Mercurial > repos > iuc > mothur_list_seqs

annotate list.seqs.xml @ 12:14742f5cf3d2 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit dfdd4c590370ecb3a9806314d43eb5668e36a01a"
author iuc
date Thu, 21 Jan 2021 21:38:57 +0000
parents 22bcd09bd771
children
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1fdda3adf67e 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_list_seqs" name="List.seqs" version="@WRAPPER_VERSION@.0">
1fdda3adf67e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Lists the names (accnos) of the sequences</description>
1fdda3adf67e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
1fdda3adf67e 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"/>
1
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9 <command><![CDATA[
3
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10 @SHELL_OPTIONS@
1
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11
3
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12 ## create symlinks to input datasets
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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13 ln -s '$search.input' search.input.dat &&
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1fdda3adf67e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14
3
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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15 echo 'list.seqs(
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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16 #if $search.intype == "fasta":
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17 fasta=search.input.dat
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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18 #elif $search.intype == "fastq":
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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19 fastq=search.input.dat
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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20 #elif $search.intype == "name":
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21 name=search.input.dat
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22 #else if $search.intype == "group":
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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23 group=search.input.dat
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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24 #elif $search.intype == "alignreport":
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25 alignreport=search.input.dat
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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26 #elif $search.intype == "list":
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27 list=search.input.dat
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28 #elif $search.intype == "taxonomy":
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29 taxonomy=search.input.dat
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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30 #elif $search.intype == "count":
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31 count=search.input.dat
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32 #end if
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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33 )'
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34 | sed 's/ //g' ## mothur trips over whitespace
8fc97e7b351c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
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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 <conditional name="search">
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40 <param name="intype" type="select" label="Type to list" help="">
1fdda3adf67e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <option value="fasta">Sequence Fasta</option>
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42 <option value="fastq">Sequence Fastq</option>
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43 <option value="name">Sequences Name reference</option>
1fdda3adf67e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 <option value="group">Groups</option>
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45 <option value="alignreport">Align Report</option>
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46 <option value="list">OTU List</option>
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47 <option value="taxonomy">Sequence Taxonomy</option>
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48 <option value="count">Count Table</option>
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49 </param>
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50 <when value="fasta">
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51 <param name="input" type="data" format="fasta" label="fasta - Fasta"/>
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52 </when>
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53 <when value="fastq">
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54 <param name="input" type="data" format="fastq" label="fasta - Fasta"/>
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55 </when>
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56 <when value="name">
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57 <param name="input" type="data" format="mothur.names" label="name - Names"/>
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58 </when>
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59 <when value="group">
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60 <param name="input" type="data" format="mothur.groups" label="group - Groups"/>
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61 </when>
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62 <when value="alignreport">
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63 <param name="input" type="data" format="mothur.align.report" label="alignreport - Align Report"/>
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64 </when>
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65 <when value="list">
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66 <param name="input" type="data" format="mothur.list" label="list - OTU List"/>
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67 </when>
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68 <when value="taxonomy">
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69 <param name="input" type="data" format="mothur.seq.taxonomy" label="taxonomy - Sequence Taxonomy"/>
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70 </when>
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71 <when value="count">
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72 <param name="input" type="data" format="mothur.count_table" label="count - Count Table"/>
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73 </when>
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74 </conditional>
5
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75 <expand macro="param-savelog"/>
0
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76 </inputs>
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77 <outputs>
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78 <expand macro="logfile-output"/>
3
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79 <data name="accnos" format="mothur.accnos" from_work_dir="search.input*.accnos" label="${tool.name} on ${on_string}: accnos"/>
0
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80 </outputs>
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81 <tests>
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82 <test><!-- test with fasta -->
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83 <param name="intype" value="fasta"/>
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84 <param name="input" value="amazon.fasta"/>
3
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85 <output name="accnos" md5="590f62ce757219c2e137a532fcd814d1" ftype="mothur.accnos"/>
5
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86 <param name="savelog" value="true"/>
0
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87 <expand macro="logfile-test"/>
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88 </test>
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89 <test><!-- test with count file -->
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90 <param name="intype" value="count"/>
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91 <param name="input" value="amazon.count_table"/>
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92 <output name="accnos" md5="360dfea2de2da4d55e75071b026c83b6" ftype="mothur.accnos"/>
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93 <param name="savelog" value="true"/>
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94 <expand macro="logfile-test"/>
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95 </test>
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96 </tests>
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97 <help><![CDATA[
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98
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99 @MOTHUR_OVERVIEW@
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100
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101 **Command Documentation**
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102
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103 The list.seqs_ command writes out the names of the sequences found within a fasta, name_, group_, list_, align.report_ or taxonomy_ file.
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104
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105 .. _name: https://www.mothur.org/wiki/Name_file
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106 .. _group: https://www.mothur.org/wiki/Group_file
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107 .. _list: https://www.mothur.org/wiki/List_file
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108 .. _align.report: https://www.mothur.org/wiki/Align.seqs
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109 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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110 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
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111
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112 v.1.20.0: Updated to mothur 1.33, added count and fastq option
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113
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114 ]]></help>
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115 <expand macro="citations"/>
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116 </tool>