alevin: alevin.xml annotate

annotate alevin.xml @ 13:e32b215b7c04 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26cff0d523671ac1e56ba7ef4965861b387727e8

author	bgruening
date	Fri, 23 Jun 2023 17:03:24 +0000
parents	e661a3269313
children	c9944a2600f1

rev	line source
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	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 changeset	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	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':
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 9 diff changeset	49 #if $pairstraight.libtype.strandedness == 'A'
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 9 diff changeset	50 A
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 9 diff changeset	51 #else
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 9 diff changeset	52 ${pairstraight.libtype.orientation}${pairstraight.libtype.strandedness}
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 9 diff changeset	53 #end if
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	54 -i $index_path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	55 -1 ./mate1.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	56 -2 ./mate2.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	57 #else:
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 9 diff changeset	58 '${pairstraight.libtype.strandedness}'
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	59 -i $index_path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	60 -r zcat ./unmate.fastq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	61 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	62 -o ./output
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	63 -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 changeset	64 ${protocol_cond.protocol}
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	65 #if $protocol_cond.protocol == '--indropV2'
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	66 --w1 '${protocol_cond.w1}'
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	67 #end if
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	68 --tgMap ./alevinmap.tsv
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	69 #if $whitelist:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	70 --whitelist '${optional.whitelist}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	71 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	72 #if $optional.numCellBootstraps:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	73 --numCellBootstraps '${optional.numCellBootstraps}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	74 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	75 #if $optional.forceCells:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	76 --forceCells '${optional.forceCells}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	77 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	78 #if $optional.expectCells:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	79 --expectCells '${optional.expectCells}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	80 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	81 #if $optional.mrna:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	82 --mrna '${optional.mrna}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	83 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	84 #if $optional.rrna:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	85 --rrna '${optional.rrna}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	86 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	87 #if $optional.keepCBFraction:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	88 --keepCBFraction '${optional.keepCBFraction}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	89 #end if
2 e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 0 diff changeset	90 ${optional.noDedup}
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	91 #if 'dumpBfh' in $output_files:
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	92 --dumpBfh
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	93 #end if
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	94 #if 'dumpFeatures' in $output_files:
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	95 --dumpFeatures
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	96 #end if
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	97 #if 'dumpUmiGraph' in $output_files:
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	98 --dumpUmiGraph
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	99 #end if
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	100 ${optional.dumpMtx}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	101 #if $optional.maxNumBarcodes:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	102 --maxNumBarcodes '${optional.maxNumBarcodes}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	103 #end if
4 917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef" bgruening parents: 3 diff changeset	104 #if $optional.freqThreshold:
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef" bgruening parents: 3 diff changeset	105 --freqThreshold '${optional.freqThreshold}'
917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef" bgruening parents: 3 diff changeset	106 #end if
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	107 ## && gunzip output/alevin/quants_tier_mat.gz -> the output is binary file
2 e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 0 diff changeset	108 #if $optional.dumpMtx != "--dumpMtx":
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 0 diff changeset	109 && python '$__tool_directory__/vpolo_convert.py' -m
7 ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	110 #else:
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	111 && gunzip output/alevin/quants_mat.mtx.gz
2 e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 0 diff changeset	112 #end if
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	113 #if 'dumpUmiGraph' in $output_files:
2 e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 0 diff changeset	114 && python '$__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	115 && 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	116 #end if
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	117 ## those gzip file include binary datasets
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	118 ## #if $optional.numCellBootstraps:
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	119 ## && gunzip output/alevin/quants_mean_mat.gz
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	120 ## && gunzip output/alevin/quants_var_mat.gz
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	121 ## #end if
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	122 #if 'auxiliar_info' in $output_files
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	123 && tar -zcvf aux_info.tar.gz output/aux_info
7 ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	124 #end if
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	125 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	126 </command>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	127 <inputs>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	128 <expand macro="index"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	129 <conditional name="pairstraight">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	130 <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	131 <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	132 <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	133 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	134 <when value="paired">
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	135 <param name="file1" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 1" help="CB+UMI raw sequence file(s)"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	136 <param name="file2" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Mate pair 2" help="Read-sequence file(s)"/>
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 9 diff changeset	137 <expand macro="stranded_pe"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	138 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	139 <when value="unmated">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	140 <param name="unmatedreads" type="data" format="fastq,fastq.gz,fastqsanger.gz,fastq.bz2" label="Unmated reads files"/>
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 9 diff changeset	141 <expand macro="stranded_se"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	142 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	143 </conditional>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	144 <conditional name="protocol_cond">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	145 <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 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	146 <option value="--dropseq">DropSeq Single Cell protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	147 <option value="--chromium">10x chromium v2 Single Cell protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	148 <option value="--chromiumV3">10x chromium v3 Single Cell protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	149 <option value="--gemcode">Gemcode v1 Single Cell protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	150 <option value="--celseq">CEL-Seq Single Cell protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	151 <option value="--celseq2">CEL-Seq2 Single Cell protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	152 <option value="--sciseq3">Sci-RNA-seq3 protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	153 <option value="--indropV2">InDrop v2 protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	154 <option value="--splitSeqV1">SplitSeqV1 protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	155 <option value="--splitSeqV2">SplitSeqV2 protocol</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	156 </param>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	157 <when value="--dropseq"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	158 <when value="--chromium"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	159 <when value="--chromiumV3"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	160 <when value="--gemcode"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	161 <when value="--celseq"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	162 <when value="--celseq2"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	163 <when value="--sciseq3"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	164 <when value="--indropV2">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	165 <param argument="--w1" type="text" value="" label="w1 adapters">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	166 <sanitizer invalid_char="">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	167 <valid initial="string.letters"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	168 </sanitizer>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	169 <validator type="regex">[ATGC]+</validator>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	170 </param>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	171 </when>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	172 <when value="--splitSeqV1"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	173 <when value="--splitSeqV2"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	174 </conditional>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	175 <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)."/>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	176 <param name="output_files" type="select" multiple="true" display="checkboxes" label="Extra output files">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	177 <option value="salmon_log">Salmon Quant log file</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	178 <option value="fragment_length">Observed fragment length distribution</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	179 <option value="auxiliar_info">Auxiliar info files</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	180 <option value="dumpUmiGraph">Per cell level parsimonious Umi graph (--dumpUmiGraph)</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	181 <option value="dumpFeatures">Features used by the CB classification and their counts at each cell level (--dumpFeatures)</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	182 <option value="dumpBfh">Full CB-EC-UMI-count data-structure (--dumpBfh)</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	183 <option value="commands">Commands info file</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	184 </param>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	185 <section name="optional" title="Advanced options" expanded="false">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	186 <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."/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	187 <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."/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	188 <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."/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	189 <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."/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	190 <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."/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	191 <param argument="--forceCells" type="integer" min="0" optional="true" label="Number of cells" help="Explicitly specify the number of cells."/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	192 <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."/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	193 <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"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	194 <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).
7 ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	195 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."/>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	196 <param argument="--keepCBFraction" type="float" min="0" max="1" optional="true" label="Fraction of cellular barcodes to keep" help="Use 1 to quantify all"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	197 <param argument="--maxNumBarcodes" type="integer" min="0" value="100000" label="Maximum allowable limit to process the cell barcodes" help="Default: 100000"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	198 <param argument="--freqThreshold" type="integer" min="0" value="10" optional="true" label="Minimum frequency for a barcode to be considered" help="Default: 10"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	199 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	200 </inputs>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	201 <outputs>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	202 <data name="quants_mat_tsv" label="${tool.name} on ${on_string}: per-cell gene-count matrix (tabular)" format="txt" from_work_dir="quants_mat.tsv">
3 0a5258e41227 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit cf916eb507ee224812b64663c1d6020eb59eb88c" bgruening parents: 2 diff changeset	203 <filter>optional["dumpMtx"] is not True</filter>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	204 </data>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	205 <data name="quants_mat_mtx" label="${tool.name} on ${on_string}: per-cell gene-count matrix (MTX)" format="mtx" from_work_dir="output/alevin/quants_mat.mtx">
2 e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 0 diff changeset	206 <filter>optional["dumpMtx"]</filter>
e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 0 diff changeset	207 </data>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	208 <data name="quants_mat_gz" label="${tool.name} on ${on_string}: per-cell level gene-count matrix (binary)" format="gz" from_work_dir="output/alevin/quants_mat.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	209 <data name="quants_mat_cols_txt" label="${tool.name} on ${on_string}: column headers (gene-ids)" format="txt" from_work_dir="output/alevin/quants_mat_cols.txt"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	210 <data name="quants_mat_rows_txt" label="${tool.name} on ${on_string}: row index (CB-ids)" format="txt" from_work_dir="output/alevin/quants_mat_rows.txt"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	211 <data name="quants_tier_mat" label="${tool.name} on ${on_string}: tier categorization" format="gz" from_work_dir="output/alevin/quants_tier_mat.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	212 <data name="featureDump_txt" label="${tool.name} on ${on_string}: cell-level information (featureDump)" format="txt" from_work_dir="output/alevin/featureDump.txt"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	213 <data name="raw_cb_frequency_txt" label="${tool.name} on ${on_string}: raw CB classification frequencies" format="txt" from_work_dir="output/alevin/raw_cb_frequency.txt">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	214 <filter>output_files and 'dumpFeatures' in output_files</filter>
4 917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef" bgruening parents: 3 diff changeset	215 </data>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	216 <data name="whitelist_txt" label="${tool.name} on ${on_string}: whitelist" format="txt" from_work_dir="output/alevin/whitelist.txt"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	217
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	218 <data name="auxiliar_files" label="${tool.name} on ${on_string}: auxiliar info files" format="tgz" from_work_dir="aux_info.tar.gz">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	219 <filter>output_files and 'auxiliar_info' in output_files</filter>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	220 </data>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	221 <data name="salmon_quant_log" format="txt" label="${tool.name} on ${on_string}: Salmon log file" from_work_dir="output/logs/salmon_quant.log">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	222 <filter>output_files and 'salmon_log' in output_files</filter>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	223 </data>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	224 <data name="cmd_info" label="${tool.name} on ${on_string}: command info (JSON)" format="json" from_work_dir="output/cmd_info.json">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	225 <filter>output_files and 'commands' in output_files</filter>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	226 </data>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	227 <data name="flenDist_txt" format="txt" label="${tool.name} on ${on_string}: observed fragment length distribution" from_work_dir="output/libParams/flenDist.txt">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	228 <filter>output_files and 'fragment_length' in output_files</filter>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	229 </data>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	230 <data name="bfh_txt" label="${tool.name} on ${on_string}: full CB-EC-UMI-count data-structure" format="txt" from_work_dir="output/alevin/bfh.txt">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	231 <filter>output_files and 'dumpBfh' in output_files</filter>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	232 </data>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	233 <data name="quants_mean_mat" label="${tool.name} on ${on_string}: count matrix mean file" format="gz" from_work_dir="output/alevin/quants_mean_mat.gz">
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	234 <filter>optional["numCellBootstraps"]</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	235 </data>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	236 <data name="quants_var_mat" label="${tool.name} on ${on_string}: count matrix variance file" format="gz" from_work_dir="output/alevin/quants_var_mat.gz">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	237 <filter>optional["numCellBootstraps"]</filter>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	238 </data>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	239 <data name="quants_boot_rows_txt" label="${tool.name} on ${on_string}: bootstraps rows" format="txt" from_work_dir="output/alevin/quants_boot_rows.txt">
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	240 <filter>optional["numCellBootstraps"]</filter>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	241 </data>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	242 <collection name="umigraphs" type="list" label="${tool.name} on ${on_string}: UMI graph PDFs">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	243 <filter>output_files and 'dumpUmiGraph' in output_files</filter>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	244 <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 parents: 0 diff changeset	245 </collection>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	246 </outputs>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	247 <tests>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	248 <test expect_num_outputs="8">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	249 <conditional name="refTranscriptSource">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	250 <param name="TranscriptSource" value="history"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	251 <section name="s_index">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	252 <param name="fasta" value="minitranscript.fa"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	253 </section>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	254 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	255 <conditional name="pairstraight">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	256 <param name="readselect" value="paired"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	257 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	258 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	259 <param name="orientation" value="I"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	260 <param name="strandedness" value="SR"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	261 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	262 <conditional name="protocol_cond">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	263 <param name="protocol" value="--chromium"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	264 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	265 <param name="tgmap" value="minitxp.tsv"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	266 <param name="output_files" value="dumpFeatures"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	267 <section name="optional">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	268 <param name="keepCBFraction" value="1"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	269 <param name="freqThreshold" value="5"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	270 <param name="dumpMtx" value="true"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	271 </section>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	272 <output name="quants_mat_mtx" file="alevin_mat_01.mtx" ftype="mtx" sort="true"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	273 </test>
4 917f8e439160 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 5dfee8ad03865f59c3e1ac9dd5865fd40e4616ef" bgruening parents: 3 diff changeset	274 <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	275 <conditional name="refTranscriptSource">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	276 <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	277 <section name="s_index">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	278 <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	279 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	280 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	281 <conditional name="pairstraight">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	282 <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	283 <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	284 <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	285 <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	286 <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	287 </conditional>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	288 <conditional name="protocol_cond">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	289 <param name="protocol" value="--chromium"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	290 </conditional>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	291 <param name="tgmap" value="minitxp.tsv"/>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	292 <param name="output_files" value="dumpFeatures"/>
8 04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f" bgruening parents: 7 diff changeset	293 <section name="optional">
04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f" bgruening parents: 7 diff changeset	294 <param name="keepCBFraction" value="1"/>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	295 <param name="numCellBootstraps" value="2"/>
8 04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f" bgruening parents: 7 diff changeset	296 <param name="freqThreshold" value="5"/>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	297 <param name="dumpMtx" value="true"/>
8 04b494623f8e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 515548aaa4b79af78c6ffc6bd55f72ee9504d30f" bgruening parents: 7 diff changeset	298 </section>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	299 <output name="quants_mat_mtx" file="alevin_mat_02.mtx" ftype="mtx" sort="true"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	300 </test>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	301 <test expect_num_outputs="8">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	302 <conditional name="refTranscriptSource">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	303 <param name="TranscriptSource" value="history"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	304 <section name="s_index">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	305 <param name="fasta" value="minitranscript.fa"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	306 </section>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	307 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	308 <conditional name="pairstraight">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	309 <param name="readselect" value="paired"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	310 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	311 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	312 <param name="orientation" value="I"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	313 <param name="strandedness" value="SR"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	314 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	315 <conditional name="protocol_cond">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	316 <param name="protocol" value="-\-indropV2"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	317 <param name="w1" value="ATCAT"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	318 </conditional>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	319 <param name="tgmap" value="minitxp.tsv"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	320 <param name="output_files" value="dumpFeatures"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	321 <section name="optional">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	322 <param name="keepCBFraction" value="1"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	323 <param name="freqThreshold" value="5"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	324 <param name="dumpMtx" value="true"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	325 </section>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	326 <output name="quants_mat_mtx" file="alevin_mat_indropV2.mtx" ftype="mtx" sort="true"/>
7 ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	327 </test>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	328 <test expect_num_outputs="14">
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	329 <conditional name="refTranscriptSource">
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	330 <param name="TranscriptSource" value="history"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	331 <section name="s_index">
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	332 <param name="fasta" value="minitranscript.fa"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	333 </section>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	334 </conditional>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	335 <conditional name="pairstraight">
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	336 <param name="readselect" value="paired"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	337 <param name="file1" value="fastqs/moreminifastq1.fastq.gz"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	338 <param name="file2" value="fastqs/moreminifastq2.fastq.gz"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	339 <param name="orientation" value="I"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	340 <param name="strandedness" value="SR"/>
ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	341 </conditional>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	342 <conditional name="protocol_cond">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	343 <param name="protocol" value="--chromium"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	344 </conditional>
7 ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	345 <param name="tgmap" value="minitxp.tsv"/>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	346 <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" bgruening parents: 4 diff changeset	347 <section name="optional">
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	348 <param name="dumpMtx" value="true"/>
7 ff78e9c7b0d8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6" bgruening parents: 4 diff changeset	349 </section>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	350 <output name="quants_mat_mtx" file="alevin_mat.mtx" ftype="mtx" sort="true"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	351 <output name="salmon_quant_log" ftype="txt">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	352 <assert_contents>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	353 <has_text text="Index contained 322 targets"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	354 <has_text text="Counted 14 total reads in the equivalence classes"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	355 </assert_contents>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	356 </output>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	357 <output name="flenDist_txt" file="length_distribution.txt" ftype="txt"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	358 <output name="auxiliar_files" ftype="tgz">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	359 <assert_contents>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	360 <has_size value="1898" delta="100"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	361 </assert_contents>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	362 </output>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	363 <output_collection name="umigraphs" type="list" count="14">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	364 <element name="AGTGGGATCTTAACCT">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	365 <assert_contents>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	366 <has_size value="4017" delta="1000"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	367 </assert_contents>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	368 </element>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	369 </output_collection>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	370 <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 parents: diff changeset	371 </test>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	372 </tests>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	373 <help><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	374 @salmonhelp@
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	375 @alevinhelp@
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	376 ]]></help>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	377 <expand macro="citations"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	378 </tool>

Mercurial > repos > bgruening > alevin

annotate alevin.xml @ 13:e32b215b7c04 draft