Mercurial > repos > iuc > mothur_filter_seqs

annotate filter.seqs.xml @ 0:32f444a36d12 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 16:30:23 -0400
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children 74e541cb0f87
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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32f444a36d12 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_filter_seqs" name="Filter.seqs" version="@WRAPPER_VERSION@.0">
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>removes columns from alignments</description>
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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
32f444a36d12 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 &&
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 #for $i in $inputs:
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$i.fasta" fasta${inputs.index($i)}.dat &&
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 #end for
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14 ln -s "$hard" hard.dat &&
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15
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16 echo 'filter.seqs(
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 fasta=fasta.dat#for $i in $inputs#-fasta${inputs.index($i)}.dat#end for#,
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 vertical=$vertical,
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19 #if $trump:
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20 trump=$trump,
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 #end if
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22 soft=$soft,
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #if $hard:
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24 hard=hard.dat,
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #end if
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26 processors='\${GALAXY_SLOTS:-8}'
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 )'
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28 | sed 's/ //g' ## mothur trips over whitespace
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29 | mothur &&
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30
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31 ## rename collection files for more transparent element naming
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta &&
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 #for i in $inputs:
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 mv fasta${inputs.index($i)}.filter.fasta ${i.fasta.element_identifier}.filter.fasta
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 #end for
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36 ]]></command>
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <inputs>
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <repeat name="inputs" title="Additional Alignment File" optional="true">
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
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41 </repeat>
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42 <param name="vertical" type="boolean" checked="true" truevalue="true" falsevalue="false" label="vertical - Vertical column" help="Ignore any column that only contains gap characters (i.e. '-' or '.')"/>
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43 <param name="trump" type="select" label="trump - Trump character" help="Remove a column if the trump character is found at that position in any sequence of the alignment">
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44 <option value="">Off</option>
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <option value=".">.</option>
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46 <option value="-">-</option>
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47 <option value="N">N</option>
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48 </param>
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49 <param name="soft" type="integer" value="0" min="0" max="100" label="soft - percentage required to retain column. (0-100)" help="Removes any column where the dominant base (i.e. A, T, G, C, or U) does not occur in at least a designated percentage of sequences"/>
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <param name="hard" type="data" format="mothur.filter" optional="True" label="hard - Hard Column Filter" help="A file should only contain one line consisting of 0's and 1's"/>
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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_filter" format="mothur.filter" from_work_dir="fasta*.filter" label="${tool.name} on ${on_string}: filter"/>
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55 <collection name="filteredfastas" type="list" label="${tool.name} on ${on_string}: filtered fastas">
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56 <discover_datasets pattern="(?P&lt;designation&gt;.*)\.filter\.fasta" format="fasta"/>
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57 </collection>
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="fasta" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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62 <repeat name="inputs">
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63 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" ftype="mothur.align"/>
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64 </repeat>
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65 <output name="out_filter" md5="3e6c2cfef46baf35d2a8b5cafe53e3a4"/>
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66 <output_collection name="filteredfastas" count="2">
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67 <element name="HMP_MOCK.v35.align" md5="ef4c6c2d9a882f7a22e5fa3c814af7cc" ftype="fasta"/>
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68 </output_collection>
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69 <expand macro="logfile-test"/>
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70 </test>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74
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75 @MOTHUR_OVERVIEW@
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76
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77 **Command Documenation**
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78
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79 The filter.seqs_ command removes columns from alignments based on a criteria defined by the user. For example, alignments generated against reference alignments (e.g. from RDP, SILVA, or greengenes) often have columns where every character is either a '.' or a '-'. These columns are not included in calculating distances because they have no information in them. By removing these columns, the calculation of a large number of distances is accelerated. Also, people also like to mask their sequences to remove variable regions using a soft or hard mask (e.g. Lane's mask). This type of masking is only encouraged for deep-level phylogenetic analysis, not fine level analysis such as that needed with calculating OTUs.
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80
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81 .. _filter.seqs: http://www.mothur.org/wiki/Filter.seqs
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82
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83 v.1.20.0: Updated to Mothur 1.33
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84
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85 ]]>
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86 </help>
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87 <expand macro="citations"/>
32f444a36d12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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88 </tool>