Mercurial > repos > iuc > mothur_make_group

annotate make.group.xml @ 8:7ea39cdd3c5d draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"
author iuc
date Tue, 08 Dec 2020 13:15:30 +0000
parents 63a75db03ecc
children
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992d380f24ea 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_group" name="Make.group" version="@WRAPPER_VERSION@.0">
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2 <description>Make a group file</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[
2
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10 @SHELL_OPTIONS@
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12 #import re
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14 #set fastas = ''
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15 #set groups = ''
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16 #set count = 0
0
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17
2
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18 #if $method.how == 'collection':
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19 #for $i in $method.fasta_collection:
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20 #set $identifier=re.sub('[^\w_]', '_', str($i.element_identifier))
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21 ln -s '$i' 'fasta_${identifier}.dat' &&
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22 #set fastas+='fasta_'+$identifier+'.dat-'
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23 #set groups+=$identifier+'-'
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24 #end for
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25 #else
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26 #for $i in $method.inputs:
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27 ln -s '$i.fasta' fasta_${count}.dat &&
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28 #set fastas+='fasta_'+str($count)+'.dat-'
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29 #set groups+=str($i.group)+'-'
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30 #set count+=1
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31 #end for
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32 #end if
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33
2
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34 echo 'make.group(
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35 fasta=${ str($fastas).rstrip('-') },
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36 groups=${ str($groups).rstrip('-') }
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37 )'
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38 | sed 's/ //g' ## mothur trips over whitespace
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39 | mothur
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40 | tee mothur.out.log
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41 ]]></command>
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42 <inputs>
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43 <conditional name="method">
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44 <param name="how" type="select" label="Method to create group file">
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45 <option value="collection"> Automatically from collection </option>
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46 <option value="manually"> Manually specify fasta files and group names</option>
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47 </param>
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48 <when value="collection">
4
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49 <param name="fasta_collection" type="data_collection" collection_type="list" format="fasta" label="Collection with fasta files to group"
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50 help="group names will be derived from the dataset names of the collection elements, please make sure these are meaningful names"/>
0
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51 </when>
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52 <when value="manually">
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53 <repeat name="inputs" title="Additional">
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54 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
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55 <param name="group" type="text" label="group - Group name"/>
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56 </repeat>
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57 </when>
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58 </conditional>
2
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59 <expand macro="param-savelog"/>
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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="output" format="mothur.groups" from_work_dir="*groups" label="${tool.name} on ${on_string}: group"/>
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64 </outputs>
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65 <tests>
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66 <test> <!-- test manual groups creation -->
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67 <param name="how" value="manually"/>
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68 <repeat name="inputs">
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69 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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70 <param name="group" value="testgroup"/>
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71 </repeat>
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72 <repeat name="inputs">
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73 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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74 <param name="group" value="testgroup2"/>
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75 </repeat>
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76 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/>
2
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77 <param name="savelog" value="true"/>
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78 <expand macro="logfile-test"/>
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79 </test>
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80 <test> <!-- test auto-creation from collection -->
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81 <param name="how" value="collection"/>
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82 <param name="fasta_collection">
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83 <collection type="list">
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84 <element name="testgroup" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
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85 <element name="testgroup2" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
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86 </collection>
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87 </param>
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88 <output name="output" file="Mock_S280_L001_R1_001_small.trim.contigs.good.Mock_S280_L001_R1_001_small.trim.contigs.good.groups"/>
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89 <param name="savelog" value="true"/>
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90 <expand macro="logfile-test"/>
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91 </test>
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92 <test> <!-- test with spaces or hyphens in element identifier -->
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93 <param name="how" value="collection"/>
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94 <param name="fasta_collection">
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95 <collection type="list">
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96 <element name="test group" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
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97 <element name="test-group2" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
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98 </collection>
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99 </param>
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100 <output name="output" file="make_group_collection.groups"/>
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101 <param name="savelog" value="true"/>
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102 <expand macro="logfile-test"/>
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103 </test>
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104 </tests>
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105 <help><![CDATA[
0
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106
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107 @MOTHUR_OVERVIEW@
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108
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109 **Command Documentation**
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110
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111 The make.group_ command reads a fasta file or series of fasta files and creates a group_ file.
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112
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113 .. _group: https://www.mothur.org/wiki/Group_file
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114 .. _make.group: https://www.mothur.org/wiki/Make.group
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115
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116 ]]></help>
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117 <expand macro="citations"/>
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118 </tool>