Mercurial > repos > iuc > mothur_get_mimarkspackage

annotate get.mimarkspackage.xml @ 0:066b8aaf5a9a 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 16:32:41 -0400
parents
children 793a04ad1837
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_get_mimarkspackage" name="Get.mimarkspackage" version="@WRAPPER_VERSION@.0">
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>creates a mimarks package form with your groups</description>
066b8aaf5a9a 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>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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
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10 ln -s "$input.infile" input.infile.dat &&
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 echo 'get.mimarkspackage(
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 #if $input.filetype == "group":
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 group=input.infile.dat,
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 #elif $input.filetype == "oligos":
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 oligos=input.infile.dat,
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #else:
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18 file=input.infile.dat,
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19 #end if
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20 package=$package,
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 requiredonly=$requiredonly
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22 )'
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 | sed 's/ //g' ## mothur trips over whitespace
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 | mothur
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25 ]]></command>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 <inputs>
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27 <conditional name="input">
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 <param name="filetype" type="select" label="input type">
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 <option value="group">group file</option>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 <option value="oligos" selected="true">oligos file</option>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 <option value="file">other file (e.g. output from mimarks.attributes)</option>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 </param>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <when value="group">
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <param name="infile" type="data" format="mothur.groups" label="group file"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 </when>
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36 <when value="oligos">
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <param name="infile" type="data" format="mothur.oligos" label="oligos"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 </when>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 <when value="file">
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <param name="infile" type="data" format="txt" label="file"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 </when>
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42 </conditional>
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43 <param name="package" type="select" label="package - select the mimarks package you would like to use">
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <option value="air">air</option>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <option value="host_associated">host_associated</option>
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46 <option value="human_associated">human_associated</option>
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47 <option value="human_gut">human_gut</option>
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48 <option value="human_oral">human_oral</option>
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49 <option value="human_skin">human_skin</option>
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50 <option value="human_vaginal">human_vaginal</option>
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51 <option value="microbial">microbial</option>
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52 <option value="miscellaneous" selected="true">miscellaneous</option>
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53 <option value="plant_associated">plant_associated</option>
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54 <option value="sediment">sediment</option>
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55 <option value="soil">soil</option>
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56 <option value="wastewater">wastewater</option>
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57 <option value="waterc">waterc</option>
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58 </param>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <param name="requiredonly" type="boolean" truevalue="true" falsevalue="false" checked="false" label="requiredonly - used to indicate you only want the required mimarks fields printed. Default=false"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 </inputs>
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61 <outputs>
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62 <expand macro="logfile-output"/>
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63 <data name="package_out" format="tabular" from_work_dir="input.infile*.tsv" label="${tool.name} on ${on_string}: mimarks package"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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64 </outputs>
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65 <tests>
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66 <test><!-- test with group file -->
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67 <param name="filetype" value="group"/>
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68 <param name="infile" value="amazon.groups" ftype="mothur.groups"/>
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69 <output name="package_out" md5="8e97dbe732b257494b796d23a3688d5a" ftype="tabular"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 <expand macro="logfile-test"/>
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71 </test>
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72 <test><!-- test with oligos -->
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73 <param name="filetype" value="oligos"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <param name="infile" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 <param name="package" value="human_associated"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <param name="requiredonly" value="true"/>
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77 <output name="package_out" md5="975cd41eb9a97725795c582dc7e903a3" ftype="tabular"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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78 <expand macro="logfile-test"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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79 </test>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <test><!-- test with other file (output from mimarks.attributes)-->
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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81 <param name="filetype" value="file"/>
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82 <param name="infile" value="biosample.source" ftype="txt"/>
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83 <output name="package_out" file="biosample.tsv" ftype="tabular"/>
066b8aaf5a9a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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84 <expand macro="logfile-test"/>
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85 </test>
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86 </tests>
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87 <help>
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88 <![CDATA[
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89
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90 @MOTHUR_OVERVIEW@
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91
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92 **Command Documenation**
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93
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94 The get.mimarkspackage_ command creates a mimarks package form with your groups.
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95
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96 .. _get.mimarkspackage: http://www.mothur.org/wiki/Get.mimarkspackage
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97
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98 ]]>
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99 </help>
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100 <citations>
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101 <citation type="doi">10.1128/AEM.01541-09</citation>
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102 </citations>
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103 </tool>