Mercurial > repos > iuc > mothur_chop_seqs

annotate chop.seqs.xml @ 0:f1d0a5a4e30c 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 17:35:55 -0400
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children b0f422397f42
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_chop_seqs" name="Chop.seqs" version="@WRAPPER_VERSION@.0">
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 ## create symlinks to input datasets
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$fasta" fasta.dat &&
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$name" name.dat &&
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$group" group.dat &&
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$count" count.dat &&
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 echo 'chop.seqs(
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 fasta=fasta.dat,
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 numbases=$numbases,
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 keep=$keep,
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 countgaps=$countgaps,
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 short=$short,
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #if $name:
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22 name=name.dat,
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #end if
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 #if $group:
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 group=group.dat,
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #end if
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 #if $count:
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 count=count.dat,
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #end if
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 processors='\${GALAXY_SLOTS:-8}'
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 )'
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32 | sed 's/ //g' ## mothur trips over whitespace
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 | mothur
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34 ]]></command>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <inputs>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <param name="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <param name="keep" type="select" label="keep - Part of the sequence to keep">
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <option value="front">front</option>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <option value="back">back</option>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 </param>
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42 <param name="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 <param name="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <param name="name" type="data" format="name" optional="true" label="name file"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <param name="group" type="data" format="group" optional="true" label="group file"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 <param name="count" type="data" format="mothur.count_table" optional="true" label="count file"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 </inputs>
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48 <outputs>
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49 <expand macro="logfile-output"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <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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51 </outputs>
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52 <tests>
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53 <test>
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54 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 <param name="name" value="Mock_S280_L001_R1_001_small.trim.contigs.good.names"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <output name="out_fasta" file="Mock_S280_L001_R1_001_small.trim.contigs.good.chop.fasta" compare="contains"/>
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <expand macro="logfile-test"/>
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58 </test>
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59 </tests>
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60 <help>
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61 <![CDATA[
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62
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63 @MOTHUR_OVERVIEW@
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64
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65 **Command Documenation**
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66
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 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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68
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69 .. _chop.seqs: http://www.mothur.org/wiki/Chop.seqs
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70
f1d0a5a4e30c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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71 v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0
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72 ]]>
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73 </help>
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74 <expand macro="citations"/>
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75 </tool>