Mercurial > repos > iuc > mothur_align_check

annotate align.check.xml @ 2:814a34469480 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:14:06 -0400
parents 9d91e7974012
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9d91e7974012 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_align_check" name="Align.check" version="@WRAPPER_VERSION@.0">
9d91e7974012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Calculate the number of potentially misaligned bases</description>
9d91e7974012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
9d91e7974012 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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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[
2
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10 @SHELL_OPTIONS@
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11
2
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12 ## create symlinks to input datasets
814a34469480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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13 ln -s '$fasta' fasta.dat &&
814a34469480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$name' name.dat &&
814a34469480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$count' count.dat &&
814a34469480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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16 ln -s '$map' map.dat &&
0
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17
2
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18 echo 'align.check(
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19 fasta=fasta.dat,
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20 #if $name:
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21 name=name.dat,
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22 #end if
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23 #if $count:
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24 count=count.dat,
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25 #end if
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26 map=map.dat
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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 | tee mothur.out.log
814a34469480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 && cat fasta.align.check
0
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32 ]]></command>
2
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33 <inputs>
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34 <param argument="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/>
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35 <conditional name="ss">
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36 <param name="source" label="Select Secondary Structure Map from" type="select">
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37 <option value="cached">Cached Secondary Structure Maps</option>
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38 <option value="history">Your History</option>
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39 </param>
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40 <when value="cached">
814a34469480 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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41 <param argument="map" type="select" label="Secondary structure map">
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42 <options from_data_table="mothur_map"/>
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43 </param>
2
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44 </when>
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45 <when value="history">
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46 <param argument="map" format="mothur.map" type="data" label="Secondary Structure Map"/>
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47 </when>
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48 </conditional>
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49 <param argument="count" type="data" format="mothur.count_table" optional="true" label="count_table file"
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50 help="You can also provide a name file associated with your fasta file"/>
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51 <param argument="name" type="data" format="mothur.names" optional="true" label="names file"
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52 help="The count file is similar to the name file in that it is used to represent the number of duplicate sequences for a given representative sequence"/>
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53 <expand macro="param-savelog"/>
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54 </inputs>
0
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55 <outputs>
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56 <expand macro="logfile-output"/>
2
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57 <data name="align.check" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/>
0
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58 </outputs>
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59 <tests>
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60 <test><!-- test with defaults -->
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61 <param name="fasta" value="amazon.align_head_short"/>
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62 <param name="source" value="history"/>
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63 <param name="map" value="silva.ss.map.head"/>
2
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64 <output name="align.check" ftype="mothur.align.check">
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65 <assert_contents>
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66 <expand macro="test-aligncheck-format"/>
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67 <has_text text="U68589"/>
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68 </assert_contents>
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69 </output>
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70 <param name="savelog" value="true"/>
0
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71 <expand macro="logfile-test"/>
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72 </test>
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73 <test><!-- test with names file -->
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74 <param name="fasta" value="amazon.align_head_short"/>
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75 <param name="source" value="history"/>
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76 <param name="map" value="silva.ss.map.head"/>
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77 <param name="name" value="amazon.align_head.names"/>
2
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78 <output name="align.check" ftype="mothur.align.check">
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79 <assert_contents>
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80 <expand macro="test-aligncheck-format"/>
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81 <has_text text="U68589"/>
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82 </assert_contents>
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83 </output>
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84 <param name="savelog" value="true"/>
0
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85 <expand macro="logfile-test"/>
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86 </test>
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87 </tests>
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88 <help><![CDATA[
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90 @MOTHUR_OVERVIEW@
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91
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92 **Command Documentation**
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93
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94 The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence
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95 alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as
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96 counting the number of ~, #, -, and = signs.
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98 .. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map
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99 .. _align.check: https://www.mothur.org/wiki/Align.check
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100
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101 ]]></help>
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102 <expand macro="citations"/>
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103 </tool>