that line of the oligos file."/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 <param name="nomatch" type="select" label="nomatch - action when no primer is found">
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <option value="reject" selected="true">reject (default)</option>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 <option value="keep">keep</option>
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65 </param>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <param name="keepprimer" type="boolean" falsevalue="" truevalue="keepprimer=true," checked="false" label="keepprimer - keep the primer in the output sequence"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 </when>
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68 <when value="reference">
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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69 <param name="ecoli" type="data" format="mothur.align" optional="true" label="ecoli - An aligned reference sequence for trimming" help="The ecoli parameter is used to provide a fasta file containing a single reference sequence (e.g. for e. coli) this must be aligned. Mothur will trim to the start and end positions of the reference sequence."/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 </when>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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71 <when value="position">
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72 <param name="start" type="integer" min="0" value="0" optional="true" label="start - a starting position to trim to"/>
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73 <param name="end" type="integer" value="" optional="true" min="0" label="end - a ending position to trim from"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 </when>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 </conditional>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <param name="keepdots" type="boolean" falsevalue="keepdots=false," truevalue="" checked="true" label="keepdots - keep the leading and trailing alignment dots in the output sequences"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Sequence Taxonomy"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequence representative name list"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Group file"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 </inputs>
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82 <outputs>
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83 <expand macro="logfile-output"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 <data name="pcr_fasta" format="mothur.align" from_work_dir="fasta*.pcr.dat" label="${tool.name} on ${on_string}: pcr.fasta"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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85 <data name="scrap_fasta" format="mothur.align" from_work_dir="fasta*.scrap.pcr.dat" label="${tool.name} on ${on_string}: pcr.scrap.fasta"/>
3a534aab3952 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pcr.dat" label="${tool.name} on ${on_string}: tax.summary">
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87 <filter>taxonomy_in</filter>
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88 </data>
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89 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.groups">
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90 <filter>group_in</filter>
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91 </data>
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92 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pcr.dat" label="${tool.name} on ${on_string}: mothur.names">
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93 <filter>name_in</filter>
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94 </data>
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95 <data name="accnos_out" format="mothur.accnos" from_work_dir="fasta*.bad.accnos" label="${tool.name} on ${on_string}: bad.accnos">
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96 <filter>trim['method'] =='oligos'</filter>
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97 </data>
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98 </outputs>
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99 <tests>
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100 <test><!-- test with position method -->
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101 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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102 <param name="keepdots" value=""/>
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103 <param name="method" value="position"/>
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104 <param name="start" value="0"/>
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105 <param name="end" value="0"/>
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106 <param name="pdiffs" value="0"/>
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107 <expand macro="logfile-test"/>
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108 <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/>
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109 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
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110 </test>
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111 <test><!-- test with reference method -->
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112 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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113 <param name="keepdots" value="keepdots=false,"/>
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114 <param name="method" value="reference"/>
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115 <param name="ecoli" value="amazon.align_head"/>
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116 <param name="name_in" value="amazon.align_head.names"/>
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117 <param name="pdiffs" value="2"/>
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118 <expand macro="logfile-test"/>
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119 <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/>
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120 <output name="scrap_fasta" md5="d41d8cd98f00b204e9800998ecf8427e" ftype="mothur.align"/>
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121 <output name="name_out" md5="0c58174137c2ecabf7da9ab492ea46fc" ftype="mothur.names"/>
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122 </test>
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123 <test><!-- test with oligos and all outputs -->
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124 <param name="fasta" value="amazon.align_head" ftype="mothur.align"/>
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125 <param name="method" value="oligos"/>
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126 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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127 <param name="name_in" value="amazon.names" ftype="mothur.names"/>
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128 <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
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129 <param name="taxonomy_in" value="amazon.wang.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
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130 <param name="start" value="5"/>
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131 <param name="end" value="50"/>
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132 <expand macro="logfile-test"/>
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133 <ouptut name="pcr_fasta" md5="1e78af5a460572e22ce199e522a70388" ftype="mothur.align"/>
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134 <output name="scrap_fasta" md5="0b63807f339dfd88cf958f7b069eba02" ftype="mothur.align"/>
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135 <output name="group_out" md5="301c358e61d38c83cc7382a8a210089a" ftype="mothur.groups"/>
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136 <output name="name_out" md5="62eb1162557408509c931496071add85" ftype="mothur.names"/>
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137 <output name="taxonomy_out" md5="4d72981cefd8b45d4f2793a28dccd9e4" ftype="mothur.seq.taxonomy"/>
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138 <output name="accnos_out" md5="48d019b92e4d303faf88a974e52f7a97" ftype="mothur.accnos"/>
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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 pcr.seqs_ command assigns sequences to chosen taxonomy outline.
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149
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150 .. _pcr.seqs: http://www.mothur.org/wiki/Pcr.seqs
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151
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152 ]]>
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153 </help>
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154 <expand macro="citations"/>
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155 </tool>