Mercurial > repos > iuc > mothur_chop_seqs

annotate chop.seqs.xml @ 2:35a4e758bbed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ca8dc573528ab7c5290bc6ca029cb989f4755db6
author iuc
date Fri, 08 Sep 2017 14:54:33 -0400
parents b7635a7037a7
children c8b6add22353
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b7635a7037a7 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_chop_seqs" name="Chop.seqs" version="@WRAPPER_VERSION@.0">
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2 <description>Trim sequences to a specified length</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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12 ## create symlinks to input datasets
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13 ln -s "$fasta" fasta.dat &&
b7635a7037a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$name" name.dat &&
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15 ln -s "$group" group.dat &&
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16 ln -s "$count" count.dat &&
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17
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18 echo 'chop.seqs(
b7635a7037a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 fasta=fasta.dat,
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20 numbases=$numbases,
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21 keep=$keep,
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22 countgaps=$countgaps,
b7635a7037a7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 short=$short,
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24 #if $name:
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25 name=name.dat,
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26 #end if
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27 #if $group:
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28 group=group.dat,
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29 #end if
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30 #if $count:
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31 count=count.dat,
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32 #end if
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33 processors='\${GALAXY_SLOTS:-8}'
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34 )'
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35 | sed 's/ //g' ## mothur trips over whitespace
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36 | mothur
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37 | tee mothur.out.log
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38 ]]></command>
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39 <inputs>
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40 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
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41 <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
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42 <param name="keep" type="select" label="keep - Part of the sequence to keep">
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43 <option value="front">front</option>
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44 <option value="back">back</option>
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45 </param>
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46 <param name="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/>
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47 <param name="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/>
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48 <param name="name" type="data" format="mothur.names" optional="true" label="name file"/>
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49 <param name="group" type="data" format="mothur.groups" optional="true" label="group file"/>
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50 <param name="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
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51 </inputs>
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52 <outputs>
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53 <expand macro="logfile-output"/>
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54 <data name="out_fasta" format_source="fasta" from_work_dir="fasta*.chop.fasta" label="${tool.name} on ${on_string}: chop.fasta"/>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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59 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names"/>
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60 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta" compare="contains"/>
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61 <expand macro="logfile-test"/>
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62 </test>
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63 </tests>
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64 <help>
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65 <![CDATA[
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66
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67 @MOTHUR_OVERVIEW@
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68
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69 **Command Documentation**
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70
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71 The chop.seqs_ command reads a fasta file of sequences and outputs a .chop.fasta file containing the trimmed sequences. It works on both aligned and unaligned sequences.
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72
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73 .. _chop.seqs: https://www.mothur.org/wiki/Chop.seqs
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74
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75 v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0
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76 ]]>
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77 </help>
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78 <expand macro="citations"/>
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79 </tool>