Mercurial > repos > iuc > mothur_shhh_flows

annotate shhh.flows.xml @ 10:af840f3c860e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
author iuc
date Mon, 17 Jun 2024 13:05:50 +0000
parents 7cca6773bc2a
children
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4f5213348132 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_shhh_flows" name="Shhh.flows" version="@WRAPPER_VERSION@.0">
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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2 <description>Denoise flowgrams (PyroNoise algorithm)</description>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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3 <macros>
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4 <import>macros.xml</import>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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5 </macros>
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af840f3c860e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab
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6 <expand macro="biotools"/>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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9 <expand macro="version_command"/>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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10 <command><![CDATA[
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11 @SHELL_OPTIONS@
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12
2
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13 ## create symlinks to input datasets
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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14 ln -s '$flow' flow.dat &&
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15 ln -s '$prob.lookup' lookup.dat &&
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4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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16
2
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17 ## Mothur can't handle scientific notation (i.e. 1e-6)
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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18 #set mindelta_decimal = "{:.12f}".format(float($mindelta))
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19 echo 'shhh.flows(
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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20 flow=flow.dat,
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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21 lookup=lookup.dat,
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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22 maxiter=$maxiter,
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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23 mindelta=$mindelta_decimal,
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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24 cutoff=$cutoff,
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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25 sigma=$sigma,
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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26 order=$order,
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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27 large=$large,
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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28 processors='\${GALAXY_SLOTS:-8}'
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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29 )'
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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30 | sed 's/ //g' ## mothur trips over whitespace
cb0fe730391d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
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31 | mothur
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32 | tee mothur.out.log
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4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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33 ]]></command>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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34 <inputs>
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35 <param name="flow" type="data" format="mothur.sff.flow" label="flow - flowgram data" help="Use sffinfo to generate flow data from an sff file and usually trimmed by trim.flows"/>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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36 <conditional name="prob">
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37 <param name="source" type="select" label="Select Taxonomy from" help="">
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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38 <option value="ref">Cached Reference</option>
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39 <option value="hist">History</option>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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40 </param>
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41 <when value="ref">
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42 <param name="lookup" type="select" format="tabular" label="lookup - intensity value per homopolymer length" help="table of the probability of observing an intensity value for a given homopolymer length">
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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43 <options from_data_table="mothur_lookup"/>
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44 </param>
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45 </when>
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46 <when value="hist">
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47 <param name="lookup" type="data" format="tabular" label="lookup - intensity value per homopolymer length" help="from https://www.mothur.org/wiki/Lookup_files"/>
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48 </when>
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49 </conditional>
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50 <param name="maxiter" type="integer" value="1000" min="10" label="maxiter - maximum iterations to run (default 1000)" help="if the delta value does not first drop below the mindelta value. "/>
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51 <param name="mindelta" type="float" value="0.000001" min="0.0" max="0.1" label="mindelta - threshold for determining how much change in the flowgram correction is allowed" help="default .000001 (10^-6)"/>
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52 <param name="cutoff" type="float" value="0.01" min="0.0" max="1.0" label="cutoff - seed the expectation-maximizaton step" help="default .01 (usually doesn't need to be changed)"/>
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53 <param name="sigma" type="float" value="0.06" min="0.0" max="1.0" label="sigma - the dispersion of the data in the expectation-maximization step of the algorithm" help="default .06 (usually doesn't need to be changed)"/>
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54 <param name="large" type="integer" value="10000" min="1" label="large - split your flow file and process the pieces separately (default 10000)" help=""/>
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55 <param name="order" type="text" value="A" label="order - flow order for nucleotides in the sequencer" help="default is A, was TACG. Also accepts B or I"/>
2
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56 <expand macro="param-savelog"/>
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57 </inputs>
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58 <outputs>
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59 <expand macro="logfile-output"/>
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60 <data name="shhh_fasta" format="fasta" from_work_dir="flow*.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
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61 <data name="shhh_qual" format="qual454" from_work_dir="flow*.qual" label="${tool.name} on ${on_string}: shhh.qual"/>
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62 <data name="shhh_names" format="mothur.names" from_work_dir="flow*.names" label="${tool.name} on ${on_string}: shhh.names"/>
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63 <data name="shhh_groups" format="mothur.groups" from_work_dir="flow*.groups" label="${tool.name} on ${on_string}: shhh.groups"/>
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64 <data name="shhh_counts" format="tabular" from_work_dir="flow*.counts" label="${tool.name} on ${on_string}: shhh.counts"/>
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="flow" value="mock.flow" ftype="mothur.sff.flow"/>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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69 <param name="source" value="hist"/>
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70 <param name="lookup" value="LookUp_Titanium.pat"/>
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71 <output name="shhh_fasta" md5="9e7ba8213d039ba2360648c79f6380da" ftype="fasta"/>
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72 <output name="shhh_qual" md5="3ff0e8f575adc95ced285cc1704097ef" ftype="qual454"/>
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73 <output name="shhh_names" md5="71c8fd857b547f237e4215306762ab3d" ftype="mothur.names"/>
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74 <output name="shhh_groups" md5="75a5293a71beeafe9f330e6f497ae350" ftype="mothur.groups"/>
4f5213348132 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
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75 <output name="shhh_counts" md5="2257f2079668a0f992a14e4576063cf0" ftype="tabular"/>
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76 <param name="savelog" value="true"/>
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77 <expand macro="logfile-test"/>
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78 </test>
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79 </tests>
2
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80 <help><![CDATA[
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81
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82 @MOTHUR_OVERVIEW@
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84 **Command Documentation**
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85
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86 The shhh.flows_ command is Pat Schloss's translation of Chris Quince's PyroNoise algorithm [1] from C to C++ with the incorporation of mothur's bells and whistles. Based on processing of test datasets provided by Quince, shhh.flows gives the same/similar output to AmpliconNoise. shhh.flows uses a expectation-maximization algorithm to correct flowgrams to identify the idealized form of each flowgram and translate that flowgram to a DNA sequence. Our testing has shown that when Titanium data are trimmed to 450 flows using trim.flows, shhh.flows provides the highest quality data for any other method available. In contrast, when we use the min/max number of flows suggested by Quince of 360/720, the error rate is not that great. This much improved error rate does come at a computational cost. Whereas the features in trim.seqs take on the order of minutes, shhh.flows can take on the order of hours. You will also need a lookup file that tells shhh.flows the probability of observing an intensity value for a given homopolymer length. You can get mothur-compatible files at: https://www.mothur.org/wiki/Lookup_files
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88 .. _shhh.flows: https://www.mothur.org/wiki/Shhh.flows
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89
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90 ]]></help>
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91 <expand macro="citations">
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92 <citation type="doi">10.1371/journal.pone.0027310</citation>
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93 <citation type="doi">10.1186/1471-2105-12-38</citation>
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94 <citation type="doi">10.1038/nmeth.1361</citation>
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95 </expand>
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96 </tool>