Mercurial > repos > iuc > mothur_make_group

annotate make.group.xml @ 2:5b28532dfc0a 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 09:13:47 -0500
parents 1cf5a6a5eb05
children e1e0c8bb9aa8
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iuc
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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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11
2
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12 #set fastas = ''
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 #set groups = ''
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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14 #set count = 0
0
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2
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16 #if $method.how == 'collection':
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17 #for $i in $method.fasta_collection:
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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18 ln -s '$i' fasta_${i.element_identifier}.dat &&
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 #set fastas+='fasta_'+$i.element_identifier+'.dat-'
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 #set groups+=$i.element_identifier+'-'
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21 #end for
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22 #else
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23 #for $i in $method.inputs:
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 ln -s '$i.fasta' fasta_${count}.dat &&
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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25 #set fastas+='fasta_'+str($count)+'.dat-'
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26 #set groups+=str($i.group)+'-'
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27 #set count+=1
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28 #end for
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29 #end if
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30
2
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31 echo 'make.group(
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32 fasta=${ str($fastas).rstrip('-') },
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 groups=${ str($groups).rstrip('-') }
5b28532dfc0a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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34 )'
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35 | sed 's/ //g' ## mothur trips over whitespace
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36 | mothur
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37 | tee mothur.out.log
0
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38 ]]></command>
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39 <inputs>
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40 <conditional name="method">
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41 <param name="how" type="select" label="Method to create group file">
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42 <option value="collection"> Automatically from collection </option>
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43 <option value="manually"> Manually specify fasta files and group names</option>
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44 </param>
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45 <when value="collection">
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46 <param name="fasta_collection" type="data_collection" collection_type="list" format="fasta" label="Collection with fasta files to group" help="group names will be named after the collection element names"/>
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47 </when>
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48 <when value="manually">
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49 <repeat name="inputs" title="Additional">
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50 <param name="fasta" type="data" format="fasta" label="fasta - Fasta to group"/>
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51 <param name="group" type="text" label="group - Group name"/>
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52 </repeat>
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <expand macro="logfile-output"/>
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58 <data name="output" format="mothur.groups" from_work_dir="*groups" label="${tool.name} on ${on_string}: group"/>
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59 </outputs>
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60 <tests>
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61 <test> <!-- test manual groups creation -->
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62 <param name="how" value="manually"/>
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63 <repeat name="inputs">
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64 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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65 <param name="group" value="testgroup"/>
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66 </repeat>
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67 <repeat name="inputs">
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68 <param name="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head"/>
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69 <param name="group" value="testgroup2"/>
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70 </repeat>
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71 <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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72 <expand macro="logfile-test"/>
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73 </test>
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74 <test> <!-- test auto-creation from collection -->
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75 <param name="how" value="collection"/>
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76 <param name="fasta_collection">
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77 <collection type="list">
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78 <element name="testgroup" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
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79 <element name="testgroup2" ftype="fasta" value="Mock_S280_L001_R1_001_small.trim.contigs.good.align_head" />
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80 </collection>
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81 </param>
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82 <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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83 <expand macro="logfile-test"/>
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84 </test>
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85 </tests>
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86 <help><![CDATA[
0
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87
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88 @MOTHUR_OVERVIEW@
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89
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90 **Command Documentation**
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91
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92 The make.group_ command reads a fasta file or series of fasta files and creates a group_ file.
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93
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94 .. _group: https://www.mothur.org/wiki/Group_file
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95 .. _make.group: https://www.mothur.org/wiki/Make.group
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96
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97 ]]></help>
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98 <expand macro="citations"/>
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99 </tool>