Mercurial > repos > iuc > mothur_make_sra

annotate make.sra.xml @ 0:eb8c2262bd1b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
author iuc
date Fri, 19 May 2017 05:03:09 -0400
parents
children 82e91bb188b2
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0
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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1 <tool profile="16.07" id="mothur_make_sra" name="Make.sra" version="@WRAPPER_VERSION@.0">
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>creates the necessary files for a NCBI submission</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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6 <expand macro="requirements"/>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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7 <expand macro="stdio"/>
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 @SHELL_OPTIONS@
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11
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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12 ## create symlinks to input datasets
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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13 ln -s "$project" project.dat &&
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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14 ln -s "$sff" sff.dat &&
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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15 ln -s "$oligos" oligos.dat &&
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16 ln -s "$mimark" mimark.dat &&
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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17 ln -s "$fastq" fastq.dat &&
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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18
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19 echo 'make.sra(
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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20 project=project.dat,
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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21 sff=sff.dat,
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22 oligos=oligos.dat,
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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23 mimark=mimark.dat,
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24 #if $fastq:
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25 fastq=fastq.dat,
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26 #end if
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27 bdiffs=$bdiffs,
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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28 pdiffs=$pdiffs,
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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29 tdiffs=$tdiffs,
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30 ldiffs=$ldiffs,
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31 sdiffs=$sdiffs,
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32 checkorient=$checkorient,
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 orientation=$orientation,
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 platform=$platform,
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35 instrument=$instrument,
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36 libstrategy=$libstrategy,
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37 libselection=$libselection,
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38 libsource=$libsource,
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39 datatype=$datatype
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40 )'
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41 | sed 's/ //g' ## mothur trips over whitespace
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42 | mothur
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43 | tee mothur.out.log
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44 ]]></command>
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45 <inputs>
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46 <param name="project" type="data" format="tabular" label="Project file"/>
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47 <param name="sff" type="data" format="sff" label="sff - provide the original sff file"/>
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48 <param name="oligos" type="data" format="mothur.oligos" label="oligos - provide an oligos file to parse your sff or fastq file by. It is required and must contain barcodes and primers"/>
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49 <param name="mimark" type="data" format="txt" label="mimarks file - you can create the template for this file using the get.mimarkspackage command"/>
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50 <param name="fastq" type="data" optional="true" format="fastq" label="fastq - provide the original fastq file"/>
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51 <param name="bdiffs" type="integer" value="0" min="0" label="bdiffs - number of differences to allow in the barcode (must be > 0; default 0)"/>
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52 <param name="pdiffs" type="integer" value="0" min="0" label="pdiffs - number of differences to allow in the primer (must be > 0; default 0)"/>
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53 <param name="tdiffs" type="integer" value="0" min="0" label="tdiffs - total number of differences to allow in primer and barcode (must be > 0; default 0)"/>
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54 <param name="ldiffs" type="integer" value="0" min="0" label="ldiffs - total number of differences to allow in linker sequence (must be > 0; default 0)"/>
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55 <param name="sdiffs" type="integer" value="0" min="0" label="sdiffs - total number of differences to allow in spacer sequence (must be > 0; default 0)"/>
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56 <param name="checkorient" type="boolean" truevalue="true" falsevalue="false" checked="false" label="checkorient - will check for the reverse compliment of the barcode or primer in the sequence. The default is false."/>
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57 <param name="orientation" type="select" label="orientation - specify the sequence orientation">
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58 <option value="forward" selected="true">forward</option>
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59 <option value="reverse">reverse</option>
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60 </param>
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61 <param name="platform" type="select" label="platform - specify platform you are using" help="This is a controlled vocabulary section in the XML file that will be generated">
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62 <option value="_LS454" selected="true">454 (_LS454)</option>
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63 <option value="ILLUMINA">Illumina (ILLUMINA)</option>
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64 <option value="ION_TORRENT">Ion Torrent (ION_TORRENT)</option>
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65 <option value="PACBIO_SMRT">PacBio (PACBIO_SMRT)</option>
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66 </param>
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67 <param name="instrument" type="select" label="instrument - specify instrument" help="This is a controlled vocabulary section in the XML file that will be generated">
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68 <option value="454_GS" selected="true">454_GS</option>
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69 <option value="454_GS_20">454_GS_20</option>
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70 <option value="454_GS_FLX">454_GS_FLX</option>
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71 <option value="454_GS_FLX_Titanium">454_GS_FLX_Titanium</option>
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72 <option value="454_GS_Junior">454_GS_Junior</option>
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73 <option value="Illumina_Genome_Analyzer">Illumina_Genome_Analyzer</option>
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74 <option value="Illumina_Genome_Analyzer_II">Illumina_Genome_Analyzer_II</option>
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75 <option value="Illumina_Genome_Analyzer_IIx">Illumina_Genome_Analyzer_IIx</option>
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76 <option value="Illumina_HiSeq_2000">Illumina_HiSeq_2000</option>
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77 <option value="Illumina_HiSeq_1000">Illumina_HiSeq_1000</option>
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78 <option value="Illumina_MiSeq">Illumina_MiSeq</option>
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79 <option value="PacBio_RS">PacBio_RS</option>
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80 <option value="Ion_Torrent_PGM">Ion_Torrent_PGM</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
81 <option value="unspecified">unspecified</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
82 </param>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
83 <param name="libstrategy" type="select" label="libstrategy - specify library strategy" help="This is a controlled vocabulary section in the XML file that will be generated">
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
84 <option value="AMPLICON" selected="true">AMPLICON</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
85 <option value="WGA">WGA</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
86 <option value="WGS">WGS</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
87 <option value="RNA-Seq">RNA-Seq</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
88 <option value="miRNA-Se">miRNA-Se</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
89 <option value="WCS">WCS</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
90 <option value="CLONE">CLONE</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
91 <option value="POOLCLONE">POOLCLONE</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
92 <option value="CLONEEND">CLONEEND</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
93 <option value="FINISHING">FINISHING</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
94 <option value="ChIP-Seq">ChIP-Seq</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
95 <option value="MNase-Seq">MNase-Seq</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
96 <option value="DNase-Hypersensitivity">DNase-Hypersensitivity</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
97 <option value="Bisulfite-Seq">Bisulfite-Seq</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
98 <option value="Tn-Seq">Tn-Seq</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
99 <option value="EST">EST</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
100 <option value="FL-cDNA">FL-cDNA</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
101 <option value="CTS">CTS</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
102 <option value="MRE-Seq">MRE-Seq</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
103 <option value="MeDIP-Seq">MeDIP-Seq</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
104 <option value="MBD-Seq">MBD-Seq</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
105 <option value="OTHER">OTHER</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
106 </param>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
107 <param name="libsource" type="select" label="libsource - specify library source" help="This is a controlled vocabulary section in the XML file that will be generated">
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
108 <option value="METAGENOMIC" selected="true">METAGENOMIC</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
109 <option value="GENOMIC">GENOMIC</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
110 <option value="TRANSCRIPTOMIC">TRANSCRIPTOMIC</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
111 <option value="METATRANSCRIPTOMIC">METATRANSCRIPTOMIC</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
112 <option value="SYNTHETIC">SYNTHETIC</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
113 <option value="VIRAL_RNA">VIRAL_RNA</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
114 <option value="OTHER">OTHER</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
115 </param>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
116 <param name="libselection" type="select" label="libselection - specify library selection" help="This is a controlled vocabulary section in the XML file that will be generated">
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
117 <option value="PCR" selected="true">PCR</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
118 <option value="RANDOM">RANDOM</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
119 <option value="RANDOM_PCR">RANDOM_PCR</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
120 <option value="RT-PCR">RT-PCR</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
121 <option value="HMPR">HMPR</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
122 <option value="MF">MF</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
123 <option value="CF-S">CF-S</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
124 <option value="CF-H">CF-H</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
125 <option value="CF-T">CF-T</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
126 <option value="CF-M">CF-M</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
127 <option value="MDA">MDA</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
128 <option value="MSLL">MSLL</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
129 <option value="cDNA">cDNA</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
130 <option value="ChIP">ChIP</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
131 <option value="MNase">MNase</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
132 <option value="Hybrid_Selection">Hybrid_Selection</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
133 <option value="Reduced_Representation">Reduced_Representation</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
134 <option value="Restriction_Digest">Restriction_Digest</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
135 <option value="5-methylcytidine_antibody">5-methylcytidine_antibody</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
136 <option value="MBD2_protein_methyl-CpG_binding_domain">MBD2_protein_methyl-CpG_binding_domain</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
137 <option value="CAGE">CAGE</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
138 <option value="RACE">RACE</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
139 <option value="size_fractionation">size_fractionation</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
140 <option value="Padlock_probes_capture_method">Padlock_probes_capture_method</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
141 <option value="other">other</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
142 </param>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
143 <param name="datatype" type="select" label="datatype - specify datatype" help="This is a controlled vocabulary section in the XML file that will be generated">
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
144 <option value="METAGENOME" selected="true">METAGENOME</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
145 <option value="GENOME_SEQUENCING">GENOME_SEQUENCING</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
146 <option value="METAGENOMIC_ASSEMBLY">METAGENOMIC_ASSEMBLY</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
147 <option value="ASSEMBLY">ASSEMBLY</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
148 <option value="TRANSCRIPTOME">TRANSCRIPTOME</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
149 <option value="PROTEOMIC">PROTEOMIC</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
150 <option value="MAP">MAP</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
151 <option value="CLONE_ENDS">CLONE_ENDS</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
152 <option value="TARGETED_LOCI">TARGETED_LOCI</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
153 <option value="RANDOM_SURVEY">RANDOM_SURVEY</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
154 <option value="EXOME">EXOME</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
155 <option value="VARIATION">VARIATION</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
156 <option value="EPIGENOMICS">EPIGENOMICS</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
157 <option value="PHENOTYPE">PHENOTYPE</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
158 <option value="GENOTYPE">GENOTYPE</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
159 <option value="OTHER">OTHER</option>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
160 </param>
eb8c2262bd1b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
iuc
parents:
diff changeset
161 </inputs>
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162 <outputs>
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163 <expand macro="logfile-output"/>
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164 <data name="fasta_out" format="fasta" from_work_dir="sff*.fasta" label="${tool.name} on ${on_string}: fasta"/>
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165 <data name="qual_out" format="qual" from_work_dir="sff*.qual" label="${tool.name} on ${on_string}: qual"/>
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166 <data name="flow_out" format="mothur.sff.flow" from_work_dir="sff*.flow" label="${tool.name} on ${on_string}: flow"/>
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167 <data name="scrap_sff" format="sff" from_work_dir="sff*.scrap.sff" label="${tool.name} on ${on_string}: scrap sff"/>
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168 <data name="submission_xml" format="xml" from_work_dir="submission.xml" label="${tool.name} on ${on_string}: submission.xml"/>
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169 </outputs>
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170 <tests>
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171 <test><!-- test with defauts -->
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172 <param name="project" value="makesra.project" ftype="tabular"/>
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173 <param name="sff" value="Fasting_Example1.sff" ftype="sff"/>
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174 <param name="oligos" value="GQY1XT001.oligos" ftype="mothur.oligos"/>
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175 <param name="mimark" value="biosample.tsv" ftype="tabular"/>
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176 <output name="fasta_out" md5="212fa15e1ed077cecb65ee87f17ef2e1" ftype="fasta"/>
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177 <output name="qual_out" md5="ffcc4831369139055e1b8e9add9a59c0" ftype="qual"/>
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178 <output name="flow_out" md5="34b17477f98ab19c1ff755a61848d968" ftype="mothur.sff.flow"/>
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179 <output name="scrap_sff" ftype="sff">
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180 <assert_contents>
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181 <has_text text="FLP3FBN01ELBSX"/>
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182 </assert_contents>
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183 </output>
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184 <output name="submission_xml" ftype="xml">
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185 <assert_contents>
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186 <has_text text="Submission"/>
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187 <has_text text="Attribute"/>
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188 <has_text text="BioProject"/>
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189 </assert_contents>
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190 </output>
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191 <expand macro="logfile-test"/>
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192 </test>
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193 </tests>
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194 <help>
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195 <![CDATA[
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196
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197 @MOTHUR_OVERVIEW@
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198
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199 **Command Documentation**
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200
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201 The make.sra_ creates the necessary files for a NCBI submission.
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202
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203 .. _make.sra: https://www.mothur.org/wiki/Make.sra
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204
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205 ]]>
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206 </help>
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207 <citations>
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208 <citation type="doi">10.1128/AEM.01541-09</citation>
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209 </citations>
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210 </tool>