Mercurial > repos > iuc > rna_starsolo
annotate rg_rnaStarSolo.xml @ 3:61cb2042581a draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 968dcb9c347b8419fd4fa62f29e036269c6f8a28"
author | iuc |
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date | Fri, 30 Aug 2019 08:08:43 -0400 |
parents | 3a1253ee137b |
children | 58b278def57e |
rev | line source |
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0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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1 <tool id="rna_starsolo" name="RNA STARSolo" version="@VERSION@@WRAPPER@" profile="17.01"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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2 <description>mapping, demultiplexing and gene quantification for single cell RNA-seq</description> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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3 <macros> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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4 <import>macros.xml</import> |
3
61cb2042581a
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 968dcb9c347b8419fd4fa62f29e036269c6f8a28"
iuc
parents:
2
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5 <token name="@WRAPPER@"></token> |
0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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6 </macros> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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7 <expand macro="requirements"/> |
2
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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8 <expand macro="stdio" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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9 <regex match="Segmentation fault" source="both" level="fatal" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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10 </expand> |
0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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11 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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12 <command><![CDATA[ |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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13 @TEMPINDEX@ |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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14 STAR |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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15 @REFGENOMEHANDLING@ |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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16 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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17 ## cDNA sequence always goes first, then barcode |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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18 --readFilesIn |
2
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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19 #set $reads2 = ','.join([ '%s' % $x.input2 for $i,$x in enumerate($input_repeats)]) |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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20 #set $reads1 = ','.join([ '%s' % $x.input1 for $i,$x in enumerate($input_repeats)]) |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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21 $reads2 $reads1 |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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22 |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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23 #if $input_repeats[0].input1.is_of_type('fastq.gz', 'fastqsanger.gz'): |
0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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24 @FASTQ_GZ_OPTION@ |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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25 #end if |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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26 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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27 ## Droplet is the only mode available for now |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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28 --soloType Droplet |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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29 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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30 ## 1 - check length of barcode, 0 - do not check |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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31 ## Good for checking custom chemistries |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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32 --soloBarcodeReadLength 1 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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33 --soloCBwhitelist '$soloCBwhitelist' |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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34 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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35 #if str($solo.params.chemistry) == "CR2": |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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36 --soloCBstart 1 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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37 --soloCBlen 16 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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38 --soloUMIstart 17 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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39 --soloUMIlen 10 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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40 #else if str($solo.params.chemistry) == "CR3": |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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41 --soloCBstart 1 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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42 --soloCBlen 16 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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43 --soloUMIstart 17 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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44 --soloUMIlen 12 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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45 #else if str($solo.params.chemistry) == "custom": |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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46 --soloCBstart '$solo.params.soloCBstart' |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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47 --soloCBlen '$solo.params.soloCBlen' |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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48 --soloUMIstart '$solo.params.soloUMIstart' |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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49 --soloUMIlen '$solo.params.soloUMIlen' |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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50 #end if |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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51 |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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52 --soloStrand '$solo.soloStrand' |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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53 --soloFeatures '$solo.soloFeatures' |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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54 --soloUMIdedup '$solo.soloUMIdedup' |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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55 ]]></command> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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56 <inputs> |
2
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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57 <repeat name="input_repeats" title="Input Pairs" min="1" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
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58 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" label="RNA-Seq FASTQ/FASTA file, Barcode reads"/> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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59 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" label="RNA-Seq FASTQ/FASTA file, cDNA reads"/> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
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60 </repeat> |
0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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61 <param format="txt,tsv" argument="--soloCBwhitelist" type="data" label="RNA-Seq Cell Barcode Whitelist" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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62 <expand macro="refgenomehandling" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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63 <section name="solo" title="Advanced Settings" expanded="true"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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64 <conditional name="params"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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65 <param name="chemistry" type="select" label="Configure Chemistry Options"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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66 <option value="CR2" selected="true">Cell Ranger v2</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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67 <option value="CR3">Cell Ranger v3</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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68 <option value="custom">Custom</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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69 </param> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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70 <when value="CR2" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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71 <when value="CR3" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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72 <when value="custom" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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73 <param argument="--soloCBstart" type="integer" min="1" value="1" label="Cell Barcode Start Base" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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74 <param argument="--soloCBlen" type="integer" min="1" value="16" label="Cell Barcode Length" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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75 <param argument="--soloUMIstart" type="integer" min="1" value="17" label="UMI Start Base" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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76 <param argument="--soloUMIlen" type="integer" min="1" value="10" label="UMI Length" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
77 </when> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
78 </conditional> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
79 <param argument="--soloStrand" type="select" label="Strandedness of Library" help="Unstranded has no strand information, Forward has the read strand the same as the original RNA molecule, Reverse has the read strand opposite to the original RNA molecule"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
80 <option value="Unstranded" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
81 <option value="Forward" selected="true" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
82 <option value="Reverse" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
83 </param> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
84 <param argument="--soloFeatures" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, None has UMIs with 1 mismatch distance to others not collapsed"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
85 <option value="Gene" selected="true">Gene: Count reads matching the Gene Transcript</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
86 <option value="SJ" >Splice Junctions: Count reads at exon-intron junctions</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
87 <option value="GeneFull" >Full: Count all reads overlapping genes' exons and introns</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
88 </param> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
89 <param argument="--soloUMIdedup" type="select" label="UMI deduplication (collapsing) algorithm" help="All has all UMIs with 1 mismatch distance to each other collapsed, Directional follows the 'directional' method given in UMI-tools, None has UMIs with 1 mismatch distance to others not collapsed"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
90 <option value="1MM_All" selected="true">All</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
91 <option value="1MM_Directional" >Directional</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
92 <option value="1MM_NotCollapsed" >None</option> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
93 </param> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
94 </section> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
95 </inputs> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
96 <outputs> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
97 <data format="txt" name="output_log" label="${tool.name} on ${on_string}: log" from_work_dir="Log.final.out"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
98 <expand macro="dbKeyActions" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
99 </data> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
100 <data format="tsv" name="output_genes" label="${tool.name} on ${on_string}: Genes" from_work_dir="Solo.out/genes.tsv" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
101 <data format="tsv" name="output_barcodes" label="${tool.name} on ${on_string}: Barcodes" from_work_dir="Solo.out/barcodes.tsv" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
102 <data format="mtx" name="output_matrix" label="${tool.name} on ${on_string}: Matrix Gene Counts" from_work_dir="Solo.out/matrix.mtx" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
103 <filter>solo['soloFeatures'] == "Gene" </filter> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
104 </data> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
105 <data format="mtx" name="output_matrixSJ" label="${tool.name} on ${on_string}: Matrix Splice Junction Counts" from_work_dir="Solo.out/matrixSJ.mtx" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
106 <filter>solo['soloFeatures'] == "SJ" </filter> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
107 </data> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
108 <data format="mtx" name="output_matrixGeneFull" label="${tool.name} on ${on_string}: Matrix Full Gene Counts" from_work_dir="Solo.out/matrixGeneFull.mtx" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
109 <filter>solo['soloFeatures'] == "GeneFull" </filter> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
110 </data> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
111 <data format="txt" name="output_stats" label="${tool.name} on ${on_string}: Feature Statistic Summaries" from_work_dir="Solo.out/Gene.stats" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
112 </outputs> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
113 <tests> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
114 <test expect_num_outputs="5"> |
2
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
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|
115 <repeat name="input_repeats" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
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|
116 <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
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|
117 <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
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|
118 </repeat> |
0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
119 <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
120 <conditional name="refGenomeSource"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
121 <param name="geneSource" value="history" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
122 <param name="genomeFastaFiles" value="SNORD83B.22.fa" /> |
2
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
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|
123 <param name="genomeSAindexNbases" value="4" /> |
0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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124 <conditional name="GTFconditional"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
125 <param name="GTFselect" value="with-gtf" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
126 <param name="sjdbOverhang" value="75"/> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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127 <param name="sjdbGTFfile" value="SNORD83B.22.gtf" ftype="gtf"/> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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128 </conditional> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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129 </conditional> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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130 <section name="solo" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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131 <conditional name="params"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
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132 <param name="chemistry" value="CR2" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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133 </conditional> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
134 <param name="soloStrand" value="Forward" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
135 <param name="soloFeatures" value="Gene" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
136 <param name="soloUMIdedup" value="1MM_All" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
137 </section> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
138 <output name="output_genes"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
139 <assert_contents> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
140 <has_line_matching expression="ENSG00000209480\sSNORD83B" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
141 </assert_contents> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
142 </output> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
143 <output name="output_matrix" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
144 <assert_contents> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
145 <has_line_matching expression="1\s137281\s0" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
146 </assert_contents> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
147 </output> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
148 <output name="output_stats" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
149 <assert_contents> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
150 <has_line_matching expression="\s+nNoFeature\s+3253" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
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|
151 <has_line_matching expression="\s+nUMIs\s+0" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
152 </assert_contents> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
153 </output> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
154 </test> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
155 <test expect_num_outputs="5"> |
2
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
156 <repeat name="input_repeats" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
157 <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
158 <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
159 </repeat> |
0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
160 <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
161 <conditional name="refGenomeSource"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
162 <param name="geneSource" value="history" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
163 <param name="genomeFastaFiles" value="SNORD83B.22.fa" /> |
2
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
164 <param name="genomeSAindexNbases" value="4" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
165 <conditional name="GTFconditional"> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
166 <param name="GTFselect" value="with-gtf" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
167 <param name="sjdbOverhang" value="75" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
168 <param name="sjdbGTFfile" value="SNORD83B.22.gtf" ftype="gtf"/> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
169 </conditional> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
170 </conditional> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
171 <section name="solo" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
172 <conditional name="params"> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
173 <param name="chemistry" value="custom" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
174 <param name="soloCBstart" value="1" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
175 <param name="soloCBlen" value="16" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
176 <param name="soloUMIstart" value="17" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
177 <param name="soloUMIlen" value="10" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
178 </conditional> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
179 <param name="soloStrand" value="Forward" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
180 <param name="soloFeatures" value="GeneFull" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
181 <param name="soloUMIdedup" value="1MM_Directional" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
182 </section> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
183 <output name="output_barcodes" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
184 <assert_contents> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
185 <has_line line="TTTGTCATCTTAGAGC" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
186 <has_line line="TTTGTCATCTTTCCTC" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
187 </assert_contents> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
188 </output> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
189 </test> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
190 <test expect_num_outputs="5"> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
191 <repeat name="input_repeats" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
192 <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
193 <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
194 </repeat> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
195 <repeat name="input_repeats" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
196 <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
197 <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
198 </repeat> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
199 <repeat name="input_repeats" > |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
200 <param name="input1" value="41737_R1_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
201 <param name="input2" value="41737_R2_sub240k.fastq.gz" ftype="fastqsanger.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
202 </repeat> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
203 <param name="soloCBwhitelist" value="737K-august-2016.small.txt.gz" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
204 <conditional name="refGenomeSource"> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
205 <param name="geneSource" value="history" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
206 <param name="genomeFastaFiles" value="SNORD83B.22.fa" /> |
3a1253ee137b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents:
0
diff
changeset
|
207 <param name="genomeSAindexNbases" value="4" /> |
0
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
208 <conditional name="GTFconditional"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
209 <param name="GTFselect" value="with-gtf" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
210 <param name="sjdbOverhang" value="75" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
211 <param name="sjdbGTFfile" value="SNORD83B.22.gtf" ftype="gtf"/> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
212 </conditional> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
213 </conditional> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
214 <section name="solo" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
215 <conditional name="params"> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
216 <param name="chemistry" value="custom" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
217 <param name="soloCBstart" value="1" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
218 <param name="soloCBlen" value="16" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
219 <param name="soloUMIstart" value="17" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
220 <param name="soloUMIlen" value="10" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
221 </conditional> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
222 <param name="soloStrand" value="Forward" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
223 <param name="soloFeatures" value="GeneFull" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
224 <param name="soloUMIdedup" value="1MM_Directional" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
225 </section> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
226 <output name="output_barcodes" > |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
227 <assert_contents> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff
changeset
|
228 <has_line line="TTTGTCATCTTAGAGC" /> |
e3c94e2933c9
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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229 <has_line line="TTTGTCATCTTTCCTC" /> |
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230 </assert_contents> |
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231 </output> |
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232 </test> |
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233 </tests> |
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234 <help><![CDATA[ |
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235 **What it does** |
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236 |
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237 **STARSolo** is a turnkey solution for analyzing droplet single cell RNA sequencing data (e.g. 10X Genomics Chromium System) built directly into STAR code. STARsolo inputs the raw FASTQ reads files, and performs the following operations: |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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238 |
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239 * Error correction and demultiplexing of cell barcodes using user-input whitelist |
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240 * Mapping the reads to the reference genome using the standard STAR spliced read alignment algorithm |
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241 * Error correction and collapsing (deduplication) of Unique Molecular Identifiers (UMIs) |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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242 * Quantification of per-cell gene expression by counting the number of reads per gene |
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243 |
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244 STARsolo output is designed to be a drop-in replacement for 10X CellRanger gene quantification output. It follows CellRanger logic for cell barcode whitelisting and UMI deduplication, and produces nearly identical gene counts in the same format. At the same time STARsolo is 10 times faster than CellRanger. |
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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245 |
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246 ]]></help> |
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247 <expand macro="citations"/> |
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248 </tool> |