Mercurial > repos > iuc > mothur_shhh_flows

annotate shhh.flows.xml @ 2:aaeb8f2dcc7f draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2
author iuc
date Tue, 05 Sep 2017 16:01:05 -0400
parents a83120484b45
children f81c31175734
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11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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1 <tool profile="16.07" id="mothur_shhh_flows" name="Shhh.flows" version="@WRAPPER_VERSION@.0">
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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2 <description>Denoise flowgrams (PyroNoise algorithm)</description>
11ff85882cfb 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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4 <import>macros.xml</import>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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5 </macros>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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6 <expand macro="requirements"/>
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7 <expand macro="stdio"/>
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11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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8 <expand macro="version_command"/>
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9 <command><![CDATA[
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10 @SHELL_OPTIONS@
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11
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11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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12 ## create symlinks to input datasets
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13 ln -s '$flow' flow.dat &&
a83120484b45 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
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14 ln -s '$prob.lookup' lookup.dat &&
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11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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16 ## Mothur can't handle scientific notation (i.e. 1e-6)
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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17 #set mindelta_decimal = "{:.12f}".format(float($mindelta))
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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18 echo 'shhh.flows(
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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19 flow=flow.dat,
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20 lookup=lookup.dat,
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11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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21 maxiter=$maxiter,
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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22 mindelta=$mindelta_decimal,
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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23 cutoff=$cutoff,
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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24 sigma=$sigma,
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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25 order=$order,
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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26 large=$large,
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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27 processors='\${GALAXY_SLOTS:-8}'
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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28 )'
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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29 | sed 's/ //g' ## mothur trips over whitespace
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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30 | mothur
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31 | tee mothur.out.log
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11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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32 ]]></command>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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33 <inputs>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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34 <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"/>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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35 <conditional name="prob">
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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36 <param name="source" type="select" label="Select Taxonomy from" help="">
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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37 <option value="ref">Cached Reference</option>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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38 <option value="hist">History</option>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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39 </param>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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40 <when value="ref">
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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41 <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">
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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42 <options from_data_table="mothur_lookup"/>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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43 </param>
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44 </when>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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45 <when value="hist">
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46 <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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47 </when>
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48 </conditional>
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49 <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. "/>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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50 <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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51 <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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52 <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)"/>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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53 <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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54 <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"/>
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55 </inputs>
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56 <outputs>
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57 <expand macro="logfile-output"/>
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58 <data name="shhh_fasta" format="fasta" from_work_dir="flow*.fasta" label="${tool.name} on ${on_string}: shhh.fasta"/>
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59 <data name="shhh_qual" format="qual454" from_work_dir="flow*.qual" label="${tool.name} on ${on_string}: shhh.qual"/>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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60 <data name="shhh_names" format="mothur.names" from_work_dir="flow*.names" label="${tool.name} on ${on_string}: shhh.names"/>
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61 <data name="shhh_groups" format="mothur.groups" from_work_dir="flow*.groups" label="${tool.name} on ${on_string}: shhh.groups"/>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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62 <data name="shhh_counts" format="tabular" from_work_dir="flow*.counts" label="${tool.name} on ${on_string}: shhh.counts"/>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="flow" value="mock.flow" ftype="mothur.sff.flow"/>
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67 <param name="source" value="hist"/>
11ff85882cfb planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 180a403421967d36f995941b1a4561349d75cfc5
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68 <param name="lookup" value="LookUp_Titanium.pat"/>
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69 <output name="shhh_fasta" md5="9e7ba8213d039ba2360648c79f6380da" ftype="fasta"/>
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70 <output name="shhh_qual" md5="3ff0e8f575adc95ced285cc1704097ef" ftype="qual454"/>
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71 <output name="shhh_names" md5="71c8fd857b547f237e4215306762ab3d" ftype="mothur.names"/>
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72 <output name="shhh_groups" md5="75a5293a71beeafe9f330e6f497ae350" ftype="mothur.groups"/>
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73 <output name="shhh_counts" md5="2257f2079668a0f992a14e4576063cf0" ftype="tabular"/>
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74 <expand macro="logfile-test"/>
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75 </test>
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76 </tests>
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77 <help>
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78 <![CDATA[
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79
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80 @MOTHUR_OVERVIEW@
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81
1
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82 **Command Documentation**
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83
1
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84 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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85
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86 .. _shhh.flows: https://www.mothur.org/wiki/Shhh.flows
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88 ]]>
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89 </help>
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90 <expand macro="citations"/>
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91 </tool>