Mercurial > repos > iuc > mothur_remove_seqs

annotate remove.seqs.xml @ 1:008f62670efc draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 16:57:34 -0400
parents e59ddb750b65
children 0b8ca0026f28
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e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
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1 <tool profile="16.07" id="mothur_remove_seqs" name="Remove.seqs" version="@WRAPPER_VERSION@.0">
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Remove sequences by name</description>
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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4 <import>macros.xml</import>
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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8 <expand macro="version_command"/>
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <command><![CDATA[
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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11
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## if accnos file is empty, just output files as-is, mothur errors if accnos empty (e.g. chimera filtering in pipeline but sample had no chimeras)
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 #import os
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 #if $os.lstat(str($accnos)).st_size == 0:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 echo "accnos file empty, nothing to remove, skipping step"
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 #if $fasta_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 && cp $fasta_in $fasta_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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19 #if $fastq_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 && cp $fastq_in $fastq_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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22 #if $count_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 && cp $count_in $count_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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24 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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25 #if $qfile_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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26 && cp $qfile_in $qfile_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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27 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 #if $name_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 && cp $name_in $name_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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30 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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31 #if $group_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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32 && cp $group_in $group_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 #if $alignreport_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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35 && cp $alignreport_in $alignreport_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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37 #if $list_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 && cp $list_in $list_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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39 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 #if $taxonomy_in:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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41 && cp $taxonomy_in $taxonomy_out
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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42 #end if
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 #else:
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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44 ## create symlinks to input datasets
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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45 ln -s "$accnos" accnos.dat &&
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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46 ln -s "$fasta_in" fasta_in.dat &&
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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47 ln -s "$fastq_in" fastq_in.dat &&
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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48 ln -s "$count_in" count_in.dat &&
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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49 ln -s "$qfile_in" qfile_in.dat &&
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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50 ln -s "$name_in" name_in.dat &&
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51 ln -s "$group_in" group_in.dat &&
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52 ln -s "$alignreport_in" alignreport_in.dat &&
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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53 ln -s "$list_in" list_in.dat &&
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54 ln -s "$taxonomy_in" taxonomy_in.dat &&
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55
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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56 echo 'remove.seqs(
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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57 accnos=accnos.dat
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58 #if $fasta_in:
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59 ,fasta=fasta_in.dat
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60 #end if
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61 #if $fastq_in:
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62 ,fastq=fastq_in.dat
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63 #end if
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64 #if $count_in:
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65 ,count=count_in.dat
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66 #end if
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67 #if $qfile_in:
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68 ,qfile=qfile_in.dat
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69 #end if
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70 #if $name_in:
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71 ,name=name_in.dat
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72 #end if
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73 #if $group_in:
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74 ,group=group_in.dat
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75 #end if
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76 #if $alignreport_in:
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77 ,alignreport=alignreport_in.dat
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78 #end if
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79 #if $list_in:
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80 ,list=list_in.dat
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81 #end if
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82 #if $taxonomy_in:
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83 ,taxonomy=taxonomy_in.dat
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84 #end if
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85 $dups
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86 )'
e59ddb750b65 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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87 | sed 's/ //g' ## mothur trips over whitespace
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88 | mothur
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89 | tee mothur.out.log
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90 #end if
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91 ]]></command>
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92 <inputs>
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93 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names of sequences to be removed"/>
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94 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
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95 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
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96 <param name="fastq_in" type="data" format="fastq" optional="true" label="fastq"/>
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97 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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98 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/>
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99 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
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100 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
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101 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
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102 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
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103 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/>
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104 </inputs>
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105 <outputs>
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106 <expand macro="logfile-output"/>
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107 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta">
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108 <filter>fasta_in</filter>
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109 </data>
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110 <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in.pick.dat" label="${tool.name} on ${on_string}: pick.fastq">
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111 <filter>fastq_in</filter>
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112 </data>
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113 <data name="count_out" format_source="count_in" from_work_dir="count_in.pick.dat" label="${tool.name} on ${on_string}: pick.count">
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114 <filter>count_in</filter>
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115 </data>
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116 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in.pick.dat" label="${tool.name} on ${on_string}: pick.qfile">
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117 <filter>qfile_in</filter>
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118 </data>
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119 <data name="name_out" format="mothur.names" from_work_dir="name_in.pick.dat" label="${tool.name} on ${on_string}: pick.names">
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120 <filter>name_in</filter>
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121 </data>
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122 <data name="group_out" format="mothur.groups" from_work_dir="group_in.pick.dat" label="${tool.name} on ${on_string}: pick.groups">
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123 <filter>group_in</filter>
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124 </data>
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125 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in.pick.dat" label="${tool.name} on ${on_string}: pick.align.report">
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126 <filter>alignreport_in</filter>
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127 </data>
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128 <data name="list_out" format="mothur.list" from_work_dir="list_in.pick.dat" label="${tool.name} on ${on_string}: pick.list">
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129 <filter>list_in</filter>
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130 </data>
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131 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in.pick.dat" label="${tool.name} on ${on_string}: pick.taxonomy">
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132 <filter>taxonomy_in</filter>
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133 </data>
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134 </outputs>
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135 <tests>
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136 <test>
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137 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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138 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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139 <param name="dups" value=""/>
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140 <expand macro="logfile-test"/>
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141 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/>
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142 </test>
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143 <test>
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144 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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145 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
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146 <expand macro="logfile-test"/>
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147 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/>
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148 </test>
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149 <test><!-- test two input files -->
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150 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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151 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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152 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
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153 <param name="dups" value=",dups=false"/>
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154 <expand macro="logfile-test"/>
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155 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/>
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156 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/>
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157 </test>
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158 <test>
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159 <param name="accnos" value="amazon.bad.accnos"/>
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160 <param name="count_in" value="amazon.count_table"/>
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161 <expand macro="logfile-test"/>
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162 <output name="count_out" md5="bd1cb7af6f277210c5c11ff7d7c54592"/>
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163 </test>
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164 <!-- TODO: make test for empty accnos file -->
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165 </tests>
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166 <help>
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167 <![CDATA[
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168
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169 @MOTHUR_OVERVIEW@
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170
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171 **Command Documentation**
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172
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173 The remove.seqs_ command takes a list of sequence names and either a fasta, name_, group_, list_, align.report_ or taxonomy_ file to generate a new file that does not contain the sequences in the list. This command may be used in conjunction with the list.seqs_ command to help screen a sequence collection.
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174
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175 .. _name: https://www.mothur.org/wiki/Name_file
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176 .. _group: https://www.mothur.org/wiki/Group_file
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177 .. _list: https://www.mothur.org/wiki/List_file
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178 .. _align.report: https://www.mothur.org/wiki/Align.seqs
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179 .. _taxonomy: https://www.mothur.org/wiki/Taxonomy_outline
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180 .. _list.seqs: https://www.mothur.org/wiki/list.seqs
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181 .. _remove.seqs: https://www.mothur.org/wiki/Remove.seqs
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182 ]]>
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183 </help>
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184 <expand macro="citations"/>
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185 </tool>