Mercurial > repos > iuc > mothur_align_check

annotate align.check.xml @ 0:5fce559c4ffa 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 17:29:43 -0400
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children cf25efc1895b
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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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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>
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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
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$fasta" fasta.dat &&
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$name" name.dat &&
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$count" count.dat &&
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$map" map.dat &&
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14
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15 echo 'align.check(
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 fasta=fasta.dat,
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17 #if $name:
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18 name=name.dat,
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19 #end if
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20 #if $count:
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 count=count.dat,
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22 #end if
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23 map=map.dat
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 )'
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 | sed 's/ //g' ## mothur trips over whitespace
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26 | mothur
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27 ]]></command>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <inputs>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <param name="fasta" type="data" format="mothur.align" label="fasta - Aligned Sequences"/>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <conditional name="ss">
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 <param name="source" label="Select Secondary Structure Map from" type="select">
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 <option value="cached">Cached Secondary Structure Maps</option>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <option value="history">Your History</option>
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34 </param>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <when value="cached">
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <param name="map" type="select" label="map - Select a secondary structure map" help="Contact Galaxy team for additions">
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <options from_data_table="mothur_map">
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38 </options>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 </param>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 </when>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <when value="history">
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <param name="map" format="mothur.map" type="data" label="Secondary Structure Map"/>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 </when>
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44 </conditional>
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45 <param name="count" type="data" format="mothur.count_table" label="count_table file" optional="true" help="You can also provide a name file associated with your fasta file"/>
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46 <param name="name" type="data" format="mothur.names" label="names file" optional="true" 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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47 </inputs>
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48 <outputs>
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49 <expand macro="logfile-output"/>
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50 <data name="out_file" format="mothur.align.check" from_work_dir="fasta.align.check" label="${tool.name} on ${on_string}: align.check"/>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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51 </outputs>
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52 <tests>
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53 <test><!-- test with defaults -->
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54 <param name="fasta" value="amazon.align_head_short"/>
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55 <param name="source" value="history"/>
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56 <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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57 <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/>
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <expand macro="logfile-test"/>
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59 </test>
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60 <test><!-- test with names file -->
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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"/>
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64 <param name="name" value="amazon.align_head.names"/>
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65 <output name="out_file" md5="a785413dc157aacca4b19adef9cefa79" ftype="mothur.align.check"/>
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66 <expand macro="logfile-test"/>
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67 </test>
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68 </tests>
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69 <help>
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70 <![CDATA[
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71
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72 @MOTHUR_OVERVIEW@
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73
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74 **Command Documenation**
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75
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76 The align.check_ command allows you to calculate the number of potentially misaligned bases in a 16S rRNA gene sequence alignment using a secondary_structure_map_. If you are familiar with the editor window in ARB, this is the same as counting the number of ~, #, -, and = signs.
5fce559c4ffa planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77
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78 .. _secondary_structure_map: http://www.mothur.org/wiki/Secondary_structure_map
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79 .. _align.check: http://www.mothur.org/wiki/Align.check
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80 ]]>
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81 </help>
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82 <expand macro="citations"/>
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83 </tool>