Mercurial > repos > bgruening > alevin
annotate alevin.xml @ 16:b0fe3e482cb7 draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 6954ddebecfe9f0975f2c7e29193e4c99c550514
author | bgruening |
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date | Mon, 28 Oct 2024 17:50:35 +0000 |
parents | c9944a2600f1 |
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rev | line source |
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11
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
10
diff
changeset
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1 <tool id="alevin" name="Alevin" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@"> |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
10
diff
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2 <description>Quantification and analysis of 3-prime tagged-end single-cell sequencing data</description> |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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3 <macros> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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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"
bgruening
parents:
diff
changeset
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5 </macros> |
14
c9944a2600f1
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a
bgruening
parents:
11
diff
changeset
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6 <expand macro="xrefs"/> |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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7 <expand macro="requirements"/> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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8 <command detect_errors="exit_code"><![CDATA[ |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
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9 mkdir ./index |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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10 && mkdir ./output |
3
0a5258e41227
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit cf916eb507ee224812b64663c1d6020eb59eb88c"
bgruening
parents:
2
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11 #if $refTranscriptSource.TranscriptSource != "indexed": |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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12 && salmon index -i ./index |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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13 --kmerLen '${refTranscriptSource.s_index.kmer}' |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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14 --gencode |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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15 --transcripts '${refTranscriptSource.s_index.fasta}' |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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16 #set $index_path = './index' |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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17 #else |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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18 #set $index_path = $refTranscriptSource.index.fields.path |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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19 #end if |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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20 #if $pairstraight.readselect == 'paired': |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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21 #if $pairstraight.file1.is_of_type("fastq.gz"): |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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22 && cp '${pairstraight.file1}' ./mate1.fastq.gz |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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23 && gunzip ./mate1.fastq.gz |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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24 && cp '${pairstraight.file2}' ./mate2.fastq.gz |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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25 && gunzip ./mate2.fastq.gz |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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26 #else if $pairstraight.file1.is_of_type("fastq.bz2"): |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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27 && cp '${pairstraight.file1}' ./mate1.fastq.bz2 |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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28 && bzip2 -d ./mate1.fastq.bz2 |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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29 && cp '${pairstraight.file2}' ./mate2.fastq.bz2 |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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30 && bzip2 -d ./mate2.fastq.bz2 |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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31 #else: |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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32 && ln -s '${pairstraight.file1}' ./mate1.fastq |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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33 && ln -s '${pairstraight.file2}' ./mate2.fastq |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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34 #end if |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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35 #else: |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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36 #if $pairstraight.unmatedreads.is_of_type("fastq.gz"): |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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37 && cp '${pairstraight.unmatedreads}' ./unmate.fastq.gz |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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38 && gunzip ./unmate.fastq.gz |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
39 #else if $pairstraight.unmatedreads.is_of_type("fastq.bz2"): |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
40 && cp '${pairstraight.unmatedreads}' ./unmate.fastq.bz2 |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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41 && bzip2 -d unmate.fastq.bz2 |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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42 #else: |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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43 && ln -s '${pairstraight.unmatedreads}' ./unmate.fastq |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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44 #end if |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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45 #end if |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
46 |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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47 && ln -s '${tgmap}' ./alevinmap.tsv |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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48 && salmon alevin -l |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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49 #if $pairstraight.readselect == 'paired': |
10
e4c01dcece8b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
9
diff
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50 #if $pairstraight.libtype.strandedness == 'A' |
e4c01dcece8b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
9
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51 A |
e4c01dcece8b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
9
diff
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52 #else |
e4c01dcece8b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
9
diff
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53 ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness} |
e4c01dcece8b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
9
diff
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54 #end if |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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55 -i $index_path |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
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56 -1 ./mate1.fastq |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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57 -2 ./mate2.fastq |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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58 #else: |
10
e4c01dcece8b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
bgruening
parents:
9
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59 '${pairstraight.libtype.strandedness}' |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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60 -i $index_path |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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61 -r zcat ./unmate.fastq |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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62 #end if |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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63 -o ./output |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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64 -p "\${GALAXY_SLOTS:-4}" |
11
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
10
diff
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65 ${protocol_cond.protocol} |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
10
diff
changeset
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66 #if $protocol_cond.protocol == '--indropV2' |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
10
diff
changeset
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67 --w1 '${protocol_cond.w1}' |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
parents:
10
diff
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68 #end if |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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69 --tgMap ./alevinmap.tsv |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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70 #if $whitelist: |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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71 --whitelist '${optional.whitelist}' |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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72 #end if |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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73 #if $optional.numCellBootstraps: |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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74 --numCellBootstraps '${optional.numCellBootstraps}' |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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75 #end if |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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76 #if $optional.forceCells: |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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77 --forceCells '${optional.forceCells}' |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
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78 #end if |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
79 #if $optional.expectCells: |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff
changeset
|
80 --expectCells '${optional.expectCells}' |
908a8d400fa2
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81 #end if |
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82 #if $optional.mrna: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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83 --mrna '${optional.mrna}' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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84 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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85 #if $optional.rrna: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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86 --rrna '${optional.rrna}' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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87 #end if |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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88 #if $optional.keepCBFraction: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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89 --keepCBFraction '${optional.keepCBFraction}' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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90 #end if |
2
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91 ${optional.noDedup} |
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92 #if 'dumpBfh' in $output_files: |
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93 --dumpBfh |
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94 #end if |
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95 #if 'dumpFeatures' in $output_files: |
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96 --dumpFeatures |
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97 #end if |
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98 #if 'dumpUmiGraph' in $output_files: |
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99 --dumpUmiGraph |
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100 #end if |
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101 ${optional.dumpMtx} |
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102 #if $optional.maxNumBarcodes: |
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103 --maxNumBarcodes '${optional.maxNumBarcodes}' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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104 #end if |
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105 #if $optional.freqThreshold: |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
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106 --freqThreshold '${optional.freqThreshold}' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
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107 #end if |
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108 ## && gunzip output/alevin/quants_tier_mat.gz -> the output is binary file |
2
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109 #if $optional.dumpMtx != "--dumpMtx": |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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110 && python '$__tool_directory__/vpolo_convert.py' -m |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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111 #else: |
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112 && gunzip output/alevin/quants_mat.mtx.gz |
2
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113 #end if |
11
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114 #if 'dumpUmiGraph' in $output_files: |
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115 && python '$__tool_directory__/vpolo_convert.py' -u |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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116 && sh '$__tool_directory__/umiout.sh' |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
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117 #end if |
11
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118 ## those gzip file include binary datasets |
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119 ## #if $optional.numCellBootstraps: |
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120 ## && gunzip output/alevin/quants_mean_mat.gz |
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121 ## && gunzip output/alevin/quants_var_mat.gz |
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122 ## #end if |
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123 #if 'auxiliar_info' in $output_files |
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124 && tar -zcvf aux_info.tar.gz output/aux_info |
7
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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125 #end if |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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126 ]]> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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127 </command> |
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128 <inputs> |
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129 <expand macro="index"/> |
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130 <conditional name="pairstraight"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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131 <param name="readselect" label="Single or paired-end reads?" type="select"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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132 <option value="paired">Paired-end</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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133 <option value="unmated">Single-end</option> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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134 </param> |
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135 <when value="paired"> |
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136 <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 1" help="CB+UMI raw sequence file(s)"/> |
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137 <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 2" help="Read-sequence file(s)"/> |
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e4c01dcece8b
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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138 <expand macro="stranded_pe"/> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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139 </when> |
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140 <when value="unmated"> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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141 <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/> |
10
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f"
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142 <expand macro="stranded_se"/> |
0
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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143 </when> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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144 </conditional> |
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145 <conditional name="protocol_cond"> |
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146 <param name="protocol" type="select" label="Type of single-cell protocol" help="In cases where single-cell protocol supports variable length cellbarcodes, alevin adds nucleotide padding to make the lengths uniform. Furthermore, the padding scheme ensures that there are no collisions added in the process."> |
e661a3269313
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147 <option value="--dropseq">DropSeq Single Cell protocol</option> |
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148 <option value="--chromium">10x chromium v2 Single Cell protocol</option> |
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149 <option value="--chromiumV3">10x chromium v3 Single Cell protocol</option> |
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150 <option value="--gemcode">Gemcode v1 Single Cell protocol</option> |
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151 <option value="--celseq">CEL-Seq Single Cell protocol</option> |
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152 <option value="--celseq2">CEL-Seq2 Single Cell protocol</option> |
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153 <option value="--sciseq3">Sci-RNA-seq3 protocol</option> |
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154 <option value="--indropV2">InDrop v2 protocol</option> |
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155 <option value="--splitSeqV1">SplitSeqV1 protocol</option> |
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156 <option value="--splitSeqV2">SplitSeqV2 protocol</option> |
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157 </param> |
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158 <when value="--dropseq"/> |
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159 <when value="--chromium"/> |
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160 <when value="--chromiumV3"/> |
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161 <when value="--gemcode"/> |
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162 <when value="--celseq"/> |
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163 <when value="--celseq2"/> |
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164 <when value="--sciseq3"/> |
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165 <when value="--indropV2"> |
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166 <param argument="--w1" type="text" value="" label="w1 adapters"> |
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167 <sanitizer invalid_char=""> |
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168 <valid initial="string.letters"/> |
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169 </sanitizer> |
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170 <validator type="regex">[ATGC]+</validator> |
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171 </param> |
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172 </when> |
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173 <when value="--splitSeqV1"/> |
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174 <when value="--splitSeqV2"/> |
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175 </conditional> |
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176 <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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177 <param name="output_files" type="select" multiple="true" display="checkboxes" label="Extra output files"> |
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178 <option value="salmon_log">Salmon Quant log file</option> |
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179 <option value="fragment_length">Observed fragment length distribution</option> |
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180 <option value="auxiliar_info">Auxiliar info files</option> |
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181 <option value="dumpUmiGraph">Per cell level parsimonious Umi graph (--dumpUmiGraph)</option> |
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182 <option value="dumpFeatures">Features used by the CB classification and their counts at each cell level (--dumpFeatures)</option> |
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183 <option value="dumpBfh">Full CB-EC-UMI-count data-structure (--dumpBfh)</option> |
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184 <option value="commands">Commands info file</option> |
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185 </param> |
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186 <section name="optional" title="Advanced options" expanded="false"> |
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187 <param argument="--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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188 <param argument="--noDedup" type="boolean" truevalue="--noDedup" falsevalue="" checked="false" label="Skip deduplication step" 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."/> |
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189 <param argument="--mrna" type="data" format="tsv" optional="true" label="Mito-RNA genes file" 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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190 <param argument="--rrna" type="data" format="tsv" optional="true" label="Ribosomal RNA file" 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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191 <param argument="--dumpMtx" type="boolean" truevalue="--dumpMtx" falsevalue="" checked="false" label=" Dump cell v transcripts count matrix in MTX format" 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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192 <param argument="--forceCells" type="integer" min="0" optional="true" label="Number of cells" help="Explicitly specify the number of cells."/> |
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193 <param argument="--expectCells" type="integer" min="0" optional="true" label="Upper bound on expected number of cells" help="define a close upper bound on expected number of cells."/> |
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194 <param argument="--numCellBootstraps" type="integer" min="0" value="0" optional="true" label="Generate mean and variance for cell x gene matrix by boostrap" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/> |
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195 <param argument="--minScoreFraction" type="float" optional="true" label="Minimum allowed score for a mapping" 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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196 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."/> |
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197 <param argument="--keepCBFraction" type="float" min="0" max="1" optional="true" label="Fraction of cellular barcodes to keep" help="Use 1 to quantify all"/> |
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198 <param argument="--maxNumBarcodes" type="integer" min="0" value="100000" label="Maximum allowable limit to process the cell barcodes" help="Default: 100000"/> |
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199 <param argument="--freqThreshold" type="integer" min="0" value="10" optional="true" label="Minimum frequency for a barcode to be considered" help="Default: 10"/> |
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200 </section> |
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201 </inputs> |
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202 <outputs> |
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203 <data name="quants_mat_tsv" label="${tool.name} on ${on_string}: per-cell gene-count matrix (tabular)" format="txt" from_work_dir="quants_mat.tsv"> |
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204 <filter>optional["dumpMtx"] is not True</filter> |
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205 </data> |
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206 <data name="quants_mat_mtx" label="${tool.name} on ${on_string}: per-cell gene-count matrix (MTX)" format="mtx" from_work_dir="output/alevin/quants_mat.mtx"> |
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207 <filter>optional["dumpMtx"]</filter> |
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208 </data> |
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209 <data name="quants_mat_gz" label="${tool.name} on ${on_string}: per-cell level gene-count matrix (binary)" format="gz" from_work_dir="output/alevin/quants_mat.gz"/> |
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210 <data name="quants_mat_cols_txt" label="${tool.name} on ${on_string}: column headers (gene-ids)" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/> |
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211 <data name="quants_mat_rows_txt" label="${tool.name} on ${on_string}: row index (CB-ids)" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/> |
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212 <data name="quants_tier_mat" label="${tool.name} on ${on_string}: tier categorization" format="gz" from_work_dir="output/alevin/quants_tier_mat.gz"/> |
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213 <data name="featureDump_txt" label="${tool.name} on ${on_string}: cell-level information (featureDump)" format="txt" from_work_dir="output/alevin/featureDump.txt"/> |
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214 <data name="raw_cb_frequency_txt" label="${tool.name} on ${on_string}: raw CB classification frequencies" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt"> |
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215 <filter>output_files and 'dumpFeatures' in output_files</filter> |
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216 </data> |
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217 <data name="whitelist_txt" label="${tool.name} on ${on_string}: whitelist" format="txt" from_work_dir="output/alevin/whitelist.txt"/> |
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218 |
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219 <data name="auxiliar_files" label="${tool.name} on ${on_string}: auxiliar info files" format="tgz" from_work_dir="aux_info.tar.gz"> |
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220 <filter>output_files and 'auxiliar_info' in output_files</filter> |
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221 </data> |
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222 <data name="salmon_quant_log" format="txt" label="${tool.name} on ${on_string}: Salmon log file" from_work_dir="output/logs/salmon_quant.log"> |
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223 <filter>output_files and 'salmon_log' in output_files</filter> |
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224 </data> |
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225 <data name="cmd_info" label="${tool.name} on ${on_string}: command info (JSON)" format="json" from_work_dir="output/cmd_info.json"> |
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226 <filter>output_files and 'commands' in output_files</filter> |
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227 </data> |
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228 <data name="flenDist_txt" format="txt" label="${tool.name} on ${on_string}: observed fragment length distribution" from_work_dir="output/libParams/flenDist.txt"> |
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229 <filter>output_files and 'fragment_length' in output_files</filter> |
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230 </data> |
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231 <data name="bfh_txt" label="${tool.name} on ${on_string}: full CB-EC-UMI-count data-structure" format="txt" from_work_dir="output/alevin/bfh.txt"> |
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232 <filter>output_files and 'dumpBfh' in output_files</filter> |
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233 </data> |
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234 <data name="quants_mean_mat" label="${tool.name} on ${on_string}: count matrix mean file" format="gz" from_work_dir="output/alevin/quants_mean_mat.gz"> |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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235 <filter>optional["numCellBootstraps"]</filter> |
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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236 </data> |
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237 <data name="quants_var_mat" label="${tool.name} on ${on_string}: count matrix variance file" format="gz" from_work_dir="output/alevin/quants_var_mat.gz"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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238 <filter>optional["numCellBootstraps"]</filter> |
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239 </data> |
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240 <data name="quants_boot_rows_txt" label="${tool.name} on ${on_string}: bootstraps rows" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt"> |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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241 <filter>optional["numCellBootstraps"]</filter> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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242 </data> |
11
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243 <collection name="umigraphs" type="list" label="${tool.name} on ${on_string}: UMI graph PDFs"> |
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244 <filter>output_files and 'dumpUmiGraph' in output_files</filter> |
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245 <discover_datasets pattern="(?P<name>.+)\.pdf" format="pdf" directory="fixed"/> |
2
e53f19161c59
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
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246 </collection> |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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247 </outputs> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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248 <tests> |
11
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249 <test expect_num_outputs="8"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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250 <conditional name="refTranscriptSource"> |
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bgruening
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251 <param name="TranscriptSource" value="history"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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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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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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255 </conditional> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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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 <conditional name="protocol_cond"> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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264 <param name="protocol" value="--chromium"/> |
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265 </conditional> |
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266 <param name="tgmap" value="minitxp.tsv"/> |
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267 <param name="output_files" value="dumpFeatures"/> |
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268 <section name="optional"> |
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269 <param name="keepCBFraction" value="1"/> |
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270 <param name="freqThreshold" value="5"/> |
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271 <param name="dumpMtx" value="true"/> |
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272 </section> |
14
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273 <output name="quants_mat_mtx" file="alevin_mat_01.mtx" compare="sim_size" ftype="mtx"> |
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274 <assert_contents> |
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275 <has_text text="MatrixMarket" /> |
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276 <has_n_columns n="5" /> |
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277 <has_n_lines n="105" /> |
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278 </assert_contents> |
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279 </output> |
11
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280 </test> |
4
917f8e439160
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
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281 <test expect_num_outputs="11"> |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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282 <conditional name="refTranscriptSource"> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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283 <param name="TranscriptSource" value="history"/> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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284 <section name="s_index"> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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285 <param name="fasta" value="minitranscript.fa"/> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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286 </section> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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287 </conditional> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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288 <conditional name="pairstraight"> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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289 <param name="readselect" value="paired"/> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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290 <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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291 <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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292 <param name="orientation" value="I"/> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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293 <param name="strandedness" value="SR"/> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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294 </conditional> |
11
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295 <conditional name="protocol_cond"> |
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296 <param name="protocol" value="--chromium"/> |
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297 </conditional> |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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298 <param name="tgmap" value="minitxp.tsv"/> |
11
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299 <param name="output_files" value="dumpFeatures"/> |
8
04b494623f8e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
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300 <section name="optional"> |
04b494623f8e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
bgruening
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301 <param name="keepCBFraction" value="1"/> |
11
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302 <param name="numCellBootstraps" value="2"/> |
8
04b494623f8e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
bgruening
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303 <param name="freqThreshold" value="5"/> |
11
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304 <param name="dumpMtx" value="true"/> |
8
04b494623f8e
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f"
bgruening
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305 </section> |
14
c9944a2600f1
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306 <output name="quants_mat_mtx" file="alevin_mat_02.mtx" compare="sim_size" ftype="mtx" > |
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307 <assert_contents> |
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308 <has_text text="MatrixMarket" /> |
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309 <has_n_columns n="5" /> |
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310 <has_n_lines n="105" /> |
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bgruening
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311 </assert_contents> |
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bgruening
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312 </output> |
11
e661a3269313
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313 </test> |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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314 <test expect_num_outputs="8"> |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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315 <conditional name="refTranscriptSource"> |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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316 <param name="TranscriptSource" value="history"/> |
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317 <section name="s_index"> |
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318 <param name="fasta" value="minitranscript.fa"/> |
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319 </section> |
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320 </conditional> |
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321 <conditional name="pairstraight"> |
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322 <param name="readselect" value="paired"/> |
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323 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/> |
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324 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/> |
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325 <param name="orientation" value="I"/> |
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326 <param name="strandedness" value="SR"/> |
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327 </conditional> |
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328 <conditional name="protocol_cond"> |
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329 <param name="protocol" value="-\-indropV2"/> |
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330 <param name="w1" value="ATCAT"/> |
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331 </conditional> |
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332 <param name="tgmap" value="minitxp.tsv"/> |
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333 <param name="output_files" value="dumpFeatures"/> |
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334 <section name="optional"> |
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335 <param name="keepCBFraction" value="1"/> |
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336 <param name="freqThreshold" value="5"/> |
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337 <param name="dumpMtx" value="true"/> |
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338 </section> |
14
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339 <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" compare="sim_size" ftype="mtx"> |
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340 <assert_contents> |
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341 <has_text text="MatrixMarket" /> |
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342 <has_n_columns n="5" /> |
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343 <has_n_lines n="105" /> |
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344 </assert_contents> |
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345 </output> |
7
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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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346 </test> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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347 <test expect_num_outputs="14"> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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348 <conditional name="refTranscriptSource"> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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349 <param name="TranscriptSource" value="history"/> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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350 <section name="s_index"> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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351 <param name="fasta" value="minitranscript.fa"/> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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352 </section> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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353 </conditional> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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354 <conditional name="pairstraight"> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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355 <param name="readselect" value="paired"/> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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356 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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357 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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358 <param name="orientation" value="I"/> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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359 <param name="strandedness" value="SR"/> |
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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360 </conditional> |
11
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361 <conditional name="protocol_cond"> |
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362 <param name="protocol" value="--chromium"/> |
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363 </conditional> |
7
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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364 <param name="tgmap" value="minitxp.tsv"/> |
11
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365 <param name="output_files" value="dumpFeatures,salmon_log,fragment_length,auxiliar_info,dumpUmiGraph,dumpBfh,commands"/> |
7
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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366 <section name="optional"> |
11
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367 <param name="dumpMtx" value="true"/> |
7
ff78e9c7b0d8
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"
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368 </section> |
14
c9944a2600f1
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369 <output name="quants_mat_mtx" file="alevin_mat.mtx" compare="sim_size" ftype="mtx"> |
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370 <assert_contents> |
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371 <has_text text="MatrixMarket" /> |
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372 <has_n_columns n="5" /> |
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373 <has_n_lines n="17" /> |
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374 </assert_contents> |
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375 </output> |
11
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376 <output name="salmon_quant_log" ftype="txt"> |
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377 <assert_contents> |
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378 <has_text text="Index contained 322 targets"/> |
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379 <has_text text="Counted 14 total reads in the equivalence classes"/> |
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380 </assert_contents> |
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381 </output> |
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382 <output name="flenDist_txt" file="length_distribution.txt" ftype="txt"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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383 <output name="auxiliar_files" ftype="tgz"> |
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384 <assert_contents> |
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385 <has_size value="1898" delta="100"/> |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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386 </assert_contents> |
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387 </output> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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388 <output_collection name="umigraphs" type="list" count="14"> |
e661a3269313
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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389 <element name="AGTGGGATCTTAACCT"> |
e661a3269313
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390 <assert_contents> |
14
c9944a2600f1
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391 <has_size value="4661" delta="1000"/> |
11
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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392 </assert_contents> |
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393 </element> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
bgruening
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394 </output_collection> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042
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395 <output name="bfh_txt" file="full_data_structure.txt" ftype="txt"/> |
0
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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396 </test> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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397 </tests> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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|
398 <help><![CDATA[ |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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|
399 @salmonhelp@ |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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400 @alevinhelp@ |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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401 ]]></help> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
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402 <expand macro="citations"/> |
908a8d400fa2
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
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403 </tool> |