Mercurial > repos > bgruening > alevin

annotate alevin.xml @ 10:e4c01dcece8b draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
author bgruening
date Thu, 22 Jul 2021 14:05:58 +0000
parents ecb9ea6269ee
children e661a3269313
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10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
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1 <tool id="alevin" name="Alevin" version="@VERSION@+@GALAXY_VERSION@" profile="@PROFILE_VERSION@">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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2 <description>Quantification and analysis of 3’ tagged-end single-cell sequencing data</description>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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3 <macros>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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4 <import>macros.xml</import>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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5 </macros>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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6 <expand macro="requirements"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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7 <command detect_errors="exit_code"><![CDATA[
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8 mkdir ./index
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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9 && mkdir ./output
3
0a5258e41227 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit cf916eb507ee224812b64663c1d6020eb59eb88c"
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10 #if $refTranscriptSource.TranscriptSource != "indexed":
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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11 && salmon index -i ./index
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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12 --kmerLen '${refTranscriptSource.s_index.kmer}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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13 --gencode
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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14 --transcripts '${refTranscriptSource.s_index.fasta}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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15 #set $index_path = './index'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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16 #else
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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17 #set $index_path = $refTranscriptSource.index.fields.path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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18 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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19 #if $pairstraight.readselect == 'paired':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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20 #if $pairstraight.file1.is_of_type("fastq.gz"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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21 && cp '${pairstraight.file1}' ./mate1.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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22 && gunzip ./mate1.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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23 && cp '${pairstraight.file2}' ./mate2.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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24 && gunzip ./mate2.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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25 #else if $pairstraight.file1.is_of_type("fastq.bz2"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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26 && cp '${pairstraight.file1}' ./mate1.fastq.bz2
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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27 && bzip2 -d ./mate1.fastq.bz2
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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28 && cp '${pairstraight.file2}' ./mate2.fastq.bz2
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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29 && bzip2 -d ./mate2.fastq.bz2
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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30 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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31 && ln -s '${pairstraight.file1}' ./mate1.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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32 && ln -s '${pairstraight.file2}' ./mate2.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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33 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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34 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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35 #if $pairstraight.unmatedreads.is_of_type("fastq.gz"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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36 && cp '${pairstraight.unmatedreads}' ./unmate.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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37 && gunzip ./unmate.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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38 #else if $pairstraight.unmatedreads.is_of_type("fastq.bz2"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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39 && cp '${pairstraight.unmatedreads}' ./unmate.fastq.bz2
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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40 && bzip2 -d unmate.fastq.bz2
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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41 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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42 && ln -s '${pairstraight.unmatedreads}' ./unmate.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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43 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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44 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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45
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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46 && ln -s '${tgmap}' ./alevinmap.tsv
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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47 && salmon alevin -l
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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48 #if $pairstraight.readselect == 'paired':
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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49 #if $pairstraight.libtype.strandedness == 'A'
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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50 A
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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51 #else
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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52 ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness}
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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53 #end if
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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54 -i $index_path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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55 -1 ./mate1.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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56 -2 ./mate2.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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57 #else:
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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58 '${pairstraight.libtype.strandedness}'
0
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59 -i $index_path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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60 -r zcat ./unmate.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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61 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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62 -o ./output
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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63 -p "\${GALAXY_SLOTS:-4}"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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64 ${protocol}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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65 --tgMap ./alevinmap.tsv
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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66 #if $whitelist:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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67 --whitelist '${optional.whitelist}'
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68 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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69 #if $optional.numCellBootstraps:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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70 --numCellBootstraps '${optional.numCellBootstraps}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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71 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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72 #if $optional.forceCells:
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73 --forceCells '${optional.forceCells}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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74 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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75 #if $optional.expectCells:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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76 --expectCells '${optional.expectCells}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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77 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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78 #if $optional.mrna:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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79 --mrna '${optional.mrna}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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80 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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81 #if $optional.rrna:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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82 --rrna '${optional.rrna}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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83 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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84 #if $optional.keepCBFraction:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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85 --keepCBFraction '${optional.keepCBFraction}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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86 #end if
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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87 ${optional.noDedup}
0
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88 ${optional.dumpBfh}
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89 ${optional.dumpFeatures}
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90 ${optional.dumpUmiGraph}
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91 ${optional.dumpMtx}
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92 #if $optional.lowRegionMinNumBarcodes:
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93 --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}'
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94 #end if
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95 #if $optional.maxNumBarcodes:
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96 --maxNumBarcodes '${optional.maxNumBarcodes}'
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97 #end if
4
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98 #if $optional.freqThreshold:
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99 --freqThreshold '${optional.freqThreshold}'
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100 #end if
2
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101
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102 #if $optional.dumpMtx != "--dumpMtx":
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103 && python '$__tool_directory__/vpolo_convert.py' -m
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104 #else:
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105 && gunzip output/alevin/quants_mat.mtx.gz
2
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106 #end if
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107 #if $optional.dumpUmiGraph:
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108 && python '$__tool_directory__/vpolo_convert.py' -u
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109 && sh '$__tool_directory__/umiout.sh'
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110 #end if
7
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111
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112 && gunzip output/alevin/quants_tier_mat.gz
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113 #if $optional.numCellBootstraps:
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114 && gunzip output/alevin/quants_mean_mat.gz
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115 && gunzip output/alevin/quants_var_mat.gz
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116 #end if
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117
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118 && gunzip output/aux_info/fld.gz
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119 && gunzip output/aux_info/observed_bias.gz
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120 && gunzip output/aux_info/observed_bias_3p.gz
0
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121 ]]>
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122 </command>
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123 <inputs>
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124 <expand macro="index"/>
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125 <conditional name="pairstraight">
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126 <param name="readselect" label="Single or paired-end reads?" type="select">
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127 <option value="paired">Paired-end</option>
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128 <option value="unmated">Single-end</option>
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129 </param>
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130 <when value="paired">
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131 <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>
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132 <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>
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133 <expand macro="stranded_pe"/>
0
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134 </when>
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135 <when value="unmated">
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136 <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
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137 <expand macro="stranded_se"/>
0
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138 </when>
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139 </conditional>
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140 <param name="protocol" type="select">
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141 <option value="--dropseq">DropSeq Single Cell protocol</option>
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142 <option value="--chromium">10x chromium v2 Single Cell protocol</option>
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143 <option value="--chromiumV3">10x chromium v3 Single Cell protocol</option>
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144 <option value="--gemcode">Gemcode v1 Single Cell protocol</option>
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145 <option value="--celseq">CEL-Seq Single Cell protocol</option>
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146 <option value="--celseq2">CEL-Seq2 Single Cell protocol</option>
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147 </param>
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148 <param name="tgmap" type="data" format="tsv,tabular" label="Transcript to gene map file" help="Tsv with no header, containing two columns mapping each transcript present in the reference to the corresponding gene (the first column is a transcript and the second is the corresponding gene)."/>
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149 <param name="allout" type="boolean" label="Retrieve all output files" truevalue="Yes" falsevalue="No" checked="false" help="If not selected, all log, info.txt, and json files output by Alevin will not be retrieved"/>
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150 <section name="optional" title="Optional commands" expanded="false">
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151 <param name="whitelist" type="data" format="tsv,tabular" optional="true" label="Whitelist file" help="Explicitly specify whitelist CP for cell detection and CB sequence correction. If not specified, putative CBs generated."/>
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152 <param name="noDedup" type="boolean" truevalue="--noDedup" falsevalue="" checked="false" help="Causes pipeline to only perform CB correction, then maps the read-sequences to the transcriptome generating the interim data-structure of CB-EqClass-UMI-count. Used in parallel with --dumpBarcodeEq or --dumpBfh for the purposes of obtaining raw information or debugging."/>
0
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153 <param name="mrna" type="data" format="tsv" optional="true" help="Single column tsv of mitochondrial genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
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154 <param name="rrna" type="data" format="tsv" optional="true" help="Single column tsv of ribosomal genes which are to be used as a feature for CB whitelising naive Bayes classification."/>
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155 <param name="dumpBfh" type="boolean" truevalue="--dumpBfh" falsevalue="" checked="false" help="Dumps the full CB-EqClass-UMI-count data-structure for the purposed of allowing raw data analysis and debugging."/>
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156 <param name="dumpFeatures" type="boolean" truevalue="--dumpFeatures" falsevalue="" checked="false" help="Dumps all features used by the CB classification and their counts at each cell level. Generally, this is used for the purposes of debugging."/>
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157 <param name="dumpUmiGraph" type="boolean" truevalue="--dumpUmiGraph" falsevalue="" checked="false" help="Dump the per-cell level umi graph"/>
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158 <param name="dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" help="Converts the default binary format of alevin for gene-count matrix into a human readable mtx (matrix market exchange) sparse format."/>
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159 <param name="forceCells" type="integer" optional="true" help="Explicitly specify the number of cells."/>
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160 <param name="expectCells" type="integer" optional="true" help="define a close upper bound on expected number of cells."/>
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161 <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
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162 <param name="minScoreFraction" type="float" optional="true" help="This value controls the minimum allowed score for a mapping to be considered valid. It matters only when --validateMappings has been passed to Salmon. The maximum possible score for a fragment is ms = read_len * ma (or ms = (left_read_len + right_read_len) * ma for paired-end reads).
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163 The argument to --minScoreFraction determines what fraction of the maximum score s a mapping must achieve to be potentially retained. For a minimum score fraction of f, only mappings with a score less than (f * s) will be kept. Mappings with lower scores will be considered as low-quality, and will be discarded."/>
0
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164 <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/>
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165 <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/>
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166 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/>
4
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167 <param name="freqThreshold" type="integer" optional="true" help="Minimum frequency for a barcode to be considered. Defaults to 10"/>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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168 </section>
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169 </inputs>
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170 <outputs>
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171 <data name="quants_mat_tsv" label="quants_mat.tsv" format="txt" from_work_dir="quants_mat.tsv">
3
0a5258e41227 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit cf916eb507ee224812b64663c1d6020eb59eb88c"
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172 <filter>optional["dumpMtx"] is not True</filter>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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173 </data>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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174 <data name="quants_mat_mtx" label="quants_mat.mtx" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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175 <filter>optional["dumpMtx"]</filter>
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176 </data>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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177 <data name="raw_cb_frequency_txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
4
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
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178 <filter>optional["dumpFeatures"]</filter>
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
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179 </data>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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180 <data name="quants_mat_cols_txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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181 <data name="quants_mat_rows_txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
7
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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182 <data name="quants_tier_mat" label="quants_tier_mat" format="mtx" from_work_dir="output/alevin/quants_tier_mat"/>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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183 <data name="alevin_log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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184 <filter>allout</filter>
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185 </data>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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186 <data name="featureDump_txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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187 <data name="whitelist_txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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188 <data name="bfh_txt" label="bfh.txt" format="txt" from_work_dir="output/alevin/bfh.txt">
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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189 <filter>optional["dumpBfh"]</filter>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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190 </data>
7
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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191 <data name="quants_mean_mat" label="quants_mean_mat" format="mtx" from_work_dir="output/alevin/quants_mean_mat">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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192 <filter>optional["numCellBootstraps"]</filter>
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193 </data>
7
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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194 <data name="quants_var_mat" label="quants_var_mat" format="mtx" from_work_dir="output/alevin/quants_var_mat">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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195 <filter>optional["numCellBootstraps"]</filter>
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196 </data>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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197 <data name="quants_boot_rows_txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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198 <filter>optional["numCellBootstraps"]</filter>
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199 </data>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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200 <data name="alevinmeta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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201 <filter>allout</filter>
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202 </data>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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203 <data name="ambig_info_tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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204 <filter>allout</filter>
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205 </data>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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206 <data name="meta_info_json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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207 <filter>allout</filter>
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208 </data>
7
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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209 <data name="expected_bias" format="txt" label="expected_bias" from_work_dir="output/aux_info/fld"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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210 <data name="observed_bias" format="txt" label="observed_bias" from_work_dir="output/aux_info/observed_bias"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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211 <data name="observed_bias_3p" format="txt" label="observed_bias_3p" from_work_dir="output/aux_info/observed_bias_3p"/>
10
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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212 <data name="flenDist_txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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213 <data name="salmon_quant_log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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214 <filter>allout</filter>
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215 </data>
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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216 <collection name="umigraphs" type="list" label="Umi graph PDFs">
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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217 <filter>optional["dumpUmiGraph"]</filter>
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218 <discover_datasets pattern="__name_and_ext__" ext="pdf" directory="fixed"/>
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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219 </collection>
9
ecb9ea6269ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit fe9dd99a14770b6c5f26e24893599acb577e304f"
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220 <data name="cmd_info.json" label="cmd_info.json" format="json" from_work_dir="output/cmd_info.json">
ecb9ea6269ee "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit fe9dd99a14770b6c5f26e24893599acb577e304f"
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221 <filter>allout</filter>
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222 </data>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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223 </outputs>
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224 <tests>
4
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225 <test expect_num_outputs="11">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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226 <conditional name="refTranscriptSource">
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227 <param name="TranscriptSource" value="history"/>
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228 <section name="s_index">
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229 <param name="fasta" value="minitranscript.fa"/>
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230 </section>
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231 </conditional>
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232 <conditional name="pairstraight">
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233 <param name="readselect" value="paired"/>
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234 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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235 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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236 <param name="orientation" value="I"/>
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237 <param name="strandedness" value="SR"/>
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238 </conditional>
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239 <param name="protocol" value="--chromium"/>
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240 <param name="tgmap" value="minitxp.tsv"/>
8
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
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241 <section name="optional">
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242 <param name="keepCBFraction" value="1"/>
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
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243 <param name="dumpFeatures" value="Yes"/>
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
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244 <param name="freqThreshold" value="5"/>
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
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245 <param name="dumpMtx" value="Yes"/>
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
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246 </section>
10
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247 <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
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248 </test>
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249 <test expect_num_outputs="14">
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250 <conditional name="refTranscriptSource">
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251 <param name="TranscriptSource" value="history"/>
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252 <section name="s_index">
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253 <param name="fasta" value="minitranscript.fa"/>
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254 </section>
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255 </conditional>
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256 <conditional name="pairstraight">
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257 <param name="readselect" value="paired"/>
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258 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
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259 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
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260 <param name="orientation" value="I"/>
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261 <param name="strandedness" value="SR"/>
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262 </conditional>
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263 <param name="protocol" value="--chromium"/>
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264 <param name="tgmap" value="minitxp.tsv"/>
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265 <section name="optional">
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266 <param name="keepCBFraction" value="1"/>
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267 <param name="dumpFeatures" value="Yes"/>
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268 <param name="numCellBootstraps" value="2"/>
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269 <param name="freqThreshold" value="5"/>
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270 <param name="dumpMtx" value="Yes"/>
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271 </section>
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272 <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true" lines_diff="62"/>
0
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273 </test>
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274 </tests>
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275 <help><![CDATA[
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276 @salmonhelp@
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277 @alevinhelp@
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278 ]]></help>
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279 <expand macro="citations"/>
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280 </tool>