Mercurial > repos > matthias > dada2_plotqualityprofile
annotate dada2_plotQualityProfile.xml @ 3:cf166b8a8e27 draft
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
| author | matthias |
|---|---|
| date | Mon, 29 Apr 2019 08:57:18 -0400 |
| parents | 4095456821e2 |
| children | 863ebf0d28d5 |
| rev | line source |
|---|---|
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4095456821e2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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1 <tool id="dada2_plotQualityProfile" name="dada2: plotQualityProfile" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@"> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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2 <description>plot a visual summary of the quality scores</description> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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3 <macros> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
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4 <import>macros.xml</import> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
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5 </macros> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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6 <expand macro="requirements"/> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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7 <expand macro="version_command"/> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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8 <command detect_errors="exit_code"><![CDATA[ |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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9 Rscript --slave '$dada2_script' |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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10 ]]></command> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
parents:
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11 <configfiles> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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12 <configfile name="dada2_script"><![CDATA[ |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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13 files = c() |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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14 #if "batch" in str($paired_cond.paired_select) |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents:
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15 #if "single" in str($paired_cond.paired_select) |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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16 files = c(files, '$paired_cond.reads') |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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17 #else |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents:
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18 files = c(files, '$paired_cond.reads.forward') |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents:
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19 files = c(files, '$paired_cond.reads.reverse') |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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20 #end if |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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21 #else |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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22 #for $read in $paired_cond.reads: |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents:
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diff
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23 #if "single" in str($paired_cond.paired_select) |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
parents:
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24 files = c(files, '$read') |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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25 #else |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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26 files = c(files, '$read.forward') |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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27 files = c(files, '$read.reverse') |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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28 #end if |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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29 #end for |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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30 #end if |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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31 |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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32 library(ggplot2, quietly=T) |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
matthias
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33 library(dada2, quietly=T) |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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34 |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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35 qp <- plotQualityProfile(files, |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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36 #if str($n) != "" |
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4095456821e2
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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37 n=$n, |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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38 #end if |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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39 aggregate = $aggregate) |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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40 |
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de5c51e1c190
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 ggsave('output.pdf', qp, width = 20,height = 15,units = c("cm")) |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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42 ]]></configfile> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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43 </configfiles> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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44 <inputs> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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45 <conditional name="paired_cond"> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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46 <param name="paired_select" type="select" label="Input data organisation and processing mode" help="Select if data is organized in a paired collection or not (note that the pairing of the data sets is not used by the tool); batch will create a separate pdf for each input data set or data set pair; non-batch will create one pdf containing a plot for each data set"> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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47 <option value="paired">paired - non batch</option> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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48 <option value="single">single - non batch</option> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
matthias
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49 <option value="paired_batch">paired - batch</option> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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50 <option value="single_batch">single - batch</option> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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51 </param> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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52 <when value="paired"> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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53 <param name="reads" type="data_collection" collection_type="list:paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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54 </when> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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55 <when value="single"> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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56 <param name="reads" type="data" multiple="true" format="fastqsanger,fastqsanger.gz" label="Short read data"/> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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57 </when> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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58 <when value="paired_batch"> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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59 <param name="reads" type="data_collection" collection_type="paired" format="fastqsanger,fastqsanger.gz" label="Short read data"/> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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60 </when> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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61 <when value="single_batch"> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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62 <param name="reads" type="data" format="fastqsanger,fastqsanger.gz" label="Short read data"/> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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63 </when> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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64 </conditional> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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65 <param argument="aggregate" type="boolean" label="Aggregate data" checked="True" truevalue="TRUE" falsevalue="FALSE" help="Create a single plot for all data sets (default) or a separate plot for each data set"/> |
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cf166b8a8e27
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit 5b1603bbcd3f139cad5c876be83fcb39697b5613-dirty
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66 <param argument="n" type="integer" value="500000" label="sample number" help="number of records to sample from the fastq file"/> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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67 </inputs> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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68 <outputs> |
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de5c51e1c190
planemo upload for repository https://github.com/bernt-matthias/mb-galaxy-tools/tree/topic/dada2/tools/dada2 commit d63c84012410608b3b5d23e130f0beff475ce1f8-dirty
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69 <data name="output" format="pdf" from_work_dir="output.pdf"/> |
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70 </outputs> |
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71 <tests> |
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72 <!-- paired non-batch, aggregate --> |
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73 <test> |
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74 <param name="aggregate" value="TRUE"/> |
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75 <param name="paired_cond|paired_select" value="paired"/> |
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76 <param name="paired_cond|reads"> |
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77 <collection type="list:paired"> |
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78 <element name="F3D0_S188_L001"> |
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79 <collection type="paired"> |
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80 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
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81 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
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82 </collection> |
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83 </element> |
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84 </collection> |
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85 </param> |
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86 <output name="output" value="qualityProfileMultiple.pdf" ftype="pdf"/> |
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87 </test> |
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88 <!-- paired, batch, no aggregate--> |
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89 <test> |
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90 <param name="aggregate" value="FALSE"/> |
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91 <param name="paired_cond|paired_select" value="paired_batch"/> |
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92 <param name="paired_cond|reads"> |
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93 <collection type="paired"> |
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94 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
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95 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
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96 </collection> |
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97 </param> |
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98 <output name="output" value="qualityProfile.pdf" ftype="pdf"/> |
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99 </test> |
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100 <!-- single, non-batch, aggregate --> |
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101 <test> |
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102 <param name="aggregate" value="TRUE"/> |
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103 <param name="paired_cond|paired_select" value="single"/> |
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104 <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz,F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
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105 <param name="n" value="10000"/> |
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106 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf"/> |
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107 </test> |
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108 <!-- single, batch, no aggregate --> |
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109 <test> |
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110 <param name="aggregate" value="FALSE"/> |
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111 <param name="paired_cond|paired_select" value="single_batch"/> |
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112 <param name="paired_cond|reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
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113 <param name="n" value="10000"/> |
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114 <output name="output" value="qualityProfileSmallSample.pdf" ftype="pdf" compare="sim_size"/> |
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115 </test> </tests> |
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116 <help><![CDATA[ |
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117 Summary |
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118 ....... |
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119 |
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120 This function plots a visual summary of the distribution of quality scores as a function of sequence position for the input fastq datasets. |
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121 |
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122 Details |
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123 ....... |
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124 |
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125 The distribution of quality scores at each position is shown as a grey-scale heat map, with dark colors corresponding to higher frequency. The plotted lines show positional summary statistics: green is the mean, orange is the median, and the dashed orange lines are the 25th and 75th quantiles. If the sequences vary in length, a red line will be plotted showing the percentage of reads that extend |
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126 to at least that position. |
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127 |
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128 Note this tool ignores the pairing of the reads, but the data is just processed as list. |
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129 ]]></help> |
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130 <expand macro="citations"/> |
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131 </tool> |