Mercurial > repos > iuc > mothur_make_lookup

annotate make.lookup.xml @ 7:a33258dc5bf8 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"
author iuc
date Mon, 02 Dec 2019 05:56:08 -0500
parents d56e5a7a9cef
children 9a074f55579e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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0c303113990d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_make_lookup" name="Make.lookup" version="@WRAPPER_VERSION@.0">
0c303113990d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>allows you to create custom lookup files for use with shhh.flows</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="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@
0
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11
3
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12 #import re
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13 ## create symlinks to input datasets
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14 ln -s '$reference.template' reference.template.dat &&
91652222f7b4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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15 ln -s '$flow' flow.dat &&
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16 ln -s '$error' error.dat &&
0
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17
3
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18 echo 'make.lookup(
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19 reference=reference.template.dat,
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20 flow=flow.dat,
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21 error=error.dat,
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22 order=$order,
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23 barcode=$re.sub("[^ACTG]","",str($barcode)),
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24 key=$re.sub("[^ACTG]","",str($key)),
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25 threshold=$threshold
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26 )'
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27 | sed 's/ //g' ## mothur trips over whitespace
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28 | mothur
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29 | tee mothur.out.log
0
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30 ]]></command>
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31 <inputs>
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32 <conditional name="reference">
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33 <param name="source" type="select" label="Select Reference Template from" help="">
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34 <option value="hist">History</option>
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35 <option value="ref">Cached Reference</option>
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36 </param>
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37 <when value="ref">
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38 <param name="template" type="select" label="reference - Select an alignment database " help="">
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39 <options from_data_table="mothur_aligndb"/>
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40 </param>
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41 </when>
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42 <when value="hist">
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43 <param name="template" type="data" format="fasta" label="reference - Reference to align with" help=""/>
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44 </when>
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45 </conditional>
2
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46 <param name="flow" type="data" format="mothur.sff.flow" label="flow - provide file with flow data"/>
0
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47 <param name="error" type="data" format="tabular" label="error - provide the error summary" help="this file is an output of seq.error tool"/>
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48 <param name="order" type="select" label="order - flow order for nucleotides in the sequencer" help="default is A, was TACG. Also accepts B or I">
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49 <option value="A" selected="true">A (TACG)</option>
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50 <option value="B">B</option>
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51 <option value="I">I</option>
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52 </param>
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53 <param name="barcode" type="text" value="AACCGTGTC" label="barcode - provide the barcode sequence"/>
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54 <param name="key" type="text" value="TCAG" label="key - provide the key sequence"/>
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55 <param name="threshold" type="integer" value="10000" min="0" label="threshold - " help=""/>
3
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56 <expand macro="param-savelog"/>
0
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57 </inputs>
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58 <outputs>
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59 <expand macro="logfile-output"/>
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60 <data name="lookup_out" format="txt" from_work_dir="flow*.lookup" label="${tool.name} on ${on_string}: lookup"/>
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61 </outputs>
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62 <tests>
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63 <test><!-- test with defaults -->
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64 <param name="source" value="hist"/>
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65 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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66 <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
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67 <param name="error" value="Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary" ftype="tabular"/>
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68 <output name="lookup_out" ftype="txt">
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69 <assert_contents>
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70 <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
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71 </assert_contents>
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72 </output>
3
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73 <param name="savelog" value="true"/>
0
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74 <expand macro="logfile-test"/>
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75 </test>
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76 <test><!-- test sanitizers -->
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77 <param name="source" value="hist"/>
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78 <param name="template" value="HMP_MOCK.v35.align" ftype="mothur.align"/>
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79 <param name="flow" value="testflow.flow" ftype="mothur.sff.flow"/>
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80 <param name="error" value="Mock_S280_L001_R1_001_small.trim.contigs.good.error.summary" ftype="tabular"/>
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81 <param name="barcode" value="XAXAXCXCXGXTXGXTXC"/><!-- should be converted to default value -->
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82 <param name="key" value="XTXCXAXGX"/><!-- should be converted to default value -->
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83 <output name="lookup_out" ftype="txt">
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84 <assert_contents>
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85 <has_line_matching expression="^(-?[(\d\.|nan)]+\t?)+$"/>
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86 </assert_contents>
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87 </output>
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88 <param name="savelog" value="true"/>
0
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89 <expand macro="logfile-test"/>
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90 </test>
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91 </tests>
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92 <help><![CDATA[
0
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93
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94 @MOTHUR_OVERVIEW@
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95
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96 **Command Documentation**
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97
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98 The make.lookup_ allows you to create custom lookup files for use with shhh.flows.
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99
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100 .. _make.lookup: https://www.mothur.org/wiki/Make.lookup
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101
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102 ]]></help>
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103 <expand macro="citations">
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104 <citation type="doi">10.1038/nmeth.1361</citation>
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105 </expand>
0
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106 </tool>