Mercurial > repos > bgruening > alevin

annotate alevin.xml @ 6:53d74155bb52 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649"
author bgruening
date Mon, 13 Jul 2020 17:14:54 -0400
parents 917f8e439160
children ff78e9c7b0d8
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
4
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
1 <tool id="alevin" name="Alevin" version="@VERSION@+galaxy1">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
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"
bgruening
parents:
diff changeset
3 <macros>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
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
5 </macros>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
6 <expand macro="requirements"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
7 <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 changeset
8 mkdir ./index
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
9 && mkdir ./output
3
0a5258e41227 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit cf916eb507ee224812b64663c1d6020eb59eb88c"
bgruening
parents: 2
diff changeset
10 #if $refTranscriptSource.TranscriptSource != "indexed":
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
11 && salmon index -i ./index
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
12 --kmerLen '${refTranscriptSource.s_index.kmer}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
13 --gencode
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
14 --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
15 #set $index_path = './index'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
16 #else
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
17 #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
18 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
19 #if $pairstraight.readselect == 'paired':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
20 #if $pairstraight.file1.is_of_type("fastq.gz"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
21 && cp '${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
22 && gunzip ./mate1.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
23 && 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
24 && gunzip ./mate2.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
25 #else if $pairstraight.file1.is_of_type("fastq.bz2"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
26 && cp '${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
27 && 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
28 && cp '${pairstraight.file2}' ./mate2.fastq.bz2
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
29 && bzip2 -d ./mate2.fastq.bz2
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
30 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
31 && ln -s '${pairstraight.file1}' ./mate1.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
32 && 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
33 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
34 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
35 #if $pairstraight.unmatedreads.is_of_type("fastq.gz"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
36 && cp '${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
37 && gunzip ./unmate.fastq.gz
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
38 #else if $pairstraight.unmatedreads.is_of_type("fastq.bz2"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
39 && cp '${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
40 && 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
41 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
42 && ln -s '${pairstraight.unmatedreads}' ./unmate.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
43 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
44 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
45
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
46 && ln -s '${tgmap}' ./alevinmap.tsv
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
47 && salmon alevin -l
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
48 #if $pairstraight.readselect == 'paired':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
49 ${pairstraight.orientation}${pairstraight.strandedness}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
50 -i $index_path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
51 -1 ./mate1.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
52 -2 ./mate2.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
53 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
54 '${pairstraight.strandedness}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
55 -i $index_path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
56 -r zcat ./unmate.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
57 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
58 -o ./output
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
59 -p "\${GALAXY_SLOTS:-4}"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
60 ${protocol}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
61 --tgMap ./alevinmap.tsv
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
62 #if $whitelist:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
63 --whitelist '${optional.whitelist}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
64 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
65 #if $optional.numCellBootstraps:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
66 --numCellBootstraps '${optional.numCellBootstraps}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
67 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
68 #if $optional.forceCells:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
69 --forceCells '${optional.forceCells}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
70 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
71 #if $optional.expectCells:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
72 --expectCells '${optional.expectCells}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
73 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
74 #if $optional.mrna:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
75 --mrna '${optional.mrna}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
76 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
77 #if $optional.rrna:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
78 --rrna '${optional.rrna}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
79 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
80 #if $optional.keepCBFraction:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
81 --keepCBFraction '${optional.keepCBFraction}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
82 #end if
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
83 ${optional.noDedup}
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
84 ${optional.dumpBfh}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
85 ${optional.dumpFeatures}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
86 ${optional.dumpUmiGraph}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
87 ${optional.dumpMtx}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
88 #if $optional.lowRegionMinNumBarcodes:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
89 --lowregionMinNumBarcodes '${optional.lowRegionMinNumBarcodes}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
90 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
91 #if $optional.maxNumBarcodes:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
92 --maxNumBarcodes '${optional.maxNumBarcodes}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
93 #end if
4
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
94 #if $optional.freqThreshold:
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
95 --freqThreshold '${optional.freqThreshold}'
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
96 #end if
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
97
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
98 #if $optional.dumpMtx != "--dumpMtx":
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
99 && python '$__tool_directory__/vpolo_convert.py' -m
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
100 #end if
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
101 #if $optional.dumpUmiGraph:
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
102 && python '$__tool_directory__/vpolo_convert.py' -u
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
103 && sh '$__tool_directory__/umiout.sh'
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
104 #end if
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
105 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
106 </command>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
107 <inputs>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
108 <expand macro="index"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
109 <conditional name="pairstraight">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
110 <param name="readselect" label="Single or paired-end reads?" type="select">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
111 <option value="paired">Paired-end</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
112 <option value="unmated">Single-end</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
113 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
114 <when value="paired">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
115 <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="CB+UMI raw sequence file(s)"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
116 <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" help="Read-sequence file(s)"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
117 <expand macro="orient"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
118 <expand macro="stranded"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
119 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
120 <when value="unmated">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
121 <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
122 <expand macro="stranded"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
123 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
124 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
125 <param name="protocol" type="select">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
126 <option value="--dropseq">DropSeq Single Cell protocol</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
127 <option value="--chromium">10x chromium v2 Single Cell protocol</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
128 <option value="--chromiumV3">10x chromium v3 Single Cell protocol</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
129 <option value="--gemcode">Gemcode v1 Single Cell protocol</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
130 <option value="--celseq">CEL-Seq Single Cell protocol</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
131 <option value="--celseq2">CEL-Seq2 Single Cell protocol</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
132 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
133 <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)."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
134 <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"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
135 <section name="optional" title="Optional commands" expanded="false">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
136 <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."/>
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
137 <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
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
138 <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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
139 <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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
140 <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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
141 <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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
142 <param name="dumpUmiGraph" type="boolean" truevalue="--dumpUmiGraph" falsevalue="" checked="false" help="Dump the per-cell level umi graph"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
143 <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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
144 <param name="forceCells" type="integer" optional="true" help="Explicitly specify the number of cells."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
145 <param name="expectCells" type="integer" optional="true" help="define a close upper bound on expected number of cells."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
146 <param name="numCellBootstraps" type="integer" optional="true" help="Performs certain number of bootstrap and generate the mean and variance of the count matrix"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
147 <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). 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
148 <param name="keepCBFraction" type="float" optional="true" help="Fraction of cellular barcodes to keep (Between 0 and 1)."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
149 <param name="lowRegionMinNumBarcodes" type="integer" optional="true" help="Minimum number of cell barcodes to use fo learning low confidence region (defaults to 200)"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
150 <param name="maxNumBarcodes" type="integer" optional="true" help="Maximum allowable limit to process the cell barcodes. Defaults to 100000"/>
4
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
151 <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"
bgruening
parents:
diff changeset
152 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
153 </inputs>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
154 <outputs>
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
155 <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"
bgruening
parents: 2
diff changeset
156 <filter>optional["dumpMtx"] is not True</filter>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
157 </data>
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
158 <data name="quants_mat.mtx.gz" label="quants_mat.mtx.gz" format="mtx" from_work_dir="output/alevin/quants_mat.mtx.gz">
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
159 <filter>optional["dumpMtx"]</filter>
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
160 </data>
4
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
161 <data name="raw_cb_frequency.txt" label="raw_cb_frequency.txt" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
162 <filter>optional["dumpFeatures"]</filter>
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
163 </data>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
164 <data name="quants_mat_cols.txt" label="quants_mat_cols.txt" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
165 <data name="quants_mat_rows.txt" label="quants_mat_rows.txt" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
166 <data name="quants_tier_mat.gz" label="quants_tier_mat.gz" format="mtx" from_work_dir="output/alevin/quants_tier_mat.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
167 <data name="alevin.log" label="alevin.log" format="txt" from_work_dir="output/alevin/alevin.log">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
168 <filter>allout</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
169 </data>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
170 <data name="featureDump.txt" label="featureDump.txt" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
171 <data name="whitelist.txt" label="whitelist.txt" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
172 <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"
bgruening
parents: 0
diff changeset
173 <filter>optional["dumpBfh"]</filter>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
174 </data>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
175 <data name="quants_mean_mat.gz" label="quants_mean_mat.gz" format="mtx" from_work_dir="output/alevin/quants_mean_mat.gz">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
176 <filter>optional["numCellBootstraps"]</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
177 </data>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
178 <data name="quants_var_mat.gz" label="quants_var_mat.gz" format="mtx" from_work_dir="output/alevin/quants_var_mat.gz">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
179 <filter>optional["numCellBootstraps"]</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
180 </data>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
181 <data name="quants_boot_rows.txt" label="quants_boot_rows.txt" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
182 <filter>optional["numCellBootstraps"]</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
183 </data>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
184 <data name="alevinmeta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/alevin_meta_info.json">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
185 <filter>allout</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
186 </data>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
187 <data name="ambig_info.tsv" format="tsv" label="ambig_info.tsv" from_work_dir="output/aux_info/ambig_info.tsv">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
188 <filter>allout</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
189 </data>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
190 <data name="meta_info.json" format="json" label="meta_info.json" from_work_dir="output/aux_info/meta_info.json">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
191 <filter>allout</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
192 </data>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
193 <data name="expected_bias.gz" format="txt" label="expected_bias.gz" from_work_dir="output/aux_info/fld.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
194 <data name="observed_bias.gz" format="txt" label="observed_bias.gz" from_work_dir="output/aux_info/observed_bias.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
195 <data name="observed_bias_3p.gz" format="txt" label="observed_bias_3p.gz" from_work_dir="output/aux_info/observed_bias_3p.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
196 <data name="flenDist.txt" format="txt" label="flenDist.txt" from_work_dir="output/libParams/flenDist.txt"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
197 <data name="salmon_quant.log" format="txt" label="salmon_quant.log" from_work_dir="output/logs/salmon_quant.log">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
198 <filter>allout</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
199 </data>
2
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
200 <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"
bgruening
parents: 0
diff changeset
201 <filter>optional["dumpUmiGraph"]</filter>
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612"
bgruening
parents: 0
diff changeset
202 <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"
bgruening
parents: 0
diff changeset
203 </collection>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
204 </outputs>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
205 <tests>
4
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
206 <test expect_num_outputs="11">
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
207 <conditional name="refTranscriptSource">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
208 <param name="TranscriptSource" value="history"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
209 <section name="s_index">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
210 <param name="fasta" value="minitranscript.fa"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
211 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
212 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
213 <conditional name="pairstraight">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
214 <param name="readselect" value="paired"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
215 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
216 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
217 <param name="orientation" value="I"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
218 <param name="strandedness" value="SR"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
219 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
220 <param name="protocol" value="--chromium"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
221 <param name="tgmap" value="minitxp.tsv"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
222 <param name="dumpMtx" value="Yes"/>
4
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
223 <param name="freqThreshold" value="5"/>
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
224 <param name="dumpFeatures" value="Yes"/>
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef"
bgruening
parents: 3
diff changeset
225 <param name="keepCBFraction" value="1"/>
0
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
226 <output name="quants_mat.mtx.gz" file="alevin_mat.mtx.gz" ftype="mtx" compare="sim_size"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
227 </test>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
228 </tests>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
229 <help><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
230 @salmonhelp@
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
231 @alevinhelp@
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
232 ]]></help>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
233 <expand macro="citations"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"
bgruening
parents:
diff changeset
234 </tool>