Mercurial > repos > iuc > dada2_filterandtrim
annotate dada2_filterAndTrim.xml @ 7:addaf9d22850 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit c2f6071f729b74540354f4a9e7084c9ac468a135
author | iuc |
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date | Mon, 07 Aug 2023 01:36:09 +0000 |
parents | 34e55239e68b |
children | 7434cc396c7b |
rev | line source |
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0
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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1 <tool id="dada2_filterAndTrim" name="dada2: filterAndTrim" version="@DADA2_VERSION@+galaxy@WRAPPER_VERSION@" profile="19.09"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
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2 <description>Filter and trim short read data</description> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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3 <macros> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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4 <import>macros.xml</import> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
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5 </macros> |
6
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
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6 <expand macro="bio_tools"/> |
0
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
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7 <expand macro="requirements"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
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8 <expand macro="stdio"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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9 <expand macro="version_command"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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10 <command detect_errors="exit_code"><![CDATA[ |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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11 Rscript '$dada2_script' |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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12 ]]></command> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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13 <configfiles> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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14 <configfile name="dada2_script"><![CDATA[ |
6
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
changeset
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15 #if $paired_cond.paired_select == "paired" |
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
changeset
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16 #set $compress_output = str($paired_cond.reads.forward.ext.endswith('gz')).upper() |
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
changeset
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17 #else |
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
changeset
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18 #set $compress_output = str($paired_cond.reads.ext.endswith('gz')).upper() |
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
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19 #end if |
0
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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20 truncQ <- c($trim.truncQ) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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21 truncLen <- c($trim.truncLen) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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22 trimLeft <- c($trim.trimLeft) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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23 trimRight <- c($trim.trimRight) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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24 #if str($filter.maxLen) == "" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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25 maxLen <- c(Inf) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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26 #else: |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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27 maxLen <- c($filter.maxLen) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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28 #end if |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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29 minLen <- c($filter.minLen) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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30 maxN <- c($filter.maxN) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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31 minQ <- c($filter.minQ) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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32 #if str($filter.maxEE) == "" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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33 maxEE <- c(Inf) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
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34 #else: |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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35 maxEE <- c($filter.maxEE) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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36 #end if |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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37 #if $paired_cond.paired_select != "single" and $seprev_cond.seprev_select == "yes" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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38 truncQ <- c(truncQ,$seprev_cond.trim.truncQ) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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39 truncLen <- c(truncLen,$seprev_cond.trim.truncLen) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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40 trimLeft <- c(trimLeft,$seprev_cond.trim.trimLeft) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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41 trimRight <- c(trimRight,$seprev_cond.trim.trimRight) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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42 #if str($seprev_cond.filter.maxLen) == "" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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43 maxLen <- c(maxLen,Inf) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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44 #else: |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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45 maxLen <- c(maxLen,$seprev_cond.filter.maxLen) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
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46 #end if |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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47 minLen <- c(minLen,$seprev_cond.filter.minLen) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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48 maxN <- c(maxN,$seprev_cond.filter.maxN) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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49 minQ <- c(minQ,$seprev_cond.filter.minQ) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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50 #if str($seprev_cond.filter.maxEE) == "" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
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51 maxEE <- c(maxEE,Inf) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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52 #else: |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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53 maxEE <- c(maxEE,$seprev_cond.filter.maxEE) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
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54 #end if |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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55 #end if |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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56 |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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57 fwd <- NULL |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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58 rev <- NULL |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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59 filt.fwd <- NULL |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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60 filt.rev <- NULL |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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61 #if $paired_cond.paired_select == "paired" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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62 fwd <- c(fwd, '$paired_cond.reads.forward') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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63 rev <- c(rev, '$paired_cond.reads.reverse') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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64 filt.fwd <- c(filt.fwd, '$paired_output.forward') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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65 filt.rev <- c(filt.rev, '$paired_output.reverse') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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66 #else if $paired_cond.paired_select == "separate" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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67 fwd <- c(fwd, '$paired_cond.reads') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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68 rev <- c(rev, '$paired_cond.sdaer') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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69 filt.fwd <- c(filt.fwd, '$output_fwd') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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70 filt.rev <- c(filt.rev, '$output_rev') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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71 #else |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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72 fwd <- c(fwd, '$paired_cond.reads') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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73 filt.fwd <- c(filt.fwd, '$output_single') |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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74 #end if |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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75 |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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76 #if str($orientFwd) == "" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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77 orientFwd <- NULL |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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78 #else |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
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79 orientFwd <- "$orientFwd" |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
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80 #end if |
cc41546adf56
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81 |
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82 library(dada2, quietly=T) |
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83 |
6
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84 ftout <- filterAndTrim(fwd, filt.fwd, rev, filt.rev, compress = $compress_output, |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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85 truncQ = truncQ, truncLen = truncLen, trimLeft = trimLeft, trimRight = trimRight, maxLen = maxLen, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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86 minLen = minLen, maxN = maxN, minQ = minQ, maxEE = maxEE, rm.lowcomplex = $rmlowcomplex, |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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87 rm.phix = $rmPhiX, orient.fwd = orientFwd) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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88 |
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89 rownames(ftout) <- c( '$paired_cond.reads.element_identifier' ) |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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90 write.table(ftout, "$outtab", quote=F, sep="\t", col.names=NA) |
2
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91 |
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92 if(0 %in% ftout){ |
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93 quit(save="no", status="1") |
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94 } |
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95 |
0
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96 ]]></configfile> |
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97 </configfiles> |
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98 <inputs> |
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99 <expand macro="fastq_input" multiple="False" collection_type="paired" argument_fwd="fwd" argument_rev="rev"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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100 <expand macro="trimmers"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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101 <expand macro="filters"/> |
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102 <conditional name="seprev_cond"> |
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103 <param name="seprev_select" type="select" label="Separate filters and trimmers for reverse reads" help="only applies to paired end data"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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104 <option value="no">no</option> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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105 <option value="yes">yes</option> |
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106 </param> |
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107 <when value="no"/> |
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108 <when value="yes"> |
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109 <expand macro="trimmers"/> |
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110 <expand macro="filters"/> |
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111 </when> |
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112 </conditional> |
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113 <param argument="rmPhiX" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Discard reads matching the PhiX genome" /> |
cc41546adf56
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114 <param name="rmlowcomplex" argument="rm.lowcomplex" type="integer" value="0" min="0" label="Low complexity filter kmer threshold" help="see below"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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115 <param name="orientFwd" argument="orient.fwd" type="text" value="" optional="true" label="String present at the start of valid reads" help="see below"/> |
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116 <param name="output_statistics" truevalue="TRUE" falsevalue="FALSE" type="boolean" checked="true" label="Output statistics" help="Create extra table with the number of reads pre and post filtering" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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117 </inputs> |
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118 <outputs> |
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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119 <collection name="paired_output" type="paired" format_source="reads['forward']" label="${tool.name} on ${on_string}: Paired reads" > |
0
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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120 <filter>paired_cond['paired_select'] == "paired"</filter> |
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121 </collection> |
6
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
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122 <data name="output_single" format_source="reads" label="${tool.name} on ${on_string}: Reads" > |
0
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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123 <filter>paired_cond['paired_select'] == "single"</filter> |
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124 </data> |
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125 <data name="output_fwd" format_source="reads" label="${tool.name} on ${on_string}: Forward reads" > |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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126 <filter>paired_cond['paired_select'] == "separate"</filter> |
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127 </data> |
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128 <data name="output_rev" format_source="sdaer" label="${tool.name} on ${on_string}: Reverse reads" > |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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129 <filter>paired_cond['paired_select'] == "separate"</filter> |
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130 </data> |
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131 <data name="outtab" format="tabular" label="${tool.name} on ${on_string}: Statistics"> |
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132 <filter>output_statistics</filter> |
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133 </data> |
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134 </outputs> |
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135 <tests> |
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136 <!-- paired data in paired collection --> |
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137 <test expect_num_outputs="4"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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138 <conditional name="paired_cond"> |
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139 <param name="paired_select" value="paired"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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140 <param name="reads"> |
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141 <collection type="paired"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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142 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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143 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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144 </collection> |
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145 </param> |
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146 </conditional> |
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147 <output_collection name="paired_output" type="paired" count="2"> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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148 <element name="forward" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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149 <element name="reverse" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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150 </output_collection> |
2
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151 <!-- in the test the used collection (the pair) has the name "Unnamed collection" hence we have two lines difference. In the real world the pair will have the sample name, i.e its OK. To be sure we test for the counts as well --> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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152 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular" lines_diff="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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153 <assert_contents> |
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154 <has_text text="745" /> |
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155 <has_text text="750" /> |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
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156 </assert_contents> |
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157 </output> |
0
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158 </test> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
159 <!-- paired data given separately --> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
160 <test expect_num_outputs="3"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
161 <conditional name="paired_cond"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
162 <param name="paired_select" value="separate"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
163 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
164 <param name="sdaer" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
165 </conditional> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
166 <output name="output_fwd" value="filterAndTrim_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
167 <output name="output_rev" value="filterAndTrim_F3D0_R2.fq.gz" ftype="fastqsanger.gz" /> |
2
23fc35093b11
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f2a33fe115fef9d711112b53136cf7619f1b19be"
iuc
parents:
0
diff
changeset
|
168 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular"/> |
0
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
169 </test> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
170 <!-- single end data --> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
171 <test expect_num_outputs="1"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
172 <conditional name="paired_cond"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
173 <param name="paired_select" value="single"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
174 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
175 </conditional> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
176 <param name="rmPhiX" value="TRUE" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
177 <param name="rmlowcomplex" value="2" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
178 <param name="orientFwd" value="TACGG" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
179 <param name="output_statistics" value="FALSE" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
180 <output name="output_fwd" value="filterAndTrim_single_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
181 </test> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
182 <!-- single end data trimming --> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
183 <test expect_num_outputs="1"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
184 <conditional name="paired_cond"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
185 <param name="paired_select" value="single"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
186 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
187 </conditional> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
188 <param name="trim|truncQ" value="30" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
189 <param name="trim|trimLeft" value="150" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
190 <param name="trim|trimRight" value="2" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
191 <param name="trim|truncLen" value="2" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
192 <param name="output_statistics" value="FALSE" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
193 <output name="output_fwd" value="filterAndTrim_single_trimmers_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
194 </test> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
195 <!-- single end data filtering --> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
196 <test expect_num_outputs="1"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
197 <conditional name="paired_cond"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
198 <param name="paired_select" value="single"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
199 <param name="reads" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
200 </conditional> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
201 <param name="filter|maxLen" value="255" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
202 <param name="filter|minLen" value="60" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
203 <param name="filter|maxN" value="100" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
204 <param name="filter|minQ" value="13" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
205 <param name="filter|maxEE" value="1" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
206 <param name="output_statistics" value="FALSE" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
207 <output name="output_fwd" value="filterAndTrim_single_filters_F3D0_R1.fq.gz" ftype="fastqsanger.gz" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
208 </test> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
209 <!-- paired data w separate filters and trimmers for reverse --> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
210 <test expect_num_outputs="3"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
211 <conditional name="paired_cond" > |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
212 <param name="paired_select" value="paired"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
213 <param name="reads"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
214 <collection type="paired"> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
215 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
216 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
217 </collection> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
218 </param> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
219 </conditional> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
220 <param name="seprev_cond|seprev_select" value="yes"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
221 <param name="seprev_cond|trim|truncQ" value="30" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
222 <param name="seprev_cond|trim|trimLeft" value="150" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
223 <param name="seprev_cond|trim|trimRight" value="2" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
224 <param name="seprev_cond|trim|truncLen" value="2" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
225 <param name="seprev_cond|filter|maxLen" value="255" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
226 <param name="seprev_cond|filter|minLen" value="60" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
227 <param name="seprev_cond|filter|maxN" value="100" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
228 <param name="seprev_cond|filter|minQ" value="13" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
229 <param name="seprev_cond|filter|maxEE" value="1" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
230 <param name="output_statistics" value="FALSE" /> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
231 <output_collection name="paired_output" type="paired" count="2"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
iuc
parents:
diff
changeset
|
232 </test> |
6
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
changeset
|
233 <!-- paired data in paired collection with uncompressed input --> |
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
changeset
|
234 <test expect_num_outputs="4"> |
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
changeset
|
235 <conditional name="paired_cond"> |
34e55239e68b
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit ea6c9c638e742c097b0ef294161eeea447c09e06
iuc
parents:
2
diff
changeset
|
236 <param name="paired_select" value="paired"/> |
34e55239e68b
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237 <param name="reads"> |
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238 <collection type="paired"> |
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239 <element name="forward" value="F3D0_S188_L001_R1_001.fastq" ftype="fastqsanger"/> |
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240 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq" ftype="fastqsanger"/> |
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241 </collection> |
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242 </param> |
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243 </conditional> |
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244 <output_collection name="paired_output" type="paired" count="2"> |
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245 <element name="forward" value="filterAndTrim_F3D0_R1.fq" ftype="fastqsanger" /> |
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246 <element name="reverse" value="filterAndTrim_F3D0_R2.fq" ftype="fastqsanger" /> |
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247 </output_collection> |
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248 <output name="outtab" value="F3D0_S188_L001_R1_001.tab" ftype="tabular" lines_diff="2"> |
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249 <assert_contents> |
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250 <has_text text="745" /> |
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251 <has_text text="750" /> |
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252 </assert_contents> |
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253 </output> |
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254 </test> |
2
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255 |
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256 <!-- test failure in case all reads are filtered --> |
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257 <test expect_exit_code="1" expect_failure="true"> |
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258 <conditional name="paired_cond" > |
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259 <param name="paired_select" value="paired"/> |
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260 <param name="reads"> |
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261 <collection type="paired"> |
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262 <element name="forward" value="F3D0_S188_L001_R1_001.fastq.gz" ftype="fastqsanger.gz"/> |
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263 <element name="reverse" value="F3D0_S188_L001_R2_001.fastq.gz" ftype="fastqsanger.gz"/> |
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264 </collection> |
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265 </param> |
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266 </conditional> |
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267 <param name="filter|minLen" value="1000" /> |
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268 <param name="output_statistics" value="FALSE" /> |
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269 </test> |
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270 |
0
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271 </tests> |
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272 |
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273 <help><![CDATA[ |
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274 Description |
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275 ........... |
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276 |
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277 Filters and trims a FASTQ dataset (can be compressed) based on several user-definable criteria, and outputs a compressed FASTQ data set containing those trimmed reads which passed the filters. For paired end data forward and reverse FASTQ datasets can be provided as pair of FASTQ datasets (or two separate data sets), in which case filtering is performed on the forward and reverse reads independently, and both reads must pass for the read pair to be in the output. |
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278 |
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279 Usage |
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280 ..... |
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281 |
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282 **Input** is a FASTQ dataset (or a pair in case of paired end data) containing all reads of a sample. It is suggested to organize them in a (paired) collection (in particular if you have multiple samples). |
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283 |
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284 **Output** is a (paired) collection of filtered and trimmed paired FASTQ datasets (again one data set or pair per sample). |
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285 |
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286 Upstream dada2 tools are *dada2: learnErrorRates* and *dada2: dada*. Note that these tools do not work on paired end data. So, if you have paired end data you need to split the generated paired collection into one containing the forward reads and one containing the reverse reads. This can be done by the *unzip collection* tool. |
cc41546adf56
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287 |
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288 An additional tabular output gives the number of reads before and after trimming. This can data set can be used as input for *dada2: sequence counts* to track the sequence counts for each sample through all dada2 pipeline step. |
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289 |
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290 Details |
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291 ....... |
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292 |
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293 *Trimming and filtering*: |
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294 |
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295 - Truncation of the read length is enforced after trimming of the right end. |
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296 - The long read filter is applied before trimming and the short read filter after trimming. |
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297 - For details on the calculation of the number of expected errors see also https://doi.org/10.1093/bioinformatics/btv401 |
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298 |
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299 |
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300 *String present at the start of valid reads* (orient.fwd): |
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301 |
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302 This string is compared to the start of each read, and the reverse complement of each read. If it exactly matches the start of the read, the read is kept. If it exactly matches the start of the reverse complement read, the read is reverse-complemented and kept. Otherwise the read if filtered out. For paired reads, the string is compared to the start of the forward and reverse reads, and if it matches the start of the reverse read the reads are swapped and kept. The primary use of this parameter is to unify the orientation of amplicon sequencing libraries that are a mixture of forward and reverse orientations, and that include the forward primer on the reads. |
cc41546adf56
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303 |
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304 *Low complexity filter kmer threshold"* |
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305 |
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306 If greater than 0, reads with an effective number of kmers less than this value will be removed. The effective number of kmers is determined as a Shannon information approximation. The default kmer-size is 2, and therefore perfectly random sequences will approachan effective kmer number of 16 = 4 (nucleotides) ^ 2 (kmer size). |
cc41546adf56
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307 |
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308 Notes |
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309 ..... |
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310 |
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311 This step may be replaced by alternative tools to filter and trim short read data if the following is ensured: |
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312 |
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313 - For paired end data unpaired reads must be removed. |
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314 - There must not be a read containing a non-canonical nucleotide (N). |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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315 |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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316 @HELP_OVERVIEW@ |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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317 ]]></help> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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318 <expand macro="citations"/> |
cc41546adf56
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/dada2 commit f8b6b6e72914ad6bcca8423dfa03f59bde80992e"
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319 </tool> |