Mercurial > repos > iuc > mothur_get_coremicrobiome

annotate get.coremicrobiome.xml @ 3:5e29cbb2fdef 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 10:09:11 -0500
parents af8e6f1110b3
children a6e3c040eb53
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1dd4d752f823 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_get_coremicrobiome" name="Get.coremicrobiome" version="@WRAPPER_VERSION@.0">
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2 <description>fraction of OTUs for samples or abundances</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
1dd4d752f823 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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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[
3
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10 @SHELL_OPTIONS@
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11
3
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12 ## create symlinks to input datasets
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13 ln -s '$otu' otu.dat &&
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14
3
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15 echo 'get.coremicrobiome(
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16 #if $otu.is_of_type("mothur.relabund"):
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17 relabund=otu.dat
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18 #elif $otu.is_of_type("mothur.shared"):
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19 shared=otu.dat
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20 #end if
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21 #if $label:
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22 ,label=${ str($label).replace(",","-") }
5e29cbb2fdef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 #end if
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24 #if $groups:
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25 ,groups=${ str($groups).replace(",","-") }
5e29cbb2fdef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 #end if
5e29cbb2fdef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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27 #if $abundance:
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28 ,abundance=$abundance
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29 #end if
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30 #if $samples:
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31 ,samples=$samples
5e29cbb2fdef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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32 #end if
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33 )'
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34 | sed 's/ //g' ## mothur trips over whitespace
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35 | mothur
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36 | tee mothur.out.log
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37 ]]></command>
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38 <inputs>
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39 <param name="otu" type="data" format="mothur.shared,mothur.relabund" label="shared or relabund - OTU Shared or Relabund"/>
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40 <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true">
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41 <expand macro="labeloptions"/>
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42 </param>
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43 <param name="groups" type="select" optional="true" label="groups - Pairwise comparision groups" multiple="true">
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44 <options>
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45 <filter type="data_meta" ref="otu" key="groups"/>
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46 </options>
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47 </param>
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48 <param name="abundance" type="integer" optional="true" value="" min="0" max="100" label="abundance - list OTU names at this abundance"/>
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49 <param name="samples" type="integer" optional="true" value="" min="1" label="samples - minimum number of samples requied to list OTU names"/>
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50 <param name="output" type="select" label="output - fraction or count">
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51 <option value="fraction" selected="true">fraction</option>
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52 <option value="count">count</option>
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53 </param>
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54 </inputs>
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55 <outputs>
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56 <expand macro="logfile-output"/>
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57 <collection name="core_microbiome" type="list" label="${tool.name} on ${on_string}: core.microbiome files">
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58 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiome$" format="tabular"/>
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59 </collection>
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60 <collection name="core_microbiome_list" type="list" label="${tool.name} on ${on_string}: core.microbiome list files">
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61 <filter>abundance or samples </filter>
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62 <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.core\.microbiomelist" format="tabular"/>
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63 </collection>
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64 </outputs>
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65 <tests>
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66 <test><!-- test with default params -->
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67 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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68 <output_collection name="core_microbiome" count="36">
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69 <element name="0.45" md5="bae9cb5f1d311fe0cfb7ecb72a177261" ftype="tabular"/>
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70 </output_collection>
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71 <expand macro="logfile-test"/>
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72 </test>
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73 <test><!-- test with list output and label and group select-->
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74 <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
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75 <param name="abundance" value="30"/>
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76 <param name="label" value="0.05,0.22,0.45"/>
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77 <param name="group" value="forest,pasture"/>
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78 <output_collection name="core_microbiome" count="3">
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79 <element name="0.05" md5="72bb437ab5f3a66965029a616fbaf317" ftype="tabular"/>
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80 </output_collection>
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81 <output_collection name="core_microbiome_list" count="3">
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82 <element name="0.05" md5="83722b4c52b7faff7fe56ce026250001" ftype="tabular"/>
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83 </output_collection>
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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><![CDATA[
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88
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89 @MOTHUR_OVERVIEW@
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90
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91 **Command Documentation**
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92
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93 The get.coremicrobiome_ command determines the fraction of OTUs that are found in varying numbers of samples for different minimum relative abundances.
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94
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95 .. _get.coremicrobiome: https://www.mothur.org/wiki/Get.coremicrobiome
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96
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97 v1.27.0: Updated to Mothur 1.33
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98
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99 ]]></help>
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100 <expand macro="citations"/>
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101 </tool>