Mercurial > repos > iuc > mothur_align_check

annotate align.check.xml @ 3:2fc7aad419ff draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:29:22 -0500
parents cf25efc1895b
children 4e7411b1aa3d
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iuc
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1 <tool profile="16.07" id="mothur_align_check" name="Align.check" version="@WRAPPER_VERSION@.0">
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Calculate the number of potentially misaligned bases</description>
5fce559c4ffa 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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iuc
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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"/>
1
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
1
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11
3
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12 ## create symlinks to input datasets
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$fasta' fasta.dat &&
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 ln -s '$name' name.dat &&
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 ln -s '$count' count.dat &&
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 ln -s '$map' map.dat &&
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5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17
3
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18 echo 'align.check(
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 fasta=fasta.dat,
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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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:
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 count=count.dat,
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 #end if
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 map=map.dat
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 )'
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28 | sed 's/ //g' ## mothur trips over whitespace
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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29 | mothur
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30 | tee mothur.out.log
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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31 && cat fasta.align.check
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32 ]]></command>
3
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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">
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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36 <param name="source" label="Select Secondary Structure Map from" type="select">
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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37 <option value="cached">Cached Secondary Structure Maps</option>
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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38 <option value="history">Your History</option>
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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39 </param>
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40 <when value="cached">
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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41 <param argument="map" type="select" label="Secondary structure map">
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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42 <options from_data_table="mothur_map"/>
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43 </param>
3
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44 </when>
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45 <when value="history">
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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46 <param argument="map" format="mothur.map" type="data" label="Secondary Structure Map"/>
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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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"
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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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"
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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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 </inputs>
0
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54 <outputs>
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55 <expand macro="logfile-output"/>
3
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56 <data name="align.check" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/>
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57 </outputs>
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58 <tests>
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59 <test><!-- test with defaults -->
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60 <param name="fasta" value="amazon.align_head_short"/>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 <param name="source" value="history"/>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 <param name="map" value="silva.ss.map.head"/>
3
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63 <output name="align.check" ftype="mothur.align.check">
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64 <assert_contents>
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65 <expand macro="test-aligncheck-format"/>
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66 <has_text text="U68589"/>
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67 </assert_contents>
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68 </output>
0
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69 <expand macro="logfile-test"/>
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70 </test>
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71 <test><!-- test with names file -->
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72 <param name="fasta" value="amazon.align_head_short"/>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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73 <param name="source" value="history"/>
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74 <param name="map" value="silva.ss.map.head"/>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <param name="name" value="amazon.align_head.names"/>
3
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76 <output name="align.check" ftype="mothur.align.check">
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77 <assert_contents>
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78 <expand macro="test-aligncheck-format"/>
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79 <has_text text="U68589"/>
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80 </assert_contents>
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81 </output>
0
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82 <expand macro="logfile-test"/>
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83 </test>
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84 </tests>
3
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85 <help><![CDATA[
0
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86
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87 @MOTHUR_OVERVIEW@
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88
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89 **Command Documentation**
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90
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91 The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence
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92 alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as
2fc7aad419ff planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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93 counting the number of ~, #, -, and = signs.
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94
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95 .. _secondary_structure_map: https://www.mothur.org/wiki/Secondary_structure_map
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96 .. _align.check: https://www.mothur.org/wiki/Align.check
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97
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98 ]]></help>
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99 <expand macro="citations"/>
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100 </tool>