Mercurial > repos > iuc > dada2_mergepairs
annotate dada2_mergePairs.xml @ 8:06be32772107 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit 6248c33a4eacc8785cac321cd4603acf06fae0fd
author | iuc |
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date | Thu, 23 May 2024 08:54:18 +0000 |
parents | 84743da21318 |
children | 35176674168c |
rev | line source |
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0
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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1 <tool id="dada2_mergePairs" name="dada2: mergePairs" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09"> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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2 <description>Merge denoised forward and reverse reads</description> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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3 <macros> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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4 <import>macros.xml</import> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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5 </macros> |
6
84743da21318
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
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6 <expand macro="bio_tools"/> |
0
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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7 <expand macro="requirements"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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8 <expand macro="stdio"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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9 <expand macro="version_command"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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10 <command detect_errors="exit_code"><![CDATA[ |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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11 Rscript '$dada2_script' |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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12 ]]></command> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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13 <configfiles> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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14 <configfile name="dada2_script"><![CDATA[ |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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15 library(dada2, quietly=T) |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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16 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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17 dadaF <- readRDS('$dadaF') |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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18 dadaR <- readRDS('$dadaR') |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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19 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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20 merged <- mergePairs(dadaF, '$derepF', dadaR, '$derepR', minOverlap = $minOverlap, maxMismatch = $maxMismatch, |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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21 ## currently not accessible by the wrapper returnRejects = FALSE, propagateCol = character(0), |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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22 justConcatenate = $justConcatenate, trimOverhang = $trimOverhang) |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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23 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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24 saveRDS(merged, file='$merged') |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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25 ##For display in Galaxy this could be transposed (..but the user could also do it herself) |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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26 ##write.table(merged, "$merged", quote=F, sep="\t", row.names = F, col.names = T) |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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27 ]]></configfile> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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28 </configfiles> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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29 <inputs> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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30 <param argument="dadaF" type="data" format="dada2_dada" label="Dada results for forward reads"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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31 <param argument="derepF" type="data" format="fastq,fastq.gz" label="Forward reads" help="despite the parameter name the sequences don't need to be dereplicated "/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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32 <param argument="dadaR" type="data" format="dada2_dada" label="Dada results for reverse reads"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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33 <param argument="derepR" type="data" format="fastq,fastq.gz" label="Reverse reads" help="despite the parameter name the sequences don't need to be dereplicated "/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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34 <param argument="minOverlap" type="integer" value="12" min="0" label="Minimum length of the overlap"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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35 <param argument="maxMismatch" type="integer" value="0" min="0" label="Maximum number of mismatches"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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36 <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"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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37 <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"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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38 </inputs> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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39 <outputs> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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40 <data name="merged" format="dada2_mergepairs" label="${tool.name} on ${on_string}"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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41 </outputs> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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42 <tests> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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43 <test> |
2
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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44 <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/> |
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805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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45 <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/> |
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69900ffd3b8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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46 <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_S188_L001_R2.Rdata"/> |
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805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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47 <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/> |
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69900ffd3b8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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48 <output name="merged" value="mergePairs_F3D0_S188_L001.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="400" /> |
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805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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49 </test> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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50 <!-- test non-default options --> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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51 <test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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52 <param name="dadaF" ftype="dada2_dada" value="dada_F3D0_S188_L001_R1.Rdata"/> |
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805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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53 <param name="derepF" ftype="fastq.gz" value="filterAndTrim_F3D0_R1.fq.gz"/> |
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69900ffd3b8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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54 <param name="dadaR" ftype="dada2_dada" value="dada_F3D0_S188_L001_R2.Rdata"/> |
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805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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55 <param name="derepR" ftype="fastq.gz" value="filterAndTrim_F3D0_R2.fq.gz"/> |
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69900ffd3b8e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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56 <output name="merged" value="mergePairs_F3D0_S188_L001_nondefault.Rdata" ftype="dada2_mergepairs" compare="sim_size" delta="700"/> |
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805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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57 <param name="minOverlap" value="8" /> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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58 <param name="maxMismatch" value="1"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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59 <param name="justConcatenate" value="TRUE" /> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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60 <param name="trimOverhang" value="TRUE" /> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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61 </test> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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62 </tests> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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63 <help><![CDATA[ |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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64 Description |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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65 ........... |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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66 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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67 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. |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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68 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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69 Usage |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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70 ..... |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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71 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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72 **Input** |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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73 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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74 - reads and learned error rates of the forward reads |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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75 - reads and learned error rates of the reverse reads |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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76 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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77 **Output** |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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78 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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79 - a data set of type dada2_mergepairs (which is a RData file containing the output of dada2's mergePairs function). |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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80 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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81 Details |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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82 ....... |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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83 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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84 @HELP_OVERVIEW@ |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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85 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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86 |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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87 ]]></help> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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88 <expand macro="citations"/> |
805daed21ef3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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89 </tool> |