annotate trim.flows.xml @ 0:8e25e5e9e75f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:35:27 -0400
parents
children 9d48c9a47566
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_trim_flows" name="Trim.flows" version="@WRAPPER_VERSION@.0">
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>partition by barcode, trim to length, cull by length and mismatches</description>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$flow" flow.dat &&
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 #if $oligo.add == "yes":
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$oligo.oligos" oligo.oligos.dat &&
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 #end if
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 echo 'trim.flows(
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 flow=flow.dat,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 minflows=$minflows,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 maxflows=$maxflows,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 #if $maxhomop:
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 maxhomop=$maxhomop,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #end if
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 order=$order,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 signal=$signal,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 noise=$noise,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 #if $oligo.add == "yes":
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 oligos=oligo.oligos.dat,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 bdiffs=$oligo.bdiffs,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 pdiffs=$oligo.pdiffs,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 tdiffs=$oligo.tdiffs,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 ldiffs=$oligo.ldiffs,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 sdiffs=$oligo.sdiffs,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 #end if
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 fasta=$fasta,
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 processors='\${GALAXY_SLOTS:-8}'
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 )'
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 | sed 's/ //g' ## mothur trips over whitespace
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 | mothur
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 | tee mothur.out.log
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 ## prevent these two files from being gathered into collection
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 && mv flow.trim.flow flow.trim
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 && mv flow.scrap.flow flow.scrap
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 ]]></command>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 <inputs>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 <param name="flow" type="data" format="mothur.sff.flow" label="flow - flowgram data" help="Use sffinfo to generate flow data from an sff file"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 <conditional name="oligo">
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 <param name="add" type="select" label="Trim with an oligos file?" 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">
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 <option value="no">no</option>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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51 <option value="yes">yes</option>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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52 </param>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 <when value="no"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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54 <when value="yes">
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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55 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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57 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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58 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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59 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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60 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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61 </when>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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62 </conditional>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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63 <param name="minflows" type="integer" value="450" min="0" label="minflows - Minimum number of flows that each sequence must contain to make it in to a &quot;trim&quot; file. (default 450)" help="(Quince uses 360)"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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64 <param name="maxflows" type="integer" value="450" min="0" label="maxflows - Maximum number of flows after which all other flows should be ignored (default 450)" help="(Quince uses 360 for GSFLX and 720 for Titanium)"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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65 <param name="maxhomop" type="integer" value="" optional="true" label="maxhomop - Maximum homopolymers" help=""/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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66 <param name="signal" type="float" value="0.5" min="0.0" max="1.0" label="signal - treat any intensity signal greater than this threshold as a real signal" help="Optional. Between 0 an 1. Default .5"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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67 <param name="noise" type="float" value="0.7" min="0.0" max="1.0" label="noise - treat any intensity signal less than this threshold as noise" help="Optional. Between 0 and 1. Default .7"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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68 <param name="order" type="select" label="order - flow order for nucleotides in the sequencer" help="default is A, was TACG. Also accepts B or I">
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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69 <option value="A" selected="true"> A (TACG) </option>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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70 <option value="B"> B </option>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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71 <option value="I"> I </option>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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72 </param>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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73 <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="false" label="fasta - translate the flowgram data to fasta sequence format"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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74 </inputs>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <outputs>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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76 <expand macro="logfile-output"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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77 <data name="trim_flow" format="mothur.sff.flow" from_work_dir="flow.trim" label="${tool.name} on ${on_string}: trim.flow"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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78 <data name="scrap_flow" format="mothur.sff.flow" from_work_dir="flow.scrap" label="${tool.name} on ${on_string}: scrap.flow"/>
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79 <data name="flow_files" format="tabular" from_work_dir="flow.flow.files" label="${tool.name} on ${on_string}: flow.files"/>
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80 <data name="flow_fasta" format="fasta" from_work_dir="flow.flow.fasta" label="${tool.name} on ${on_string}: flow.fasta">
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81 <filter>fasta</filter>
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82 </data>
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83 <collection name="flow_oligos" type="list" label="${tool.name} on ${on_string}: oligos.flow">
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84 <filter>oligo['add'] == 'yes'</filter>
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85 <discover_datasets pattern="flow\.(?P&lt;designation&gt;.*)\.flow" format="mothur.sff.flow"/>
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86 </collection>
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87 </outputs>
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88 <tests>
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89 <test><!-- test with defaults -->
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90 <param name="flow" value="mock.flow" ftype="mothur.sff.flow"/>
8e25e5e9e75f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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91 <output name="trim_flow" md5="6850bb59570822aec6cd7aa7ce4675c4" ftype="mothur.sff.flow"/>
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92 <output name="scrap_flow" md5="e5d39459c28f5e7245bae7c509f05cba" ftype="mothur.sff.flow"/>
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93 <output name="flow_files" ftype="tabular">
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94 <assert_contents>
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95 <has_text text="flow"/>
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96 </assert_contents>
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97 </output>
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98 <expand macro="logfile-test"/>
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99 </test>
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100 <test><!-- test with oligos file and fasta output -->
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101 <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
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102 <param name="add" value="yes"/>
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103 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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104 <param name="order" value="I"/>
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105 <param name="fasta" value="true"/>
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106 <param name="pdiffs" value="10"/>
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107 <param name="bdiffs" value="10"/>
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108 <output name="trim_flow" md5="fdb1634899e8a6f8490ace953382591e" ftype="mothur.sff.flow"/>
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109 <output name="scrap_flow" md5="dd2497eb1e3da8d513d2b0bc111cdf11" ftype="mothur.sff.flow"/>
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110 <output name="flow_files" ftype="tabular">
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111 <assert_contents>
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112 <has_text text="flow"/>
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113 </assert_contents>
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114 </output>
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115 <output_collection name="flow_oligos" count="2">
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116 <element name="F003D006" md5="5ea6613d7aa26f87ca9b983152e14a4b" ftype="mothur.sff.flow"/>
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117 </output_collection>
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118 <output name="flow_fasta" md5="0725967a9ed731c049d48ea876b0e308" ftype="fasta"/>
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119 <expand macro="logfile-test"/>
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120 </test>
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121 </tests>
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122 <help>
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123 <![CDATA[
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124
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125 @MOTHUR_OVERVIEW@
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126
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127 **Command Documentation**
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128
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129 The trim.flows_ command is analogous to the trim.seqs command, except that it uses the flowgram data that comes bundled in the sff file that is generated by 454 sequencing. It's primary usage is as a preliminary step to running shhh.seqs. Chris Quince has a series of perl scripts that fulfill a similar role [1]. This command will allow you to partition your flowgram data by sample based on the barcode, trim the flows to a specified length range, and cull sequences that are too short or have too many mismatches to barcodes and primers.
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130
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131 .. _trim.flows: https://www.mothur.org/wiki/Trim.flows
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132
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133 ]]>
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134 </help>
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135 <expand macro="citations"/>
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136 </tool>