Mercurial > repos > iuc > presto_filterseq
annotate presto_filterseq.xml @ 3:196b83ac37f2 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
author | iuc |
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date | Sat, 25 Sep 2021 18:30:46 +0000 |
parents | 33a09d40751f |
children | 4a4e086f6e38 |
rev | line source |
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3
196b83ac37f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
iuc
parents:
2
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1 <tool id="presto_filterseq" name="pRESTO FilterSeq" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@"> |
0
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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2 <description>Filters and/or masks reads based on length, quality, missing bases and repeats.</description> |
3
196b83ac37f2
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit d52e3c9c53dd358e14e65a3a083e7d5c102f8697"
iuc
parents:
2
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3 <expand macro="bio_tools"/> |
0
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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changeset
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4 <macros> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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5 <import>presto_macros.xml</import> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
changeset
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6 </macros> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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7 |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
changeset
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8 <expand macro="requirements"/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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9 |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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10 <version_command>FilterSeq.py --version</version_command> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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11 <command detect_errors="exit_code"><![CDATA[ |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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12 ln -s '$fastq_in' in.fastq && |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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13 FilterSeq.py '$cc.command' |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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14 --nproc "\${GALAXY_SLOTS:-1}" |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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15 -s in.fastq |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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16 #if $varExists('cc.q') |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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17 -q '$cc.q' |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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18 #end if |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
changeset
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19 #if $getVar('cc.inner', False) |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
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20 --inner |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
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21 #end if |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
changeset
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22 #if $varExists('cc.win') |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
changeset
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23 --win '$cc.win' |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
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24 #end if |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
changeset
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25 #if $getVar('cc.reverse', False) |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
changeset
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26 --reverse |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
changeset
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27 #end if |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
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28 #if $varExists('cc.n') |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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29 -n '$cc.n' |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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30 #end if |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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31 --outdir=. |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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32 --outname=tmp_filter_seq |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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33 #if $capture_log |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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34 --log '$log_out' |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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35 #end if |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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36 && |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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37 mv ./tmp_filter_seq_${cc.command}-pass.fastq $fastq_out |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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38 ]]></command> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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39 <inputs> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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40 <param argument="-s" name="fastq_in" type="data" format="fastq" label="Input FASTQ file"/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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41 <conditional name="cc"> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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42 <param name="command" type="select" label="Command"> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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43 <option value="length">Filters reads by length (length)</option> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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44 <option value="missing">Filters reads by N or gap character count (missing)</option> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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45 <option value="repeats">Filters reads by consecutive nucleotide repeats (repeats)</option> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
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46 <option value="quality">Filters reads by quality score (quality)</option> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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47 <option value="maskqual">Masks low quality positions (maskqual)</option> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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48 <option value="trimqual">Trims sequences by quality score decay (trimqual)</option> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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49 </param> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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50 <when value="length"> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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51 <param argument="-n" type="integer" value="" label="Minimum Length" help="Discard reads shorter than this number of bases long."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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52 </when> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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53 <when value="missing"> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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54 <param argument="-n" type="integer" value="" label="Max Missing" help="Dicard reads with more than this many no-calls or gaps."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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55 </when> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
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56 <when value="repeats"> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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57 <param argument="-n" type="integer" value="" label="Max Repeat Length" help="Discard reads with simple repeats of this length of longer."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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58 </when> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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59 <when value="quality"> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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60 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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61 <param argument="--inner" type="boolean" value="false" label="End-Trim Ns" help="Exclude Ns at the ends of the reads from calculation."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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62 </when> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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63 <when value="maskqual"> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
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64 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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65 </when> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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66 <when value="trimqual"> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
diff
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67 <param argument="-q" type="integer" value="20" label="Minimum Quality" help="Discard reads with mean quality below this value."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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68 <param argument="--win" type="integer" value="10" label="Window Size" help="Window size for moving average quality calculation."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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69 <param argument="--reverse" type="boolean" value="false" label="Reverse" help="If true trim the start of the reads instead of the ends."/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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70 </when> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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71 </conditional> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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72 <expand macro="presto-log-param"/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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73 </inputs> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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74 |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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75 <outputs> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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76 <data name="fastq_out" format="fastq"/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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77 <expand macro="presto-log-output"/> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
parents:
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78 </outputs> |
7b102129b1e8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit 5d4da3eb59439ce5b1eea211b4ad1d47807d7acb
iuc
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79 |
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80 <tests> |
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81 <test> |
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82 <param name="command" value="length"/> |
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83 <param name="n" value="299"/> |
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84 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> |
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85 <output name="fastq_out" file="presto_filterseq_length_test_out.fastq" sort="true"/> |
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86 </test> |
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87 <test> |
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88 <param name="command" value="missing"/> |
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89 <param name="n" value="281"/> |
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90 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> |
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91 <output name="fastq_out" file="presto_filterseq_missing_test_out.fastq" sort="true"/> |
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92 </test> |
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93 <test> |
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94 <param name="command" value="repeats"/> |
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95 <param name="n" value="8"/> |
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96 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> |
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97 <output name="fastq_out" file="presto_filterseq_repeats_test_out.fastq" sort="true"/> |
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98 </test> |
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99 <test> |
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100 <param name="command" value="quality"/> |
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101 <param name="q" value="30"/> |
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102 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> |
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103 <output name="fastq_out" file="presto_filterseq_quality_test_out.fastq" sort="true"/> |
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104 </test> |
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105 <test> |
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106 <param name="command" value="maskqual"/> |
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107 <param name="q" value="30"/> |
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108 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> |
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109 <output name="fastq_out" file="presto_filterseq_maskqual_test_out.fastq" sort="true"/> |
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110 </test> |
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111 <test> |
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112 <param name="command" value="trimqual"/> |
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113 <param name="q" value="30"/> |
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114 <param name="fastq_in" value="presto_filterseq_test_in.fastq"/> |
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115 <output name="fastq_out" file="presto_filterseq_trimqual_test_out.fastq" sort="true"/> |
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116 </test> |
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117 </tests> |
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118 |
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119 <help><![CDATA[ |
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120 Filters and/or masks reads based on length, quality, missing bases and repeats. |
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121 |
1
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/presto commit a42c43c1528ae7b7efe2c5ef848681d574df0405"
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122 See the `pRESTO online help <@PRESTO_BASE_URL@/en/stable>`_ for more information. |
0
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123 |
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124 @HELP_NOTE@ |
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125 ]]></help> |
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126 <expand macro="citations" /> |
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127 </tool> |