Mercurial > repos > iuc > mothur_remove_seqs

annotate remove.seqs.xml @ 0:f9e64904c5dd 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 16:48:28 -0400
parents
children 87747f00c377
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
f9e64904c5dd 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_remove_seqs" name="Remove.seqs" version="@WRAPPER_VERSION@.0">
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
iuc
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2 <description>Remove sequences by name</description>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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3 <macros>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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4 <import>macros.xml</import>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
f9e64904c5dd 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"/>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <command detect_errors="aggressive"><![CDATA[
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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10 ln -s "$accnos" accnos.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11 ln -s "$fasta_in" fasta_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ln -s "$fastq_in" fastq_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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13 ln -s "$count_in" count_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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14 ln -s "$qfile_in" qfile_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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15 ln -s "$name_in" name_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 ln -s "$group_in" group_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 ln -s "$alignreport_in" alignreport_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 ln -s "$list_in" list_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 ln -s "$taxonomy_in" taxonomy_in.dat &&
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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20
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 echo 'remove.seqs(
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 accnos=accnos.dat
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 #if $fasta_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 #if $fastq_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 #if $count_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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31 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 #if $qfile_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 #if $name_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 #if $group_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 #if $alignreport_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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44 #if $list_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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46 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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47 #if $taxonomy_in:
f9e64904c5dd 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
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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49 #end if
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 $dups
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51 )'
f9e64904c5dd 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
f9e64904c5dd 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>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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55 <inputs>
f9e64904c5dd 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 of sequences to be removed"/>
f9e64904c5dd 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"/>
f9e64904c5dd 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"/>
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59 <param name="fastq_in" type="data" format="fastq" optional="true" label="fastq"/>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <param name="name_in" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference"/>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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61 <param name="group_in" type="data" format="mothur.groups" optional="true" label="group - Sequences Groups"/>
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62 <param name="alignreport_in" type="data" format="mothur.align.report" optional="true" label="alignreport - Align Report"/>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 <param name="list_in" type="data" format="mothur.list" optional="true" label="list - OTU List"/>
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64 <param name="taxonomy_in" type="data" format="mothur.seq.taxonomy" optional="true" label="taxonomy - Taxonomy"/>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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65 <param name="count_in" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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66 <param name="dups" type="boolean" truevalue="" falsevalue=",dups=false" checked="true" label="dups - Apply to duplicates"/>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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67 </inputs>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <outputs>
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69 <expand macro="logfile-output"/>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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70 <data name="fasta_out" format_source="fasta_in" from_work_dir="fasta_in.pick.dat" label="${tool.name} on ${on_string}: pick.fasta">
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71 <filter>fasta_in</filter>
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72 </data>
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73 <data name="fastq_out" format_source="fastq_in" from_work_dir="fastq_in.pick.dat" label="${tool.name} on ${on_string}: pick.fastq">
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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74 <filter>fastq_in</filter>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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75 </data>
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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76 <data name="count_out" format_source="count_in" from_work_dir="count_in.pick.dat" label="${tool.name} on ${on_string}: pick.count">
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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77 <filter>count_in</filter>
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78 </data>
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79 <data name="qfile_out" format_source="qfile_in" from_work_dir="qfile_in.pick.dat" label="${tool.name} on ${on_string}: pick.qfile">
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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80 <filter>qfile_in</filter>
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81 </data>
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82 <data name="name_out" format="mothur.names" from_work_dir="name_in.pick.dat" label="${tool.name} on ${on_string}: pick.names">
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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83 <filter>name_in</filter>
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84 </data>
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85 <data name="group_out" format="mothur.groups" from_work_dir="group_in.pick.dat" label="${tool.name} on ${on_string}: pick.groups">
f9e64904c5dd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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86 <filter>group_in</filter>
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87 </data>
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88 <data name="alignreport_out" format="mothur.align.report" from_work_dir="alignreport_in.pick.dat" label="${tool.name} on ${on_string}: pick.align.report">
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89 <filter>alignreport_in</filter>
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90 </data>
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91 <data name="list_out" format="mothur.list" from_work_dir="list_in.pick.dat" label="${tool.name} on ${on_string}: pick.list">
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92 <filter>list_in</filter>
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93 </data>
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94 <data name="taxonomy_out" format="mothur.seq.taxonomy" from_work_dir="taxonomy_in.pick.dat" label="${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 <expand macro="logfile-test"/>
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104 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/>
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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 <expand macro="logfile-test"/>
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110 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/>
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111 </test>
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112 <test><!-- test two input files -->
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113 <param name="accnos" value="Mock_S280_L001_R1_001_small.trim.contigs.bad.accnos"/>
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114 <param name="fasta_in" value="Mock_S280_L001_R1_001_small.trim.contigs.fasta"/>
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115 <param name="fastq_in" value="Mock_S280_L001_R1_001_small.fastq"/>
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116 <param name="dups" value=",dups=false"/>
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117 <expand macro="logfile-test"/>
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118 <output name="fasta_out" md5="2357e1429647afbe21521a60935919bf"/>
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119 <output name="fastq_out" md5="1e10d0793f1c5f12388156d5922c0eb8"/>
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120 </test>
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121 <test>
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122 <param name="accnos" value="amazon.bad.accnos"/>
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123 <param name="count_in" value="amazon.count_table"/>
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124 <expand macro="logfile-test"/>
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125 <output name="count_out" md5="bd1cb7af6f277210c5c11ff7d7c54592"/>
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126 </test>
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127 </tests>
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128 <help>
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129 <![CDATA[
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130
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131 @MOTHUR_OVERVIEW@
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132
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133 **Command Documenation**
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134
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135 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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136
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137 .. _name: http://www.mothur.org/wiki/Name_file
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138 .. _group: http://www.mothur.org/wiki/Group_file
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139 .. _list: http://www.mothur.org/wiki/List_file
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140 .. _align.report: http://www.mothur.org/wiki/Align.seqs
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141 .. _taxonomy: http://www.mothur.org/wiki/Taxonomy_outline
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142 .. _list.seqs: http://www.mothur.org/wiki/list.seqs
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143 .. _remove.seqs: http://www.mothur.org/wiki/Remove.seqs
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144 ]]>
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145 </help>
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146 <expand macro="citations"/>
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147 </tool>