Mercurial > repos > iuc > mothur_sffinfo

annotate sffinfo.xml @ 0:b2c31e79e969 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 16:40:20 -0400
parents
children 32a19ce534d1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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b2c31e79e969 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_sffinfo" name="Sffinfo" version="@WRAPPER_VERSION@.0">
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Summarize the quality of sequences</description>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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3 <macros>
b2c31e79e969 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>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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5 </macros>
b2c31e79e969 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"/>
b2c31e79e969 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"/>
b2c31e79e969 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[
b2c31e79e969 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
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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10 ln -s "$sff" sff.dat &&
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$accnos" accnos.dat &&
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 #if $oligo.add == "yes":
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$oligo.oligos" oligo.oligos.dat &&
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 #end if
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 echo 'sffinfo(
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 sff=sff.dat,
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 fasta=$fasta,
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 qfile=$qfile,
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 $sfftxt
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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21 flow=$flow,
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 trim=$trim
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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23 #if $accnos:
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 ,accnos=accnos.dat
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #end if
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #if $oligo.add == "yes":
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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27 ,oligos=oligo.oligos.dat
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 ,bdiffs=$oligo.bdiffs
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 ,pdiffs=$oligo.pdiffs
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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30 ,tdiffs=$oligo.tdiffs
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 ,ldiffs=$oligo.ldiffs
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 ,sdiffs=$oligo.sdiffs
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #end if
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 )'
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 | sed 's/ //g' ## mothur trips over whitespace
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 | mothur
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 ]]></command>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <inputs>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <param name="sff" type="data" format="sff" label="sff - Sff data"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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40 <conditional name="oligo">
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <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.">
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <option value="no" selected="true">no</option>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <option value="yes">yes</option>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 </param>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <when value="no"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <when value="yes">
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 <param name="oligos" type="data" format="mothur.oligos" label="oligos - barcodes and primers"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (default 0)"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (default 0)"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (default 0)"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (default 0)"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (default 0)"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 </when>
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54 </conditional>
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55 <param name="fasta" type="boolean" truevalue="true" falsevalue="false" checked="true" label="fasta - Add fasta to your history"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <param name="qfile" type="boolean" truevalue="true" falsevalue="false" checked="true" label="qfile - Add qfile to your history"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <param name="sfftxt" type="boolean" truevalue="sfftxt=true," falsevalue="" checked="false" label="sfftxt - Add sfftxt to your history"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <param name="flow" type="boolean" truevalue="true" falsevalue="false" checked="true" label="flow - Add flow to your history"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <param name="trim" type="boolean" truevalue="true" falsevalue="false" checked="true" label="trim - Trim sequences and quality scores"/>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <param name="accnos" type="data" format="mothur.accnos" optional="true" label="accnos - Limit output to named Accessions"/>
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61 </inputs>
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62 <outputs>
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63 <expand macro="logfile-output"/>
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64 <data name="out_fasta" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta">
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <filter>fasta</filter>
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66 </data>
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67 <data name="out_qfile" format="qual454" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual">
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <filter>qfile</filter>
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69 </data>
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 <data name="out_sfftxt" format="txt" from_work_dir="sff*.sff.txt" label="${tool.name} on ${on_string}: sff.txt">
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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71 <filter>sfftxt</filter>
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72 </data>
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73 <data name="out_flow" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flowgram">
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <filter>flow</filter>
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75 </data>
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76 <data name="out_scrap" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap.sff">
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77 <filter>oligo['add'] == 'yes'</filter>
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78 </data>
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79 </outputs>
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80 <tests>
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81 <test><!-- test without oligos -->
b2c31e79e969 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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82 <param name="sff" value="Fasting_Example1.sff"/>
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83 <param name="sfftxt" value="true"/>
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84 <output name="out_fasta" md5="fbe6f4d51959d4723a8417636476d0e0" ftype="fasta"/>
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85 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
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86 <output name="out_sfftxt" md5="fdc80c8e476016632d317cfd7893713c" ftype="txt"/>
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87 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
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88 <expand macro="logfile-test"/>
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89 </test>
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90 <test><!-- test with oligos file -->
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91 <param name="sff" value="Fasting_Example1.sff"/>
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92 <param name="add" value="yes"/>
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93 <param name="oligos" value="GQY1XT001.oligos"/>
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94 <output name="out_fasta" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
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95 <output name="out_qfile" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual454"/>
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96 <output name="out_flow" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
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97 <output name="out_scrap" md5="f03c422fe364815e7214ad31ad135aca" ftype="sff"/>
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98 <expand macro="logfile-test"/>
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99 </test>
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100 </tests>
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101 <help>
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102 <![CDATA[
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103
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104 @MOTHUR_OVERVIEW@
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105
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106 **Command Documenation**
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107
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108 The sffinfo_ command will summarize the quality of sequences in an unaligned or aligned fasta-formatted sequence file.
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109
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110
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111 .. _sffinfo: http://www.mothur.org/wiki/Sffinfo
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112 ]]>
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113 </help>
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114 <expand macro="citations"/>
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115 </tool>