Mercurial > repos > erasmus-medical-center > mycrobiota

annotate krona_mothur.xml @ 1:e93e39c121b1 draft default tip

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit aadbfac9c48191cac625f10590082a6d1a0bfd09
author erasmus-medical-center
date Tue, 29 Jan 2019 12:13:23 -0500
parents 607c5e7e0a64
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607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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1 <tool id="mycrobiota-krona-mothur" name="Krona" version="1">
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2 <description>for mothur datasets</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 <requirements>
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7 <requirement type="package" version="2.7">krona</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive"><![CDATA[
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10 ## create symlinks to taxonomy files for nicer display names in output
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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11 #if $input.haveshared == 'no':
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12 #for $tax in $input.taxonomy:
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13 ln -s '$tax' '$tax.name' &&
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14 #end for
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15 #end if
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16
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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17 python '$__tool_directory__/mycrobiota.py'
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18 #if $input.haveshared == 'yes':
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19 --command create_krona_plot_multisample
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20 --shared_file '$input.shared_file'
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21 #if $input.level == 'None':
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22 --level '$input.taxonomy.name'
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23 #else:
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24 --level '$input.level'
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25 #end if
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26 --taxonomy $input.taxonomy
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27 #else:
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28 --command create_krona_plot
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29 #for $tax in $input.taxonomy:
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30 --taxonomy '$tax.name'
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31 #end for
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32 #end if
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33 ${with_otu}
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34 ]]></command>
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35 <inputs>
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36 <conditional name="input">
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37 <param name="haveshared" type="select" label="Would you like to supply a mothur shared file?"
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38 help="This will create a multisample plot. If you select 'no', you can still create a multisample plot by providing a taxonomy file per sample">
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39 <option value="no">No</option>
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40 <option value="yes">Yes</option>
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41 </param>
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42 <when value="no">
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43 <param argument="--taxonomy" type="data" multiple="true" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/>
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44 </when>
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45 <when value="yes">
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46 <param argument="--taxonomy" type="data" format="mothur.ref.taxonomy,mothur.seq.taxonomy,mothur.cons.taxonomy" label="Select mothur taxonomy file" help=""/>
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47 <param argument="--shared_file" type="data" optional="true" format="mothur.shared" label="Supply a mothur shared file" help=""/>
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48 <param argument="--level" type="select" optional="true" label="label - pick (one) OTU Label" help="leave blank for collections, will try to determine level from element names">
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49 <options>
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50 <filter type="data_meta" ref="shared_file" key="labels"/>
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51 </options>
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52 </param>
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53 </when>
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54 </conditional>
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55 <param argument="--with_otu" type="boolean" checked="false" truevalue="--with-otu" falsevalue="" label="differentiate between different OTUs of same taxonomy?" help=""/>
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56 </inputs>
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57 <outputs>
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58 <data name="krona_plot" format="html" from_work_dir="text.krona.html" label="Krona plot of ${on_string}: HTML"/>
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59 </outputs>
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60 <tests>
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61 <test> <!-- test single sample -->
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62 <param name="haveshared" value="no"/>
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63 <param name="taxonomy" value="multisample.taxonomy"/>
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64 <param name="with_otu" value="--with-otu"/>
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65 <output name="krona_plot">
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66 <assert_contents>
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67 <has_text text="Krona"/>
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68 <has_text text="Actinobacteria"/>
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69 <not_has_text text="F3D0"/>
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70 <not_has_text text="F3D148"/>
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71 <not_has_text text="krona.test1.mothur.cons"/>
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72 <has_text text="Otu0127"/>
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73 </assert_contents>
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74 </output>
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75 </test>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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76 <test> <!-- test multi samples (multiple single-sample taxonomy files) -->
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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77 <param name="haveshared" value="no"/>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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78 <param name="taxonomy" value="multisample.taxonomy,krona.test1.mothur.cons.taxonomy"/>
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79 <param name="with_otu" value=""/>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
erasmus-medical-center
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80 <output name="krona_plot">
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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81 <assert_contents>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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82 <has_text text="Krona"/>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
erasmus-medical-center
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83 <has_text text="krona.test1.mothur.cons"/>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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84 <has_text text="Actinobacteria"/>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
erasmus-medical-center
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85 <not_has_text text="F3D0"/>
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erasmus-medical-center
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86 <not_has_text text="F3D148"/>
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87 <not_has_text text="Otu0127"/>
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88 </assert_contents>
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89 </output>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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90 </test>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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91 <test> <!-- test multi sample (single multisample taxonomy file with shared file) -->
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92 <param name="haveshared" value="yes"/>
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93 <param name="taxonomy" value="multisample.taxonomy"/>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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94 <param name="shared_file" ftype="mothur.shared" value="example.mothur.shared"/>
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95 <param name="with_otu" value="--with-otu"/>
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96 <param name="level" value="0.03"/>
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97 <output name="krona_plot">
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98 <assert_contents>
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99 <has_text text="Krona"/>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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100 <has_text text="Actinobacteria"/>
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101 <has_text text="F3D0"/>
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102 <has_text text="F3D148"/>
607c5e7e0a64 planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/mycrobiota commit 1c4c58018b64ff3531a719e789ce71cb0a1244c5
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103 </assert_contents>
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104 </output>
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105 </test>
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106 </tests>
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107 <help><![CDATA[
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108 **What it does**
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109 ]]></help>
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110 <expand macro="citations">
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111 <citation type="doi">10.1007/978-1-4614-6418-1_802-1</citation>
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112 </expand>
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113 </tool>