Mercurial > repos > iuc > mothur_get_seqs

annotate get.seqs.xml @ 0:d54a9887df4a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
author iuc
date Fri, 24 Jun 2016 16:34:46 -0400
parents
children fa04cbc39523
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0
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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1 <tool profile="16.07" id="mothur_get_seqs" name="Get.seqs" version="@WRAPPER_VERSION@.0">
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Picks sequences by name</description>
d54a9887df4a 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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iuc
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4 <import>macros.xml</import>
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5 </macros>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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7 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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9 ## create symlinks to input datasets
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$accnos" accnos.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$fasta_in" fasta_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$fastq_in" fastq_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$count_in" count_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$qfile_in" qfile_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$name_in" name_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 ln -s "$group_in" group_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 ln -s "$alignreport_in" alignreport_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 ln -s "$list_in" list_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 ln -s "$taxonomy_in" taxonomy_in.dat &&
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 echo 'get.seqs(
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 accnos=accnos.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #if $fasta_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 fasta=fasta_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #end if
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #if $fastq_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 fastq=fastq_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 #end if
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #if $count_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 count=count_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 #end if
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 #if $qfile_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 qfile=qfile_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 #end if
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 #if $name_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 name=name_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 #end if
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 #if $group_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 group=group_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 #end if
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 #if $alignreport_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 alignreport=alignreport_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 #end if
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 #if $list_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 list=list_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 #end if
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 #if $taxonomy_in:
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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48 taxonomy=taxonomy_in.dat,
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 #end if
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50 dups=$dups
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51 )'
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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52 | sed 's/ //g' ## mothur trips over whitespace
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 | mothur
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54 ]]></command>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 <inputs>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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56 <param name="accnos" type="data" format="mothur.accnos" label="accnos - Accession Names"/>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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57 <param name="fasta_in" type="data" format="fasta" optional="true" label="fasta - Fasta Sequences"/>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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58 <param name="qfile_in" type="data" format="qual" optional="true" label="qfile - Fasta Quality"/>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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59 <param name="fastq_in" type="data" format="fastq" optional="true" label="count - a count_table" help="fastq - allows you to select sequences from your fastq file"/>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
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62 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/>
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63 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
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64 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
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66 <param name="dups" type="boolean" truevalue="dups" falsevalue="false" checked="true" label="dups - Apply to duplicates"/>
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67 </inputs>
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68 <outputs>
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69 <expand macro="logfile-output"/>
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70 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in*.pick.*" label="${tool.name} on ${on_string}: pick.fasta">
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71 <filter>fasta_in</filter>
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72 </data>
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73 <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in*.pick.*" label="${tool.name} on ${on_string}: pick.fastq">
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <filter>fastq_in</filter>
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75 </data>
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76 <data name="count_out" format_source="count_in" from_work_dir="count_in*.pick.*" label="${tool.name} on ${on_string}: pick.count">
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <filter>count_in</filter>
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78 </data>
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79 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in*.pick.*" label="${tool.name} on ${on_string}: pick.qfile">
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <filter>qfile_in</filter>
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81 </data>
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82 <data name="name_out" format="mothur.names" from_work_dir="name_in*.pick.*" label="${tool.name} on ${on_string}: pick.names">
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83 <filter>name_in</filter>
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84 </data>
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85 <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
d54a9887df4a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <filter>group_in</filter>
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87 </data>
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88 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in*.pick.*" label="${tool.name} on ${on_string}: pick.align.report">
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89 <filter>alignreport_in</filter>
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90 </data>
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91 <data name="list_out" format="mothur.list" from_work_dir="list_in*.pick.*" label="${tool.name} on ${on_string}: pick.list">
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92 <filter>list_in</filter>
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93 </data>
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94 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in*.pick.*" label="${tool.name} on ${on_string}: pick.taxonomy">
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95 <filter>taxonomy_in</filter>
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96 </data>
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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101 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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102 <param name="dups" value=""/>
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103 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
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104 <expand macro="logfile-test"/>
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105 </test>
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106 <test>
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107 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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108 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
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109 <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/>
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110 <expand macro="logfile-test"/>
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111 </test>
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112 <test>
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113 <!-- test two input files -->
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114 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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115 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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116 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
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117 <param name="dups" value="false"/>
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118 <output name="fasta_out" md5="f9335b6b70dc639e420d33809e51431d"/>
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119 <output name="fastq_out" md5="e9aae546bf9c00cb7e884dff267d4ba1"/>
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120 <expand macro="logfile-test"/>
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121 </test>
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122 <test>
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123 <param name="accnos" value="amazon.bad.accnos"/>
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124 <param name="count_in" value="amazon.count_table"/>
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125 <output name="count_out" md5="6892dd99850ce9e9f8f15e77b28f57e2"/>
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126 <expand macro="logfile-test"/>
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127 </test>
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128 </tests>
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129 <help>
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130 <![CDATA[
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131
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132 @MOTHUR_OVERVIEW@
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133
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134 **Command Documenation**
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135
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136 The get.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 contains only 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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137
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138 .. _name: http://www.mothur.org/wiki/Name_file
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139 .. _group: http://www.mothur.org/wiki/Group_file
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140 .. _list: http://www.mothur.org/wiki/List_file
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141 .. _align.report: http://www.mothur.org/wiki/Align.seqs
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142 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
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143 .. _list.seqs: http://www.mothur.org/wiki/list.seqs
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144 .. _get.seqs: http://www.mothur.org/wiki/Get.seqs
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145
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146 v.1.27.0 : Updated to Mothur 1.33, added count and fastq params
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147 ]]>
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148 </help>
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149 <expand macro="citations"/>
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150 </tool>