Mercurial > repos > matthias > dada2_mergepairs
annotate dada2_mergePairs.xml @ 12:7f01a44f6321 draft default tip
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit df2dfeb75f88b326f567cab8df4e6c4a7f2e548c
author | matthias |
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date | Tue, 15 Oct 2019 07:27:58 -0400 |
parents | 9fae5010b6bf |
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9fae5010b6bf
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit b59ed2476188176bb5b2973f59899b7d733e7641-dirty
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1 <tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09"> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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2 <description>Merge denoised forward and reverse reads</description> |
44230c777694
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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3 <macros> |
44230c777694
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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4 <import>macros.xml</import> |
44230c777694
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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5 </macros> |
44230c777694
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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6 <expand macro="requirements"/> |
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9fae5010b6bf
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit b59ed2476188176bb5b2973f59899b7d733e7641-dirty
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7 <expand macro="stdio"/> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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8 <expand macro="version_command"/> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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9 <command detect_errors="exit_code"><![CDATA[ |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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10 Rscript '$dada2_script' |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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11 ]]></command> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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12 <configfiles> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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13 <configfile name="dada2_script"><![CDATA[ |
44230c777694
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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14 library(dada2, quietly=T) |
44230c777694
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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15 |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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16 dadaF <- readRDS('$dadaF') |
e76f2213f0cc
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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17 dadaR <- readRDS('$dadaR') |
e76f2213f0cc
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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18 derepF <- readRDS('$derepF') |
e76f2213f0cc
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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19 derepR <- readRDS('$derepR') |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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20 |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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21 merged <- mergePairs(dadaF, derepF, dadaR, derepR, minOverlap = $minOverlap, maxMismatch = $maxMismatch, |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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22 ## currently not accessible by the wrapper returnRejects = FALSE, propagateCol = character(0), |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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23 justConcatenate = $justConcatenate, trimOverhang = $trimOverhang) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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24 |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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25 saveRDS(merged, file='$merged') |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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26 ##For display in Galaxy this could be transposed (..but the user could also do it herself) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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27 ##write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T) |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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28 ]]></configfile> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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29 </configfiles> |
44230c777694
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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30 <inputs> |
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31 <param argument="dadaF" type="data" format="dada2_dada" label="Dada results for forward reads"/> |
e76f2213f0cc
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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32 <param argument="derepF" type="data" format="dada2_derep" label="Dereplicated forward reads"/> |
e76f2213f0cc
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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33 <param argument="dadaR" type="data" format="dada2_dada" label="Dada results for reverse reads"/> |
e76f2213f0cc
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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34 <param argument="derepR" type="data" format="dada2_derep" label="Dereplicated reverse reads"/> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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35 <param argument="minOverlap" type="integer" value="12" min="0" label="Minimum length of the overlap"/> |
caae353b2928
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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36 <param argument="maxMismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/> |
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37 <param argument="justConcatenate" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Concatenated rather than merge" help="The forward and reverse-complemented reverse read are concatenated rather than merged, with a 10 Ns spacer inserted between them"/> |
e76f2213f0cc
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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38 <param argument="trimOverhang" type="boolean" checked="false" truevalue="TRUE" falsevalue="FALSE" label="Trim overhangs" help="Overhangs are when the reverse read extends past the start of the forward read, and vice-versa, as can happen when reads are longer than the amplicon and read into the other-direction primer region"/> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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39 </inputs> |
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40 <outputs> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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41 <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/> |
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42 </outputs> |
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43 <tests> |
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44 <test> |
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45 <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_R1.Rdata"/> |
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46 <param name="derepF" ftype="dada2_derep" value="derepFastq_F3D0_R1.Rdata"/> |
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47 <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_R2.Rdata"/> |
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planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 990192685955e9cda0282e348c28ef6462d88a38
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48 <param name="derepR" ftype="dada2_derep" value="derepFastq_F3D0_R2.Rdata"/> |
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49 <output name="merged" value="mergePairs_F3D0.Rdata" ftype="dada2_mergepairs" /> |
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50 </test> |
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51 <!-- test non-default options --> |
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52 <test> |
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53 <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_R1.Rdata"/> |
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54 <param name="derepF" ftype="dada2_derep" value="derepFastq_F3D0_R1.Rdata"/> |
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55 <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_R2.Rdata"/> |
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56 <param name="derepR" ftype="dada2_derep" value="derepFastq_F3D0_R2.Rdata"/> |
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57 <output name="merged" value="mergePairs_F3D0_nondefault.Rdata" ftype="dada2_mergepairs" /> |
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58 <param name="minOverlap" value="8" /> |
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59 <param name="maxMismatch" value="1"/> |
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60 <param name="justConcatenate" value="TRUE" /> |
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61 <param name="trimOverhang" value="TRUE" /> |
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62 </test> |
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63 </tests> |
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64 <help><![CDATA[ |
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65 Description |
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66 ........... |
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67 |
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68 This function attempts to merge each denoised pair of forward and reverse reads, rejecting any pairs which do not sufficiently overlap (at least 12bp by default) or which contain too many (>0 by default) mismatches in the overlap region. |
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69 |
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70 Usage |
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71 ..... |
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72 |
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73 **Input** |
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74 |
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75 - dereplicated reads and learned error rates of the forward reads |
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76 - dereplicated reads and learned error rates of the reverse reads |
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77 |
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78 **Output** |
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79 |
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80 - a data set of type dada2_mergepairs (which is a RData file containing the output of dada2's mergePairs function). |
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81 |
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82 Details |
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83 ....... |
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84 |
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85 @HELP_OVERVIEW@ |
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86 |
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87 |
0
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88 ]]></help> |
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89 <expand macro="citations"/> |
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90 </tool> |