changeset 3:ca73bbac615a draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 8533fe71d1d50f09348da2dc34941724407a1ffe"
author iuc
date Tue, 14 Jul 2020 07:38:55 -0400
parents 23fc35093b11
children f732237754fc
files macros.xml static/images/pairpipe.png static/images/pairpipe.svg test-data/gentest.R test-data/learnErrors.pdf test-data/learnErrors_R1.pdf
diffstat 6 files changed, 206 insertions(+), 193 deletions(-) [+]
line wrap: on
line diff
--- a/macros.xml	Mon Mar 16 07:33:38 2020 -0400
+++ b/macros.xml	Tue Jul 14 07:38:55 2020 -0400
@@ -7,7 +7,7 @@
         </requirements>
     </xml>
 
-    <token name="@DADA2_VERSION@">1.14</token>
+    <token name="@DADA2_VERSION@">1.16</token>
     <token name="@WRAPPER_VERSION@">0</token>
 
     <xml name="version_command">
@@ -124,6 +124,9 @@
 
 .. image:: pairpipe.png
 
+Note: In particular for the analysis of paired collections the collections should be sorted lexicographical
+before the analysis.
+
 For single end data you the steps "Unzip collection" and "mergePairs" are not necessary.
 
 More information may be found on the dada2 homepage:: https://benjjneb.github.io/dada2/index.html (in particular tutorials) or the documentation of dada2's R package https://bioconductor.org/packages/release/bioc/html/dada2.html (in particular the pdf which contains the full documentation of all parameters)
Binary file static/images/pairpipe.png has changed
--- a/static/images/pairpipe.svg	Mon Mar 16 07:33:38 2020 -0400
+++ b/static/images/pairpipe.svg	Tue Jul 14 07:38:55 2020 -0400
@@ -24,7 +24,7 @@
         <dc:format>image/svg+xml</dc:format>
         <dc:type
            rdf:resource="http://purl.org/dc/dcmitype/StillImage" />
-        <dc:title></dc:title>
+        <dc:title />
       </cc:Work>
     </rdf:RDF>
   </metadata>
@@ -37,16 +37,16 @@
      guidetolerance="10"
      inkscape:pageopacity="0"
      inkscape:pageshadow="2"
-     inkscape:window-width="1920"
-     inkscape:window-height="1016"
+     inkscape:window-width="1680"
+     inkscape:window-height="986"
      id="namedview386"
      showgrid="false"
      inkscape:snap-global="true"
      inkscape:snap-bbox="false"
      inkscape:object-paths="true"
-     inkscape:zoom="1"
-     inkscape:cx="650.80177"
-     inkscape:cy="176.12189"
+     inkscape:zoom="2"
+     inkscape:cx="336.68624"
+     inkscape:cy="192.12189"
      inkscape:window-x="0"
      inkscape:window-y="27"
      inkscape:window-maximized="1"
@@ -443,22 +443,22 @@
     </marker>
   </defs>
   <path
-     style="stroke:#000000;marker-end:url(#id2)"
-     d="m 117.55976,114.5 h 42"
+     style="stroke:#000000;stroke-width:0.93333333;marker-end:url(#id2);stroke-miterlimit:4;stroke-dasharray:none"
+     d="m 117.55976,114.5 h 34.86"
      id="line138"
      inkscape:connector-curvature="0"
      sodipodi:nodetypes="cc" />
   <rect
      height="30.245491"
      width="116.46159"
-     x="165.14262"
-     y="0.37725419"
+     x="174.14262"
+     y="3.3772583"
      id="rect80"
      style="fill:#ebd9b2;stroke:#000000;stroke-width:0.75450838" />
   <text
      id="text188"
-     y="20.499996"
-     x="170.26537"
+     y="23.5"
+     x="179.26537"
      style="font-size:14px;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif">plotQualityProfile</text>
   <rect
      height="30.184877"
@@ -483,9 +483,9 @@
      inkscape:connector-curvature="0"
      id="path5591"
      d="m 971.55976,116.5 h 42.00004"
-     style="stroke:#000000;marker-end:url(#id2)" />
+     style="stroke:#000000;marker-end:url(#id2);stroke-width:0.93333333;stroke-miterlimit:4;stroke-dasharray:none" />
   <path
-     style="stroke:#000000;marker-end:url(#id2)"
+     style="stroke:#000000;marker-end:url(#id2);stroke-width:0.93333333;stroke-miterlimit:4;stroke-dasharray:none"
      d="m 1167.5598,116.5 h 42"
      id="path5593"
      inkscape:connector-curvature="0"
@@ -494,8 +494,8 @@
      sodipodi:nodetypes="cc"
      inkscape:connector-curvature="0"
      id="path5557"
-     d="m 255.55976,114.5 h 42"
-     style="stroke:#000000;marker-end:url(#id2)" />
+     d="m 283.77925,110.5 h 33.78051"
+     style="stroke:#000000;stroke-width:0.93333333;marker-end:url(#id2);stroke-miterlimit:4;stroke-dasharray:none" />
   <g
      id="g5364"
      transform="translate(-1226.0934,-496.75423)">
@@ -524,7 +524,7 @@
          sodipodi:role="line">and addSpecies</tspan></text>
   </g>
   <path
-     style="stroke:#000000;marker-end:url(#id2)"
+     style="stroke:#000000;marker-end:url(#id2);stroke-width:0.93333333;stroke-miterlimit:4;stroke-dasharray:none"
      d="m 545.55976,90.499996 h 42"
      id="path5573"
      inkscape:connector-curvature="0"
@@ -534,21 +534,21 @@
      inkscape:connector-curvature="0"
      id="path5575"
      d="m 545.55976,150.5 h 42"
-     style="stroke:#000000;marker-end:url(#id2)" />
+     style="stroke:#000000;marker-end:url(#id2);stroke-width:0.93333333;stroke-miterlimit:4;stroke-dasharray:none" />
   <path
      sodipodi:nodetypes="cc"
      inkscape:connector-curvature="0"
      id="path5597"
      d="m 645.55976,90.499996 555.87494,-54.3773"
-     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2)" />
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.93333333;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2);stroke-miterlimit:4;stroke-dasharray:none" />
   <path
-     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2)"
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.93333333;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2);stroke-miterlimit:4;stroke-dasharray:none"
      d="M 645.55976,150.5 1201.4347,46.233626"
      id="path5599"
      inkscape:connector-curvature="0"
      sodipodi:nodetypes="cc" />
   <path
-     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2)"
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.93333333;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2);stroke-miterlimit:4;stroke-dasharray:none"
      d="M 779.55976,116.5 1201.4347,40.196646"
      id="path5601"
      inkscape:connector-curvature="0"
@@ -576,9 +576,9 @@
      inkscape:connector-curvature="0"
      id="path5583"
      d="m 645.55976,90.499996 46,20.000004"
-     style="stroke:#000000;marker-end:url(#id2)" />
+     style="stroke:#000000;marker-end:url(#id2);stroke-width:0.93333333;stroke-miterlimit:4;stroke-dasharray:none" />
   <path
-     style="stroke:#000000;marker-end:url(#id2)"
+     style="stroke:#000000;marker-end:url(#id2);stroke-width:0.93333333;stroke-miterlimit:4;stroke-dasharray:none"
      d="M 645.55976,150.5 692.7316,122.10054"
      id="path5585"
      inkscape:connector-curvature="0"
@@ -588,7 +588,7 @@
      inkscape:connector-curvature="0"
      id="path5561"
      d="m 421.55976,124.5 37.062,24"
-     style="stroke:#000000;marker-end:url(#id2)" />
+     style="stroke:#000000;marker-end:url(#id2);stroke-width:0.93333333;stroke-miterlimit:4;stroke-dasharray:none" />
   <path
      sodipodi:nodetypes="cc"
      inkscape:connector-curvature="0"
@@ -602,14 +602,14 @@
      inkscape:connector-curvature="0"
      sodipodi:nodetypes="cc" />
   <path
-     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2)"
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.93333333;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2);stroke-miterlimit:4;stroke-dasharray:none"
      d="M 257.55976,114.5 C 274.37974,61.579996 445.40374,44.875026 606.50218,44.875906 739.16074,44.87663 971.24276,28.390716 1201.4347,30.159676"
      id="path5595"
      inkscape:connector-curvature="0"
      sodipodi:nodetypes="csc" />
   <g
      id="g5293"
-     transform="translate(-212.17332,-513.99998)">
+     transform="translate(-52.17332,-509.99998)">
     <rect
        style="fill:#ebd9b2;stroke:#000000;stroke-width:0.73455542"
        id="rect84"
@@ -624,48 +624,12 @@
        id="text194">filterAndTrim</text>
   </g>
   <circle
-     cx="257.11923"
-     cy="114"
+     cx="417.11923"
+     cy="110.5"
      r="5"
      id="circle5305"
      style="font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;fill:#ffffff;stroke:#000000" />
   <rect
-     height="30.07983"
-     width="111.46966"
-     x="304.38879"
-     y="101.46008"
-     id="rect88"
-     style="fill:#ebd9b2;stroke:#000000;stroke-width:0.92017078" />
-  <text
-     id="text202"
-     y="121.5"
-     x="309.42871"
-     style="font-size:14px;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif">Unzip Collection</text>
-  <circle
-     style="font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;fill:#ffffff;stroke:#000000"
-     id="circle320"
-     r="5"
-     cy="109.5"
-     cx="416.42871" />
-  <circle
-     style="font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;fill:#ffffff;stroke:#000000"
-     id="circle324"
-     r="5"
-     cy="109.5"
-     cx="416.42871" />
-  <circle
-     style="font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;fill:#ffffff;stroke:#000000"
-     id="circle328"
-     r="5"
-     cy="124.5"
-     cx="416.42871" />
-  <circle
-     style="font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;fill:#ffffff;stroke:#000000"
-     id="circle332"
-     r="5"
-     cy="124.5"
-     cx="416.42871" />
-  <rect
      height="30.25116"
      width="82.581673"
      x="463.61261"
@@ -756,7 +720,7 @@
      inkscape:connector-curvature="0"
      id="path5605"
      d="M 971.55976,116.5 1201.4347,52.270596"
-     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2)" />
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.93333333;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;marker-end:url(#id2);stroke-miterlimit:4;stroke-dasharray:none" />
   <g
      id="g5353"
      transform="translate(-994.97942,-607.3983)">
@@ -815,34 +779,34 @@
      sodipodi:nodetypes="cc"
      inkscape:connector-curvature="0"
      id="path5609"
-     d="M 117.55976,114.5 161.14262,20.499995"
-     style="stroke:#000000;marker-end:url(#id2)" />
+     d="M 121.78486,109.34886 167.41518,39.34955"
+     style="stroke:#000000;stroke-width:0.93333334;stroke-miterlimit:4;stroke-dasharray:none;marker-end:url(#id2)" />
   <rect
      style="fill:#ebd9b2;stroke:#000000;stroke-width:0.74489039"
      id="rect5370"
-     y="92.711388"
+     y="95.906334"
      x="0.3724452"
      width="117.18732"
      height="42.187313" />
   <text
      id="text5376"
-     y="107.53393"
+     y="111.53393"
      x="2.1782999"
      style="font-style:normal;font-weight:normal;font-size:20px;line-height:100%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
      xml:space="preserve"><tspan
        style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14.66666698px;line-height:0.99999998%;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;-inkscape-font-specification:'Helvetica, Arial, FreeSans, Sans, sans, sans-serif'"
-       y="107.53393"
+       y="111.53393"
        x="2.1782999"
        id="tspan5372"
        sodipodi:role="line">Paired input </tspan><tspan
        id="tspan5380"
        style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14.66666698px;line-height:0.99999998%;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;-inkscape-font-specification:'Helvetica, Arial, FreeSans, Sans, sans, sans-serif'"
-       y="127.53393"
+       y="131.53394"
        x="2.1782999"
        sodipodi:role="line">dataset collection</tspan><tspan
        style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14.66666698px;line-height:0.99999998%;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;-inkscape-font-specification:'Helvetica, Arial, FreeSans, Sans, sans, sans-serif'"
        id="tspan5374"
-       y="147.53392"
+       y="151.53394"
        x="2.1782999"
        sodipodi:role="line" /></text>
   <circle
@@ -866,15 +830,15 @@
      inkscape:connector-curvature="0"
      id="path1289"
      d="m 421.55976,110.5 37.062,-21.830514"
-     style="stroke:#000000;marker-end:url(#id2)" />
+     style="stroke:#000000;marker-end:url(#id2);stroke-width:0.93333333;stroke-miterlimit:4;stroke-dasharray:none" />
   <path
-     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.93333333;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none"
      d="m 421.55976,110.5 c 37.23584,-60.959159 95.4379,-71.01965 170,-20.000004"
      id="path1291"
      inkscape:connector-curvature="0"
      sodipodi:nodetypes="cc" />
   <path
-     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.93333333;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none"
      d="m 421.55976,124.5 c 26.21758,79.15744 93.37522,68.88106 170,26"
      id="path1293"
      inkscape:connector-curvature="0"
@@ -886,26 +850,78 @@
      inkscape:connector-curvature="0"
      sodipodi:nodetypes="cc" />
   <path
-     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+     style="fill:none;fill-rule:evenodd;stroke:#000000;stroke-width:0.93333333;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1;stroke-miterlimit:4;stroke-dasharray:none"
      d="m 421.55976,124.5 274.19828,-2.49999"
      id="path1297"
      inkscape:connector-curvature="0" />
   <rect
      style="fill:#ebd9b2;stroke:#000000;stroke-width:0.70499283"
      id="rect1299"
-     y="40.352497"
-     x="165.11786"
+     y="43.352493"
+     x="174.11786"
      width="101.51111"
      height="30.295006" />
   <text
      style="font-size:14px;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif"
-     x="170.26537"
-     y="60.499992"
+     x="179.26537"
+     y="63.5"
      id="text1301">plotComplexity</text>
   <path
-     style="stroke:#000000;marker-end:url(#id2)"
-     d="M 117.55976,114.5 161.14262,60.499995"
+     style="stroke:#000000;stroke-width:0.93333334;stroke-miterlimit:4;stroke-dasharray:none;marker-end:url(#id2)"
+     d="M 121.78486,109.34886 168.30515,76.42082"
      id="path1307"
      inkscape:connector-curvature="0"
      sodipodi:nodetypes="cc" />
+  <circle
+     style="font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;fill:#ffffff;stroke:#000000"
+     id="circle1296"
+     r="5"
+     cy="123.25001"
+     cx="417.11923" />
+  <rect
+     height="42.187313"
+     width="117.18732"
+     x="160.37244"
+     y="95.906334"
+     id="rect1298"
+     style="fill:#ebd9b2;stroke:#000000;stroke-width:0.74489039" />
+  <text
+     xml:space="preserve"
+     style="font-style:normal;font-weight:normal;font-size:20px;line-height:100%;font-family:sans-serif;letter-spacing:0px;word-spacing:0px;fill:#000000;fill-opacity:1;stroke:none;stroke-width:1px;stroke-linecap:butt;stroke-linejoin:miter;stroke-opacity:1"
+     x="162.1783"
+     y="111.53393"
+     id="text1306"><tspan
+       sodipodi:role="line"
+       id="tspan1300"
+       x="162.1783"
+       y="111.53393"
+       style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14.66666698px;line-height:0.99999998%;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;-inkscape-font-specification:'Helvetica, Arial, FreeSans, Sans, sans, sans-serif'">Unzip &amp; Sort</tspan><tspan
+       sodipodi:role="line"
+       x="162.1783"
+       y="131.53394"
+       style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14.66666698px;line-height:0.99999998%;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;-inkscape-font-specification:'Helvetica, Arial, FreeSans, Sans, sans, sans-serif'"
+       id="tspan1302">dataset collection</tspan><tspan
+       sodipodi:role="line"
+       x="162.1783"
+       y="151.53394"
+       id="tspan1304"
+       style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:14.66666698px;line-height:0.99999998%;font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;-inkscape-font-specification:'Helvetica, Arial, FreeSans, Sans, sans, sans-serif'" /></text>
+  <circle
+     style="font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;fill:#ffffff;stroke:#000000"
+     id="circle1310"
+     r="5"
+     cy="110.5"
+     cx="277.11923" />
+  <circle
+     cx="277.11923"
+     cy="123.25001"
+     r="5"
+     id="circle1312"
+     style="font-family:Helvetica, Arial, FreeSans, Sans, sans, sans-serif;fill:#ffffff;stroke:#000000" />
+  <path
+     style="stroke:#000000;stroke-width:0.93333333;marker-end:url(#id2);stroke-miterlimit:4;stroke-dasharray:none"
+     d="m 283.77925,122.5 h 33.78051"
+     id="path1314"
+     inkscape:connector-curvature="0"
+     sodipodi:nodetypes="cc" />
 </svg>
--- a/test-data/gentest.R	Mon Mar 16 07:33:38 2020 -0400
+++ b/test-data/gentest.R	Tue Jul 14 07:38:55 2020 -0400
@@ -1,192 +1,186 @@
-library(dada2, quietly=T)
-library(ggplot2, quietly=T)
+library(dada2, quietly = T)
+library(ggplot2, quietly = T)
 
-sample.names <- c('F3D0_S188_L001', 'F3D141_S207_L001')
-fwd <- c('F3D0_S188_L001_R1_001.fastq.gz', 'F3D141_S207_L001_R1_001.fastq.gz')
-rev <- c('F3D0_S188_L001_R2_001.fastq.gz', 'F3D141_S207_L001_R2_001.fastq.gz')
+sample_names <- c("F3D0_S188_L001", "F3D141_S207_L001")
+fwd <- c("F3D0_S188_L001_R1_001.fastq.gz", "F3D141_S207_L001_R1_001.fastq.gz")
+rev <- c("F3D0_S188_L001_R2_001.fastq.gz", "F3D141_S207_L001_R2_001.fastq.gz")
 
-filt.fwd <- c('filterAndTrim_F3D0_R1.fq.gz', 'filterAndTrim_F3D141_R1.fq.gz')
-filt.rev <- c('filterAndTrim_F3D0_R2.fq.gz', 'filterAndTrim_F3D141_R2.fq.gz')
+filt_fwd <- c("filterAndTrim_F3D0_R1.fq.gz", "filterAndTrim_F3D141_R1.fq.gz")
+filt_rev <- c("filterAndTrim_F3D0_R2.fq.gz", "filterAndTrim_F3D141_R2.fq.gz")
 
 print("filterAndTrim")
 
-for(i in 1:length(fwd)){
-	ftout <- filterAndTrim(fwd[i], filt.fwd[i], rev[i], filt.rev[i])
-    b <- paste(strsplit(fwd[i], ".", fixed=T)[[1]][1], "tab", sep=".")
-    write.table(ftout, b, quote=F, sep="\t", col.names=NA)
+for (i in seq_len(fwd)) {
+    ftout <- dada2::filterAndTrim(fwd[i], filt_fwd[i], rev[i], filt_rev[i])
+    b <- paste(strsplit(fwd[i], ".", fixed = T)[[1]][1], "tab", sep = ".")
+    write.table(ftout, b, quote = F, sep = "\t", col.names = NA)
 }
 
 # In the test only the 1st data set is used
 t <- data.frame()
-t <- rbind(t, ftout[1,])
+t <- rbind(t, ftout[1, ])
 colnames(t) <- colnames(ftout)
 rownames(t) <- rownames(ftout)[1]
-write.table(t, "filterAndTrim.tab", quote=F, sep="\t", col.names=NA)
+write.table(t, "filterAndTrim.tab", quote = F, sep = "\t", col.names = NA)
 
-names(fwd) <- sample.names
-names(rev) <- sample.names
-names(filt.fwd) <- sample.names
-names(filt.rev) <- sample.names
+names(fwd) <- sample_names
+names(rev) <- sample_names
+names(filt_fwd) <- sample_names
+names(filt_rev) <- sample_names
 
 # Plot quality profile (just for one file, Galaxy compares with sim_size)
 print("plots")
-qp <- plotQualityProfile(fwd)
-ggsave('qualityProfile_fwd.pdf', qp, width = 20,height = 15,units = c("cm"))
-qp <- plotQualityProfile(rev)
-ggsave('qualityProfile_rev.pdf', qp, width = 20,height = 15,units = c("cm"))
-qp <- plotQualityProfile(fwd[1])
-ggsave('qualityProfile.pdf', qp, width = 20,height = 15,units = c("cm"))
+qp <- dada2::plotQualityProfile(fwd)
+ggsave("qualityProfile_fwd.pdf", qp, width = 20, height = 15, units = c("cm"))
+qp <- dada2::plotQualityProfile(rev)
+ggsave("qualityProfile_rev.pdf", qp, width = 20, height = 15, units = c("cm"))
+qp <- dada2::plotQualityProfile(fwd[1])
+ggsave("qualityProfile.pdf", qp, width = 20, height = 15, units = c("cm"))
 
 # Plot complexity (just for one file, Galaxy compares with sim_size)
 
-cp <- plotComplexity(fwd)
-ggsave('complexity_fwd.pdf', cp, width = 20,height = 15,units = c("cm"))
-cp <- plotComplexity(rev)
-ggsave('complexity_rev.pdf', cp, width = 20,height = 15,units = c("cm"))
-cp <- plotComplexity(fwd[1])
-ggsave('complexity.pdf', cp, width = 20,height = 15,units = c("cm"))
+cp <- dada2::plotComplexity(fwd)
+ggsave("complexity_fwd.pdf", cp, width = 20, height = 15, units = c("cm"))
+cp <- dada2::plotComplexity(rev)
+ggsave("complexity_rev.pdf", cp, width = 20, height = 15, units = c("cm"))
+cp <- dada2::plotComplexity(fwd[1])
+ggsave("complexity.pdf", cp, width = 20, height = 15, units = c("cm"))
 
 
 # learn Errors
 print("learnErrors")
-err.fwd <- learnErrors(filt.fwd) 
-saveRDS(err.fwd, file='learnErrors_R1.Rdata')
-plot <- plotErrors(err.fwd)
-ggsave('learnErrors_R1.pdf', plot, width = 20,height = 15,units = c("cm"))
+err_fwd <- dada2::learnErrors(filt_fwd)
+saveRDS(err_fwd, file = "learnErrors_R1.Rdata")
+plot <- dada2::plotErrors(err_fwd)
+ggsave("learnErrors_R1.pdf", plot, width = 20, height = 15, units = c("cm"))
 
-err.rev <- learnErrors(filt.rev) 
-saveRDS(err.rev, file='learnErrors_R2.Rdata')
-plot <- plotErrors(err.rev)
-ggsave('learnErrors.pdf', plot, width = 20,height = 15,units = c("cm"))
+err_rev <- dada2::learnErrors(filt_rev)
+saveRDS(err_rev, file = "learnErrors_R2.Rdata")
+plot <- dada2::plotErrors(err_rev)
+ggsave("learnErrors.pdf", plot, width = 20, height = 15, units = c("cm"))
 
 # dada
 print("dada")
-dada.fwd <- dada(filt.fwd, err.fwd)
-dada.rev <- dada(filt.rev, err.rev)
-for( id in sample.names ){
-	saveRDS(dada.fwd[[id]], file=paste("dada_", id,"_R1.Rdata", sep=""))
-	saveRDS(dada.rev[[id]], file=paste("dada_", id,"_R2.Rdata", sep=""))
+dada_fwd <- dada2::dada(filt_fwd, err_fwd)
+dada_rev <- dada2::dada(filt_rev, err_rev)
+for (id in sample_names) {
+    saveRDS(dada_fwd[[id]], file = paste("dada_", id, "_R1.Rdata", sep = ""))
+    saveRDS(dada_rev[[id]], file = paste("dada_", id, "_R2.Rdata", sep = ""))
 }
 
 # merge pairs
 print("mergePairs")
-merged <- mergePairs(dada.fwd, filt.fwd, dada.rev, filt.rev)
-for( id in sample.names ){
-	saveRDS(merged[[id]], file=paste("mergePairs_", id,".Rdata", sep=""))
+merged <- dada2::mergePairs(dada_fwd, filt_fwd, dada_rev, filt_rev)
+for (id in sample_names) {
+    saveRDS(merged[[id]], file = paste("mergePairs_", id, ".Rdata", sep = ""))
 }
 
 
 # make sequence table
 print("makeSequenceTable")
 seqtab <- makeSequenceTable(merged)
-write.table(t(seqtab), file="makeSequenceTable.tab", quote=F, sep="\t", row.names = T, col.names = NA)
+write.table(t(seqtab), file = "makeSequenceTable.tab", quote = F, sep = "\t", row.names = T, col.names = NA)
 
-reads.per.seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
-df <- data.frame(length=as.numeric(names(reads.per.seqlen)), count=reads.per.seqlen)
-pdf( 'makeSequenceTable.pdf' )
-ggplot(data=df, aes(x=length, y=count)) +
+reads_per_seqlen <- tapply(colSums(seqtab), factor(nchar(getSequences(seqtab))), sum)
+df <- data.frame(length = as.numeric(names(reads_per_seqlen)), count = reads_per_seqlen)
+pdf("makeSequenceTable.pdf")
+ggplot(data = df, aes(x = length, y = count)) +
     geom_col() +
     theme_bw()
 bequiet <- dev.off()
 
 # remove bimera
 print("removeBimera")
-seqtab.nochim <- removeBimeraDenovo(seqtab)
-write.table(t(seqtab), file="removeBimeraDenovo.tab", quote=F, sep="\t", row.names = T, col.names = NA)
+seqtab_nochim <- dada2::removeBimeraDenovo(seqtab)
+write.table(t(seqtab), file = "removeBimeraDenovo.tab", quote = F, sep = "\t", row.names = T, col.names = NA)
 
 # assign taxonomy/species
-tl <- 'Level1,Level2,Level3,Level4,Level5'
+tl <- "Level1,Level2,Level3,Level4,Level5"
 tl <- strsplit(tl, ",")[[1]]
 
 set.seed(42)
 print("assignTaxonomyAndSpecies")
-taxa <- assignTaxonomy(seqtab.nochim, 'reference.fa.gz', outputBootstraps = T, taxLevels=tl, multithread = 1)
+taxa <- dada2::assignTaxonomy(seqtab_nochim, "reference.fa.gz", outputBootstraps = T, taxLevels = tl, multithread = 1)
 
-taxa$tax <- addSpecies(taxa$tax, 'reference_species.fa.gz')
-write.table(taxa$tax, file = 'assignTaxonomyAddspecies.tab', quote = F, sep = "\t", row.names = T, col.names = NA)
+taxa$tax <- dada2::addSpecies(taxa$tax, "reference_species.fa.gz")
+write.table(taxa$tax, file = "assignTaxonomyAddspecies.tab", quote = F, sep = "\t", row.names = T, col.names = NA)
 
-write.table(taxa$boot, file = 'assignTaxonomyAddspecies_boot.tab', quote = F, sep = "\t", row.names = T, col.names = NA)
+write.table(taxa$boot, file = "assignTaxonomyAddspecies_boot.tab", quote = F, sep = "\t", row.names = T, col.names = NA)
 
 
-## Generate extra test data for parameter testing 
+## Generate extra test data for parameter testing
 print("alternatives")
-filterAndTrim(fwd, c('filterAndTrim_single_F3D0_R1.fq.gz', 'filterAndTrim_single_F3D141_R1.fq.gz'), rm.phix = T, orient.fwd = 'TACGG')
+dada2::filterAndTrim(fwd, c("filterAndTrim_single_F3D0_R1.fq.gz", "filterAndTrim_single_F3D141_R1.fq.gz"), rm.phix = T, orient.fwd = "TACGG")
 
-filterAndTrim(fwd, c('filterAndTrim_single_trimmers_F3D0_R1.fq.gz', 'filterAndTrim_single_trimmers_F3D141_R1.fq.gz'), truncQ = 30, truncLen = 2, trimLeft = 150, trimRight = 2)
+dada2::filterAndTrim(fwd, c("filterAndTrim_single_trimmers_F3D0_R1.fq.gz", "filterAndTrim_single_trimmers_F3D141_R1.fq.gz"), truncQ = 30, truncLen = 2, trimLeft = 150, trimRight = 2)
 
-filterAndTrim(fwd, c('filterAndTrim_single_filters_F3D0_R1.fq.gz', 'filterAndTrim_single_filters_F3D141_R1.fq.gz'), maxLen = 255, minLen = 60, maxN = 100, minQ = 13, maxEE = 1)
+dada2::filterAndTrim(fwd, c("filterAndTrim_single_filters_F3D0_R1.fq.gz", "filterAndTrim_single_filters_F3D141_R1.fq.gz"), maxLen = 255, minLen = 60, maxN = 100, minQ = 13, maxEE = 1)
 
 
-merged_nondef <- mergePairs(dada.fwd, filt.fwd, dada.rev, filt.rev, minOverlap = 8, maxMismatch = 1, justConcatenate = TRUE, trimOverhang = TRUE)
-for( id in sample.names ){
-	saveRDS(merged_nondef[[id]], file=paste("mergePairs_", id,"_nondefault.Rdata", sep=""))
+merged_nondef <- dada2::mergePairs(dada_fwd, filt_fwd, dada_rev, filt_rev, minOverlap = 8, maxMismatch = 1, justConcatenate = TRUE, trimOverhang = TRUE)
+for (id in sample_names) {
+    saveRDS(merged_nondef[[id]], file = paste("mergePairs_", id, "_nondefault.Rdata", sep = ""))
 }
-rb.dada.fwd <- removeBimeraDenovo(dada.fwd[["F3D0_S188_L001"]])
-write.table(rb.dada.fwd, file = 'removeBimeraDenovo_F3D0_dada_uniques.tab', quote = F, sep = "\t", row.names = T, col.names = F)
+rb_dada_fwd <- dada2::removeBimeraDenovo(dada_fwd[["F3D0_S188_L001"]])
+write.table(rb_dada_fwd, file = "removeBimeraDenovo_F3D0_dada_uniques.tab", quote = F, sep = "\t", row.names = T, col.names = F)
 
-rb.merged <- removeBimeraDenovo(merged, method="pooled")
-saveRDS(rb.merged, file='removeBimeraDenovo_F3D0_mergepairs.Rdata')
- 
+rb_merged <- dada2::removeBimeraDenovo(merged, method = "pooled")
+saveRDS(rb_merged, file = "removeBimeraDenovo_F3D0_mergepairs.Rdata")
+
 # SeqCounts
-getN <- function(x){ sum(getUniques(x)) }
-
-read.uniques <- function ( fname ) {
-    p <- read.table(fname, header=F, sep="\t")
-    n <-x[,2]
-    names(n)<-x[,1]
+get_n <- function(x) {
+    sum(dada2::getUniques(x))
 }
 
-
 print("seqCounts ft")
-samples = list()
-samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header=T, sep="\t", row.names=1)
+samples <- list()
+samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header = T, sep = "\t", row.names = 1)
 dname <- "filter"
 tdf <- samples[["F3D0_S188_L001_R1_001.tab"]]
-names(tdf) <- paste( dname, names(tdf) )
-tdf <- cbind( data.frame(samples=names( samples )), tdf)
-write.table(tdf, "seqCounts_filter.tab", quote=F, sep="\t", row.names = F, col.names = T)
+names(tdf) <- paste(dname, names(tdf))
+tdf <- cbind(data.frame(samples = names(samples)), tdf)
+write.table(tdf, "seqCounts_filter.tab", quote = F, sep = "\t", row.names = F, col.names = T)
 
-samples = list()
-samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header=T, sep="\t", row.names=1)
-samples[["F3D141_S207_L001_R1_001.tab"]] <- read.table("F3D141_S207_L001_R1_001.tab", header=T, sep="\t", row.names=1)
+samples <- list()
+samples[["F3D0_S188_L001_R1_001.tab"]] <- read.table("F3D0_S188_L001_R1_001.tab", header = T, sep = "\t", row.names = 1)
+samples[["F3D141_S207_L001_R1_001.tab"]] <- read.table("F3D141_S207_L001_R1_001.tab", header = T, sep = "\t", row.names = 1)
 dname <- "filter"
 tdf <- samples[["F3D0_S188_L001_R1_001.tab"]]
 tdf <- rbind(tdf, samples[["F3D141_S207_L001_R1_001.tab"]])
-names(tdf) <- paste( dname, names(tdf) )
-tdf <- cbind( data.frame(samples=names( samples )), tdf)
-write.table(tdf, "seqCounts_filter_both.tab", quote=F, sep="\t", row.names = F, col.names = T)
+names(tdf) <- paste(dname, names(tdf))
+tdf <- cbind(data.frame(samples = names(samples)), tdf)
+write.table(tdf, "seqCounts_filter_both.tab", quote = F, sep = "\t", row.names = F, col.names = T)
 
 print("seqCounts dada")
-samples = list()
-samples[["dada_F3D0_S188_L001_R1.Rdata"]] <- readRDS('dada_F3D0_S188_L001_R1.Rdata')
-samples[["dada_F3D141_S207_L001_R1.Rdata"]] <- readRDS('dada_F3D141_S207_L001_R1.Rdata')
+samples <- list()
+samples[["dada_F3D0_S188_L001_R1.Rdata"]] <- readRDS("dada_F3D0_S188_L001_R1.Rdata")
+samples[["dada_F3D141_S207_L001_R1.Rdata"]] <- readRDS("dada_F3D141_S207_L001_R1.Rdata")
 dname <- "dadaF"
-tdf <- data.frame( samples = names(samples) )
-tdf[[ dname ]] <- sapply(samples, getN)
-write.table(tdf, "seqCounts_dadaF.tab", quote=F, sep="\t", row.names = F, col.names = T)
+tdf <- data.frame(samples = names(samples))
+tdf[[dname]] <- sapply(samples, get_n)
+write.table(tdf, "seqCounts_dadaF.tab", quote = F, sep = "\t", row.names = F, col.names = T)
 
 print("seqCounts mp")
-samples = list()
-samples[["mergePairs_F3D0_S188_L001.Rdata"]] <- readRDS('mergePairs_F3D0_S188_L001.Rdata')
-samples[["mergePairs_F3D141_S207_L001.Rdata"]] <- readRDS('mergePairs_F3D141_S207_L001.Rdata')
+samples <- list()
+samples[["mergePairs_F3D0_S188_L001.Rdata"]] <- readRDS("mergePairs_F3D0_S188_L001.Rdata")
+samples[["mergePairs_F3D141_S207_L001.Rdata"]] <- readRDS("mergePairs_F3D141_S207_L001.Rdata")
 dname <- "merge"
-tdf <- data.frame( samples = names(samples) )
-tdf[[ dname ]] <- sapply(samples, getN)
-write.table(tdf, "seqCounts_merge.tab", quote=F, sep="\t", row.names = F, col.names = T)
+tdf <- data.frame(samples = names(samples))
+tdf[[dname]] <- sapply(samples, get_n)
+write.table(tdf, "seqCounts_merge.tab", quote = F, sep = "\t", row.names = F, col.names = T)
 
 print("seqCounts st")
-samples = list()
-samples <- t(as.matrix( read.table("makeSequenceTable.tab", header=T, sep="\t", row.names=1) ))
+samples <- list()
+samples <- t(as.matrix(read.table("makeSequenceTable.tab", header = T, sep = "\t", row.names = 1)))
 dname <- "seqtab"
-tdf <- data.frame( samples = row.names(samples) )
-tdf[[ dname ]] <- rowSums(samples)
-write.table(tdf, "seqCounts_seqtab.tab", quote=F, sep="\t", row.names = F, col.names = T)
+tdf <- data.frame(samples = row.names(samples))
+tdf[[dname]] <- rowSums(samples)
+write.table(tdf, "seqCounts_seqtab.tab", quote = F, sep = "\t", row.names = F, col.names = T)
 
 print("seqCounts rb")
-samples = list()
-samples <- t(as.matrix( read.table("removeBimeraDenovo.tab", header=T, sep="\t", row.names=1) ))
+samples <- list()
+samples <- t(as.matrix(read.table("removeBimeraDenovo.tab", header = T, sep = "\t", row.names = 1)))
 dname <- "nochim"
-tdf <- data.frame( samples = row.names(samples) )
-tdf[[ dname ]] <- rowSums(samples)
-write.table(tdf, "seqCounts_nochim.tab", quote=F, sep="\t", row.names = F, col.names = T)
-
+tdf <- data.frame(samples = row.names(samples))
+tdf[[dname]] <- rowSums(samples)
+write.table(tdf, "seqCounts_nochim.tab", quote = F, sep = "\t", row.names = F, col.names = T)
Binary file test-data/learnErrors.pdf has changed
Binary file test-data/learnErrors_R1.pdf has changed