salmonquantmerge: macros.xml annotate

annotate macros.xml @ 5:cfb0849582e1 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit dee6a6f4aa8cbee9f81692fc6f3a2e4ad1f3abf6"

author	bgruening
date	Sat, 03 Oct 2020 18:22:17 +0000
parents	85b3dc9b6830
children	88c07fc4024c

rev	line source
0 43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	1 <macros>
4 85b3dc9b6830 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 3 diff changeset	2 <token name="@VERSION@">1.3.0</token>
0 43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	3 <token name="@GALAXY_VERSION@">galaxy0</token>
4 85b3dc9b6830 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 3 diff changeset	4 <token name="@IDX_VERSION@">q7</token>
0 43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	5 <xml name="requirements">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	6 <requirements>
4 85b3dc9b6830 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 3 diff changeset	7 <requirement type="package" version="@VERSION@">salmon</requirement>
3 f6e3a10a88e5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664" bgruening parents: 2 diff changeset	8 <requirement type="package" version="1.3">seqtk</requirement>
f6e3a10a88e5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664" bgruening parents: 2 diff changeset	9 <requirement type="package" version="1.10">samtools</requirement>
2 178ebdfe5a7e "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 1 diff changeset	10 <requirement type="package" version="0.2.0">vpolo</requirement>
4 85b3dc9b6830 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 3 diff changeset	11 <requirement type="package" version="1.0.3">pandas</requirement>
85b3dc9b6830 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 3 diff changeset	12 <requirement type="package" version="1.4.1">scipy</requirement>
0 43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	13 </requirements>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	14 </xml>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	15 <xml name="stranded">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	16 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	17 <option value="U" selected="True">Not stranded (U)</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	18 <option value="SF">read comes from the forward strand (SF)</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	19 <option value="SR">read comes from the reverse strand (SR)</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	20 </param>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	21 </xml>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	22 <xml name="orient">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	23 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	24 <option value="M">Mates are oriented in the same direction (M = matching)</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	25 <option value="O">Mates are oriented away from each other (O = outward)</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	26 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	27 </param>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	28 </xml>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	29 <xml name="index">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	30 <conditional name="refTranscriptSource">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	31 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	32 help="Built-ins were indexed using default options">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	33 <option value="indexed">Use a built-in index</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	34 <option value="history" selected="True">Use one from the history</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	35 </param>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	36 <when value="indexed">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	37 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	38 <options from_data_table="salmon_indexes_versioned">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	39 <filter type="sort_by" column="2"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	40 <filter type="static_value" column="4" value="@IDX_VERSION@" />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	41 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	42 </options>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	43 </param>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	44 </when> <!-- build-in -->
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	45 <when value="history">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	46 <section name="s_index" title="Salmon index" expanded="true">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	47 <param name="fasta" type="data" format="fasta" label="Transcripts fasta file"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	48 <param name="kmer" type="integer" value="31" label="Kmer length"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	49 <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	50 help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification), but will take longer to construct"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	51 </section>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	52 </when>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	53 </conditional>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	54 </xml>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	55 <xml name="reads">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	56 <section name="input" title="Data input" expanded="True">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	57 <conditional name="single_or_paired">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	58 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	59 <option value="single">Single-end</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	60 <option value="paired">Paired-end</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	61 <option value="paired_collection">Paired-end Dataset Collection</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	62 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	63 </param>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	64 <when value="single">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	65 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	66 <expand macro="stranded"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	67 </when>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	68 <when value="paired">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	69 <param name="input_mate1" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 1" help="FASTQ file." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	70 <param name="input_mate2" type="data" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="Mate pair 2" help="FASTQ file." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	71 <expand macro="orient"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	72 <expand macro="stranded"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	73 </when>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	74 <when value="paired_collection">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	75 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="Must be of datatype "fastqsanger" or "fasta"" />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	76 <expand macro="orient"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	77 <expand macro="stranded"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	78 </when>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	79 <when value="paired_interleaved">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	80 <param name="input_1" format="fastq,fasta,fastq.gz,fastq.bz2,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data" label="Interleaved FASTQ file" help="Must be of datatype "fastqsanger" or "fasta". --interleaved"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	81 <expand macro="orient"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	82 <expand macro="stranded"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	83 </when>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	84 </conditional>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	85 </section>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	86 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	87 <option value="quasi" selected="True">quasi</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	88 </param>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	89 <!--Salmon quant type select: reads-based or alignment-based-->
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	90 <param name="discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	91 label="Discard orphan quasi"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	92 help="Discard orphan mappings in quasi-mapping mode. If this flag is passed then only paired mappings will be considered toward quantification estimates. The default behavior is to consider orphan mappings if no valid paired mappings exist."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	93 <conditional name="validmap">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	94 <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	95 label="Validate mappings"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	96 help="Validate mappings using alignment-based verifcation. If this flag is passed, quasi-mappings will be validated to ensure that they could give rise to a reasonable alignment before they are further used for quantification."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	97 <when value="--validateMappings">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	98 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	99 label="Min Score Fraction"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	100 help="The fraction of the optimal possible alignment score that a mapping must achieve in order to be considered valid. Should be in (0,1]."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	101 <param name="maxMMPExtension" type="integer" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	102 label="Sets the maximum allowable MMP extension when collecting suffix array intervals to be used in chaining. This prevents MMPs from becoming too long, and potentially masking intervals that would uncover other good quasi-mappings for the read. This heuristic mimics the idea of the maximum mappable safe prefix (MMSP) in selective alignment. Setting a smaller value will potentially allow for more sensitive, but slower, mapping."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	103 <param name="matchScore" argument="--ma" type="integer" value="2"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	104 label="Match Score"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	105 help="The value given to a match between read and reference nucleotides in an alignment."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	106 <param name="mismatchPenalty" argument="--mp" type="integer" value="4"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	107 label="Mismatch Penalty"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	108 help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	109 <param name="gapOpenPenalty" argument="--go" type="integer" value="5"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	110 label="Gap Open Penalty"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	111 help="The value given to a gap opening in an alignment."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	112 <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	113 label="Gap Extension Penalty"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	114 help="The value given to a gap extension in an alignment."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	115 <param name="mimicBT2" type="boolean" truevalue="--mimicBT2" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	116 label="Mimic Bowtie 2"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	117 help=" Set flags to mimic parameters similar to Bowtie2 with --no-discordant and --no-mixed flags. This increases disallows dovetailing reads, and discards orphans. Note, this does not impose the very strict parameters assumed by RSEM+Bowtie2, like gapless alignments. For that behavior, use the --mimiStrictBT2 flag "/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	118 <param name="mimicStrictBT2" type="boolean" truevalue="--mimicStrictBT2" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	119 label="Mimic Strict Bowtie 2"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	120 help="Set flags to mimic the very strict parameters used by RSEM+Bowtie2. This increases --minScoreFraction to 0.8, disallows dovetailing reads, discards orphans, and disallows gaps in alignments."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	121 <param name="hardFilter" type="boolean" truevalue="--hardFilter" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	122 label="Hard Filter"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	123 help="Instead of weighting mappings by their alignment score, this flag will discard any mappings with sub-optimal alignment score. The default option of soft-filtering (i.e. weighting mappings by their alignment score) usually yields slightly more accurate abundance estimates but this flag may be desirable if you want more accurate 'naive' equivalence classes, rather than range factorized equivalence classes."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	124 </when>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	125 <when value=""/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	126 </conditional>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	127 <param name="consensusSlack" type="integer" optional="True" value="0"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	128 label="Consensus Slack"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	129 help="The amount of slack allowed in the quasi-mapping consensus mechanism. Normally, a transcript must cover all hits to be considered for mapping. If this is set to a value, X, greater than 0, then a transcript can fail to cover up to X hits before it is discounted as a mapping candidate. The default value of this option is 1 if --validateMappings is given and 0 otherwise."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	130 <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	131 <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	132 help="Attempt to recover the mates of orphaned reads. This uses edlib for orphan recovery, and so introduces some computational overhead, but it can improve sensitivity."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	133 <param name="writeMappings" type="boolean" truevalue="--writeMappings=./output/samout.sam" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	134 label="Write Mappings to Bam File"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	135 help="If this option is provided, then the quasi-mapping results will be written out in SAM-compatible format. By default, output will be directed to stdout, but an alternative file name can be provided instead"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	136 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	137 label="Consistent Hits"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	138 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	139 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	140 help="[Experimental]: The fraction of the read that must be covered by MMPs (of length >= 31) if this read is to be considered as 'mapped'. This may help to avoid 'spurious' mappings. A value of 0 (the default) denotes no coverage threshold (a single 31-mer can yield a mapping). Since coverage by exact matching, large, MMPs is a rather strict condition, this value should likely be set to something low, if used."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	141 </xml>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	142 <xml name="align">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	143 <param name="afile" type="data" format="bam" label="Alignment file"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	144 <param name="transcript" type="data" format="fasta,fa" label="Transcript file"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	145 <expand macro="stranded"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	146 <param name="discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	147 label="Discard orphans"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	148 help="Discard orphan alignments in the input. If this flag is passed, then only paired alignments will be considered toward quantification estimates. The default behavior is to consider orphan alignments if no valid paired mappings exist."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	149 <param name="noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	150 label="No Error Model"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	151 help="Turn off the alignment error model, which takes into account the the observed frequency of different types of mismatches / indels when computing the likelihood of a given alignment. Turning this off can speed up alignment-based salmon, but can harm quantification accuracy."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	152 <param name="numErrorBins" type="integer" optional="True" value="6"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	153 label="Number of Error Bins"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	154 help="The number of bins into which to divideeach read when learning and applying the error model. For example, a value of 10 would mean that effectively, a separate error model is learned and applied to each 10th of the read, whilea value of 3 would mean that a separate error model is applied to the read beginning (first third), middle (second third) and end (final third)."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	155 <param name="sampleOut" type="boolean" truevalue="--sampleOut" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	156 label="Sample out"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	157 help="Write a 'postSample.bam' file in the output directory that will sample the input alignments according to the estimated transcript abundances. If you're going to perform downstream analysis of the alignments with tools which don't, themselves, take fragment assignment ambiguity into account, you should use this output"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	158 <param name="sampleUnaligned" type="boolean" truevalue="--sampleUnaligned" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	159 label="Sample unaligned"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	160 help="In addition to sampling the aligned reads, also write the un-aligned reads to 'postSample.bam'."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	161 <param name="gencode" type="boolean" truevalue="--gencode" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	162 label="Gencode"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	163 help="This flag will expect the input transcript fasta to be in GENCODE format, and will split the transcript name at the first '\|' character. These reduced names will be used in the output and when looking for these transcripts in a gene to transcript GTF."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	164 </xml>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	165 <xml name="quantboth">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	166 <param name="geneMap" type="data" format="tabular,gff,gtf" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	167 label="File containing a mapping of transcripts to genes"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	168 help="If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	169 <param name="seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	170 label="Perform sequence-specific bias correction"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	171 <param name="gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	172 label="Perform fragment GC bias correction"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	173 <param name="incompatPrior" type="float" optional="True" min="0.0" max="1" value="0"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	174 help="Sets the prior probability that an alignment that disagrees with the specified library type (orientation and strandedness) results from the true fragment origin. Setting this to 0 specifies that alignments that disagree with the library type should be 'impossible', while setting it to 1 says that alignments that disagree with the library type are no less likely than those that do"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	175 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	176 label="Meta"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	177 help="If you're using Salmon on a metagenomic dataset, consider setting this flag to disable parts of the abundance estimation model that make less sense for metagenomic data."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	178 <!--Salmon quant advanced options: available to both kinds of quant-->
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	179 <section name="adv" title="Additional Options">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	180 <param name="skipQuant" type="boolean" truevalue="--skipQuant" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	181 label="skipQuant" help="Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	182 <param name="dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	183 label="Dump equivalence class counts"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	184 help="Dump the equivalence class counts that were computed during quasi-mapping."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	185 <param name="dumpEqWeights" type="boolean" truevalue="--dumpEqWeights" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	186 label="Dump equivalence class counts including rich weights"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	187 help="Includes 'rich' equivlance class weights in the output when equivalence class information is being dumped to file."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	188 <param name="minAssignedFrags" type="integer" optional="True" label="Minimum assigned fragments"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	189 help="The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	190 <param name="biasSpeedSamp" type="integer" value="5" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	191 label="The value at which the fragment length PMF is down-sampled when evaluating GC fragment bias." help="Larger values speed up effective length correction, but may decrease the fidelity of bias modeling results."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	192 <param name="fldMax" type="integer" value="1000" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	193 label="The maximum fragment length to consider when building the empirical distribution."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	194 <param name="fldMean" type="integer" value="250" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	195 label="The mean used in the fragment length distribution prior"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	196 help="If single end reads are being used for quantification, or there are an insufficient number of uniquely mapping reads when performing paired-end quantification to estimate the empirical fragment length distribution, then use this value to calculate effective lengths."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	197 <param name="fldSD" type="integer" value="25" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	198 label="Standard deviation"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	199 help="The standard deviation used in the fragment length distribution prior."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	200 <param name="forgettingFactor" type="float" value="0.65000000000000002" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	201 label="The forgetting factor used in the online learning schedule."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	202 help=" A smaller value results in quicker learning, but higher variance and may be unstable. A larger value results in slower learning but may be more stable. Value should be in the interval (0.5, 1.0]." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	203 <param name="initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	204 label="Initialization with uniform parameters"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	205 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	206 <param name="maxReadOcc" type="integer" value="100" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	207 label="Maximal read mapping occurence"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	208 help="Reads mapping to more than this many places won't be considered."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	209 <param name="noLengthCorrection" type="boolean" truevalue="--noLengthCorrection" falsevalue=""
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	210 label="No length correction"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	211 help="[experimental] : Entirely disables length correction when estimating the abundance of transcripts. This option can be used with protocols where one expects that fragments derive from their underlying targets without regard to that target's length (e.g. QuantSeq)"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	212 <param name="noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	213 label="Disable effective length correction"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	214 help="Disables effective length correction when computing the probability that a fragment was generated from a transcript. If this flag is passed in, the fragment length distribution is not taken into account when computing this probability."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	215 <param name="noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	216 label="Ignore fragment length distribution"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	217 help="[experimental] : Don't consider concordance with the learned fragment length distribution when trying to determine the probability that a fragment has originated from a specified location. Normally, Fragments with unlikely lengths will be assigned a smaller relative probability than those with more likely lengths. When this flag is passed in, the observed fragment length has no effect on that fragment's a priori probability." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	218 <param name="noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	219 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	220 help="This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	221 <param name="numBiasSamples" type="integer" value="2000000" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	222 label="Number of fragment mappings to use when learning the sequence-specific bias model."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	223 <param name="numAuxModelSamples" type="integer" value="5000000" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	224 label="The first numAuxModelSamples are used to train the auxiliary model parameters."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	225 help="(e.g. fragment length distribution, bias, etc.). After ther first numAuxModelSamples observations the auxiliary model parameters will be assumed to have converged and will be fixed." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	226 <param name="numPreAuxModelSamples" type="integer" value="5000" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	227 label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	228 help=" The purpose of ignoring the auxiliary models for the first numPreAuxModelSamples observations is to avoid applying these models before thier parameters have been learned sufficiently well." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	229 <param name="useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	230 label="Use the traditional EM algorithm for optimization in the batch passes."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	231 help=""/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	232 <param name="rangeFactorizationBins" type="integer" value="0" label="Range of factorization bins"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	233 help="Factorizes the likelihood used in quantification by adopting a new notionof equivalence classes based on the conditional probabilities with which fragments are generated from different transcripts. This is a more fine-grained factorization than the normal rich equivalence classes. The default value (0) corresponds to the standard rich equivalence classes, and larger values imply a more fine-grained factorization. If range factorization is enabled, a common value to select for this parameter is 4."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	234 <param name="numGibbsSamples" type="integer" value="0" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	235 label="Number of Gibbs sampling rounds to perform."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	236 help="" />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	237 <param name="noGammaDraw" type="boolean" truevalue="--noGammaDraw" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	238 label="No gamma draw"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	239 help="This switch will disable drawing transcript fractions from a Gamma distribution during Gibbs sampling. In this case the sampler does not account for shot-noise, but only assignment ambiguity"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	240 <param name="numBootstraps" type="integer" value="0" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	241 label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	242 help="" />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	243 <param name="bootstrapReproject" type="boolean" truevalue="--bootstrapReproject" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	244 label="Bootstrap reproject"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	245 help="This switch will learn the parameter distribution from the bootstrapped counts for each sample, but will reproject those parameters onto the original equivalence class counts."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	246 <param name="thinningFactor" type="integer" value="16" optional="true" label="Thinning factor"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	247 help="Number of steps to discard for every sample kept from the Gibbs chain. The larger this number, the less chance that subsequent samples are auto-correlated, but the slower sampling becomes."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	248 <param name="perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	249 label="The prior will be interpreted as a transcript-level prior."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	250 help="either the default or the argument provided via --vbPrior" />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	251 <param name="sigDigits" type="integer" value="3"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	252 label="Significant Digits"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	253 help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	254 <param name="vbPrior" type="float" value="1.0000000000000001e-05" optional="True"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	255 label="The prior that will be used in the VBEM algorithm."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	256 help="This is interpreted as a per-nucleotide prior, unless the --perTranscriptPrior flag is also given, in which case this is used as a transcript-level prior." />
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	257 <param name="writeOrphanLinks" type="boolean" truevalue="--writeOrphanLinks" falsevalue="" checked="False" label="Write orphan links"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	258 help="Write the transcripts that are linked by orphaned reads."/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	259 <param name="writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	260 label="Write the names of un-mapped reads to the file unmapped_names.txt."
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	261 help=""/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	262 </section>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	263 </xml>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	264 <xml name="quantmerge">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	265 <repeat name="quantfiles" title="Quant file and names">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	266 <param name="quants" type="data" format="tsv,tabular"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	267 label="Salmon quant tabular output files"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	268 <param name="names" type="text" label="One-word sample names" optional="True"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	269 </repeat>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	270 <param name="column" type="select" label="Columns"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	271 help="Name of columns that will be merged in the output file">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	272 <option value="len" selected="True">Length</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	273 <option value="elen">Effective Length</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	274 <option value="tpm">Transcripts per Million</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	275 <option value="numreads">NumReads</option>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	276 </param>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	277 <param name="genes" type="boolean" truevalue="--genes" falsevalue="" checked="False"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	278 label="Genes" help="Use gene quantifications instead of transcript"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	279 <param name="missing" type="integer" label="Missing" optional="True" help="The value of missing values"/>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	280 </xml>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	281 <xml name="citations">
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	282 <citations>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	283 <citation type="doi">10.1186/s13059-019-1670-y</citation>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	284 <citation type="doi">10.1038/nmeth.4197</citation>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	285 </citations>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	286 </xml>
3 f6e3a10a88e5 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664" bgruening parents: 2 diff changeset	287 <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
0 43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	288 <token name="@indexing@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	289 mkdir ./index &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	290 mkdir ./output &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	291 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	292 salmon index -i ./index
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	293 --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	294 --gencode
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	295 --transcripts '${quant_type.refTranscriptSource.s_index.fasta}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	296 &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	297 #set $index_path = './index'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	298 #else
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	299 #set $index_path = $quant_type.refTranscriptSource.index.fields.path
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	300 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	301 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	302 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	303 <token name="@salreads@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	304 #set compressed = 'no'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	305 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	306 #if $quant_type.input.single_or_paired.input_singles.ext == 'fasta':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	307 #set $ext = 'fasta'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	308 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	309 #if $quant_type.input.single_or_paired.input_singles.is_of_type("fastq.gz", "fastqsanger.gz"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	310 #set compressed = 'GZ'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	311 #else if $quant_type.input.single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	312 #set compressed = 'BZ2'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	313 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	314 #set $ext = 'fastq'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	315 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	316 ln -s $quant_type.input.single_or_paired.input_singles ./single.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	317 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	318 #if $quant_type.input.single_or_paired.input_mate1.ext == 'fasta':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	319 #set $ext = 'fasta'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	320 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	321 #if $quant_type.input.single_or_paired.input_mate1.is_of_type("fastq.gz", "fastqsanger.gz"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	322 #set compressed = 'GZ'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	323 #else if $quant_type.input.single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	324 #set compressed = 'BZ2'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	325 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	326 #set $ext = 'fastq'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	327 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	328 ln -s $quant_type.input.single_or_paired.input_mate1 ./mate1.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	329 ln -s $quant_type.input.single_or_paired.input_mate2 ./mate2.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	330 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_collection':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	331 #if $quant_type.input.single_or_paired.input_1.forward.ext == 'fasta':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	332 #set $ext = 'fasta'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	333 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	334 #if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastq.gz", "fastqsanger.gz"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	335 #set compressed = 'GZ'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	336 #else if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	337 #set compressed = 'BZ2'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	338 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	339 #set $ext = 'fastq'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	340 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	341 ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	342 ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	343 #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	344 #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	345 #set $ext = 'fasta'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	346 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	347 #if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.gz", "fastqsanger.gz"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	348 #set compressed = 'GZ'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	349 #else if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	350 #set compressed = 'BZ2'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	351 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	352 #set $ext = 'fastq'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	353 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	354 ln -s '$quant_type.input.single_or_paired.input_1' ./mate1.$ext &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	355 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	356 #if $geneMap:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	357 ln -s '$geneMap' ./geneMap.${geneMap.ext} &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	358 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	359
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	360 salmon quant
4 85b3dc9b6830 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 3 diff changeset	361 --index '$index_path'
0 43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	362 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	363 --libType ${quant_type.input.single_or_paired.strandedness}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	364 #if $compressed == 'GZ':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	365 --unmatedReads <(zcat < ./single.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	366 #else if $compressed == 'BZ2':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	367 --unmatedReads <(bzcat < ./single.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	368 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	369 --unmatedReads ./single.$ext
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	370 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	371 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	372 --libType '${quant_type.input.single_or_paired.orientation}${quant_type.input.single_or_paired.strandedness}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	373 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	374 #if $compressed == 'BZ2':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	375 --mates1 <(bzcat < ./mate1.$ext \| seqtk seq -1)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	376 --mates2 <(bzcat < ./mate1.$ext \| seqtk seq -2)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	377 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	378 --mates1 <(seqtk seq -1 ./mate1.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	379 --mates2 <(seqtk seq -2 ./mate1.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	380 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	381 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	382 #if $compressed == 'GZ':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	383 --mates1 <(zcat < ./mate1.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	384 --mates2 <(zcat < ./mate2.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	385 #else if $compressed == 'BZ2':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	386 --mates1 <(bzcat < ./mate1.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	387 --mates2 <(bzcat < ./mate2.$ext)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	388 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	389 --mates1 ./mate1.$ext
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	390 --mates2 ./mate2.$ext
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	391 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	392 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	393 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	394 --threads "\${GALAXY_SLOTS:-4}"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	395 ${quant_type.discardOrphansQuasi}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	396 ${quant_type.validmap.validateMappings}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	397 #if $quant_type.validmap.validateMappings:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	398 #if $quant_type.validmap.minScoreFraction:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	399 --minScoreFraction '${quant_type.validmap.minScoreFraction}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	400 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	401 #if $quant_type.validmap.maxMMPExtension:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	402 --maxMMPExtension '${quant_type.validmap.maxMMPExtension}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	403 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	404 #if $quant_type.validmap.matchScore:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	405 --ma '${$quant_type.validmap.matchScore}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	406 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	407 #if $quant_type.validmap.mismatchPenalty:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	408 --mp '${$quant_type.validmap.mismatchPenalty}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	409 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	410 #if $quant_type.validmap.gapOpenPenalty:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	411 --go '${$quant_type.validmap.gapOpenPenalty}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	412 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	413 #if $quant_type.validmap.gapExtensionPenalty:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	414 --ge '${$quant_type.validmap.gapExtensionPenalty}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	415 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	416 ${$quant_type.validmap.mimicBT2}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	417 ${$quant_type.validmap.mimicStrictBT2}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	418 ${$quant_type.validmap.hardFilter}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	419 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	420 #if $quant_type.consensusSlack:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	421 --consensusSlack '${quant_type.consensusSlack}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	422 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	423 ${quant_type.dovetail}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	424 ${quant_type.recoverOrphans}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	425 ${quant_type.writeMappings}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	426 ${quant_type.consistentHits}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	427 #if $quant_type.quasiCoverage:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	428 --quasiCoverage '${quant_type.quasiCoverage}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	429 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	430 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	431 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	432 <token name="@salalign@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	433 #if $geneMap:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	434 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	435 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	436 salmon quant
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	437 -t '${quant_type.transcript}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	438 -l '${quant_type.strandedness}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	439 -a '${quant_type.afile}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	440 --threads "\${GALAXY_SLOTS:-4}"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	441 ${quant_type.discardOrphans}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	442 ${quant_type.noErrorModel}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	443 #if $quant_type.numErrorBins:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	444 --numErrorBins '${quant_type.numErrorBins}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	445 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	446 ${quant_type.sampleOut}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	447 ${quant_type.sampleUnaligned}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	448 ${quant_type.gencode}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	449 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	450 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	451 <token name="@salquant@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	452 #if $geneMap:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	453 --geneMap ./geneMap.${geneMap.ext}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	454 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	455
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	456 ##Further basic options##
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	457
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	458 ${seqBias}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	459 ${gcBias}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	460 --incompatPrior '${incompatPrior}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	461 ${meta}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	462
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	463 ##Advanced options##
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	464
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	465 ${adv.skipQuant}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	466 ${adv.dumpEq}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	467 ${adv.dumpEqWeights}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	468 #if $adv.minAssignedFrags:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	469 --minAssignedFrags '${adv.minAssignedFrags}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	470 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	471 #if $adv.biasSpeedSamp:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	472 --biasSpeedSamp '${adv.biasSpeedSamp}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	473 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	474 #if $adv.fldMax:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	475 --fldMax '${adv.fldMax}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	476 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	477 #if $adv.fldMean:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	478 --fldMean '${adv.fldMean}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	479 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	480 #if $adv.fldSD:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	481 --fldSD '${adv.fldSD}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	482 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	483 #if $adv.forgettingFactor:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	484 --forgettingFactor '${adv.forgettingFactor}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	485 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	486 ${adv.initUniform}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	487 #if str($adv.maxReadOcc):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	488 --maxReadOcc '${adv.maxReadOcc}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	489 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	490 ${adv.noLengthCorrection}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	491 ${adv.noEffectiveLengthCorrection}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	492 ${adv.noFragLengthDist}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	493 ${adv.noBiasLengthThreshold}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	494 #if str($adv.numBiasSamples):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	495 --numBiasSamples '${adv.numBiasSamples}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	496 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	497 #if str($adv.numAuxModelSamples):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	498 --numAuxModelSamples '${adv.numAuxModelSamples}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	499 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	500 #if str($adv.numPreAuxModelSamples):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	501 --numPreAuxModelSamples '${adv.numPreAuxModelSamples}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	502 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	503 ${adv.useEM}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	504 #if $adv.rangeFactorizationBins:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	505 --rangeFactorizationBins '${adv.rangeFactorizationBins}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	506 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	507 #if str($adv.numGibbsSamples):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	508 --numGibbsSamples '${adv.numGibbsSamples}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	509 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	510 ${adv.noGammaDraw}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	511 #if str($adv.numBootstraps):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	512 --numBootstraps '${adv.numBootstraps}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	513 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	514 ${adv.bootstrapReproject}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	515 #if $adv.thinningFactor:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	516 --thinningFactor '${adv.thinningFactor}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	517 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	518 ${adv.perTranscriptPrior}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	519 --sigDigits '${adv.sigDigits}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	520 #if $adv.vbPrior:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	521 --vbPrior '${adv.vbPrior}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	522 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	523 ${adv.writeOrphanLinks}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	524 ${adv.writeUnmappedNames}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	525 -o ./output
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	526 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	527 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	528 <token name="@qmerge@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	529 #import re
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	530
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	531 #for $counter, $input_data in enumerate($quantfiles):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	532 rank_of_series=$counter
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	533 mkdir ${counter}.quantmerge &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	534 ln -s $input_data.quants ${counter}.quantmerge/quant.sf &&
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	535 #end for
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	536 salmon quantmerge
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	537 --quants *.quantmerge
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	538 --names
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	539 #for $counter, $input_data in enumerate($quantfiles):
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	540 #if $input_data.names and re.sub(' ', '', '$input_data.names') != '':
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	541 '${input_data.names}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	542 #else:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	543 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_data.quants.element_identifier))
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	544 "$identifier"
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	545 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	546 #end for
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	547 --column '${column}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	548 ${genes}
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	549 #if $missing:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	550 --missing '${missing}'
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	551 #end if
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	552 -o qmergeout.tab
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	553 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	554 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	555 <token name="@salmonhelp@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	556 Salmon is a lightweight method for quantifying transcript abundance from RNA–seq reads, combining a dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	557
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	558 The salmon package contains 4 tools:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	559
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	560 * Index: creates a salmon index
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	561
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	562 * Quant: quantifies a sample (Reads or mapping-based)
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	563
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	564 * Alevin: Single-cell analysis
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	565
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	566 * Quantmerge: Merges multiple quantifications into a single file
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	567
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	568 Galaxy divides these four into three separate tools in the IUC toolshed:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	569
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	570 * Salmon quant
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	571
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	572 * Salmon quantmerge
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	573
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	574 * Alevin
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	575 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	576 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	577 <token name="@alevinhelp@"><![CDATA[
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	578 Alevin is a tool — integrated with the salmon software — that introduces a family of algorithms for quantification and analysis of 3’ tagged-end single-cell sequencing data. Currently alevin supports the following two major droplet based single-cell protocols:
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	579
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	580 * Drop-seq
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	581
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	582 * 10x-Chromium v1/2/3
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	583
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	584 Alevin works under the same indexing scheme (as salmon) for the reference, and consumes the set of FASTA/Q files(s) containing the Cellular Barcode(CB) + Unique Molecule identifier (UMI) in one read file and the read sequence in the other. Given just the transcriptome and the raw read files, alevin generates a cell-by-gene count matrix (in a fraction of the time compared to other tools).
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	585
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	586 Alevin works in two phases. In the first phase it quickly parses the read file containing the CB and UMI information to generate the frequency distribution of all the observed CBs, and creates a lightweight data-structure for fast-look up and correction of the CB. In the second round, alevin utilizes the read-sequences contained in the files to map the reads to the transcriptome, identify potential PCR/sequencing errors in the UMIs, and performs hybrid de-duplication while accounting for UMI collisions. Finally, a post-abundance estimation CB whitelisting procedure is done and a cell-by-gene count matrix is generated.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	587
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	588 For further information regarding the tool and its optional parameters, visit the `Alevin <https://salmon.readthedocs.io/en/latest/alevin.html?highlight=alevin>`__ and `Salmon <https://salmon.readthedocs.io/en/latest/index.html>`__ wikis.
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	589 ]]>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	590 </token>
43658f594542 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	591 </macros>

Mercurial > repos > bgruening > salmonquantmerge

annotate macros.xml @ 5:cfb0849582e1 draft