alevin: macros.xml annotate

annotate macros.xml @ 0:908a8d400fa2 draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3"

author	bgruening
date	Mon, 09 Sep 2019 11:12:51 -0400
parents
children	c0ea43315baf

rev	line source
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	1 <macros>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	2 <token name="@VERSION@">0.14.1</token>
908a8d400fa2 "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>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	4 <token name="@IDX_VERSION@">q5</token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	5 <xml name="requirements">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	6 <requirements>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	7 <requirement type="package" version="1.0.6">bzip2</requirement>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	8 <requirement type="package" version="1.2">seqtk</requirement>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	9 <requirement type="package" version="0.14.1">salmon</requirement>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	10 <requirement type="package" version="1.9">samtools</requirement>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	11 </requirements>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	12 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	13 <xml name="stranded">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	14 <param name="strandedness" type="select" label="Specify the strandedness of the reads">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	15 <option value="U" selected="True">Not stranded (U)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	16 <option value="SF">read comes from the forward strand (SF)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	17 <option value="SR">read comes from the reverse strand (SR)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	18 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	19 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	20 <xml name="orient">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	21 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	22 <option value="M">Mates are oriented in the same direction (M = matching)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	23 <option value="O">Mates are oriented away from each other (O = outward)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	24 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	25 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	26 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	27 <xml name="index">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	28 <conditional name="refTranscriptSource">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	29 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	30 help="Built-ins were indexed using default options">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	31 <option value="indexed">Use a built-in index</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	32 <option value="history" selected="True">Use one from the history</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	33 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	34 <when value="indexed">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	35 <param name="index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	36 <options from_data_table="salmon_indexes_versioned">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	37 <filter type="sort_by" column="2"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	38 <filter type="static_value" column="4" value="@IDX_VERSION@" />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	39 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	40 </options>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	41 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	42 </when> <!-- build-in -->
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	43 <when value="history">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	44 <section name="s_index" title="Salmon index" expanded="true">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	45 <param name="fasta" type="data" format="fasta" label="Transcripts fasta file"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	46 <param name="kmer" type="integer" value="31" label="Kmer length"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	47 <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	48 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"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	49 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	50 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	51 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	52 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	53 <xml name="reads">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	54 <section name="input" title="Data input" expanded="True">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	55 <conditional name="single_or_paired">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	56 <param name="single_or_paired_opts" type="select" label="Is this library mate-paired?">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	57 <option value="single">Single-end</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	58 <option value="paired">Paired-end</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	59 <option value="paired_collection">Paired-end Dataset Collection</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	60 <option value="paired_interleaved">Paired-end data from single interleaved dataset</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	61 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	62 <when value="single">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	63 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	64 <expand macro="stranded"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	65 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	66 <when value="paired">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	67 <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." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	68 <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." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	69 <expand macro="orient"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	70 <expand macro="stranded"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	71 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	72 <when value="paired_collection">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	73 <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"" />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	74 <expand macro="orient"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	75 <expand macro="stranded"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	76 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	77 <when value="paired_interleaved">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	78 <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"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	79 <expand macro="orient"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	80 <expand macro="stranded"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	81 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	82 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	83 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	84 <param argument="--type" type="select" label="Type of index" help="When using quasi, orphaned reads will be considered when performing lightweight-alignment.">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	85 <option value="quasi" selected="True">quasi</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	86 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	87 <!--Salmon quant type select: reads-based or alignment-based-->
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	88 <param name="discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	89 label="Discard orphan quasi"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	90 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	91 <conditional name="validmap">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	92 <param name="validateMappings" type="boolean" truevalue="--validateMappings" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	93 label="Validate mappings"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	94 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	95 <when value="--validateMappings">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	96 <param name="minScoreFraction" type="float" value="0.65" min="0.0" max="0.99"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	97 label="Min Score Fraction"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	98 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]."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	99 <param name="maxMMPExtension" type="integer" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	100 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	101 <param name="matchScore" argument="--ma" type="integer" value="2"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	102 label="Match Score"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	103 help="The value given to a match between read and reference nucleotides in an alignment."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	104 <param name="mismatchPenalty" argument="--mp" type="integer" value="4"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	105 label="Mismatch Penalty"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	106 help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	107 <param name="gapOpenPenalty" argument="--go" type="integer" value="5"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	108 label="Gap Open Penalty"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	109 help="The value given to a gap opening in an alignment."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	110 <param name="gapExtensionPenalty" argument="--ge" type="integer" value="3"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	111 label="Gap Extension Penalty"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	112 help="The value given to a gap extension in an alignment."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	113 <param name="mimicBT2" type="boolean" truevalue="--mimicBT2" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	114 label="Mimic Bowtie 2"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	115 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 "/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	116 <param name="mimicStrictBT2" type="boolean" truevalue="--mimicStrictBT2" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	117 label="Mimic Strict Bowtie 2"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	118 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	119 <param name="hardFilter" type="boolean" truevalue="--hardFilter" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	120 label="Hard Filter"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	121 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	122 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	123 <when value=""/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	124 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	125 <param name="consensusSlack" type="integer" optional="True" value="0"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	126 label="Consensus Slack"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	127 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	128 <param name="dovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="False" help="Allow dovetail mappings"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	129 <param name="recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	130 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	131 <param name="writeMappings" type="boolean" truevalue="--writeMappings=./output/samout.sam" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	132 label="Write Mappings to Bam File"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	133 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"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	134 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	135 label="Consistent Hits"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	136 help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	137 <param name="quasiCoverage" type="integer" optional="True" label="Quasi Coverage"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	138 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	139 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	140 <xml name="align">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	141 <param name="afile" type="data" format="bam" label="Alignment file"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	142 <param name="transcript" type="data" format="fasta,fa" label="Transcript file"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	143 <expand macro="stranded"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	144 <param name="discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	145 label="Discard orphans"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	146 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	147 <param name="noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	148 label="No Error Model"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	149 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	150 <param name="numErrorBins" type="integer" optional="True" value="6"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	151 label="Number of Error Bins"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	152 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)."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	153 <param name="sampleOut" type="boolean" truevalue="--sampleOut" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	154 label="Sample out"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	155 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"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	156 <param name="sampleUnaligned" type="boolean" truevalue="--sampleUnaligned" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	157 label="Sample unaligned"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	158 help="In addition to sampling the aligned reads, also write the un-aligned reads to 'postSample.bam'."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	159 <param name="gencode" type="boolean" truevalue="--gencode" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	160 label="Gencode"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	161 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	162 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	163 <xml name="quantboth">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	164 <param name="geneMap" type="data" format="tabular,gff,gtf" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	165 label="File containing a mapping of transcripts to genes"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	166 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	167 <param name="seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	168 label="Perform sequence-specific bias correction"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	169 <param name="gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	170 label="Perform fragment GC bias correction"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	171 <param name="incompatPrior" type="float" optional="True" min="0.0" max="1" value="0"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	172 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"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	173 <param name="meta" type="boolean" truevalue="--meta" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	174 label="Meta"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	175 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	176 <!--Salmon quant advanced options: available to both kinds of quant-->
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	177 <section name="adv" title="Additional Options">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	178 <param name="skipQuant" type="boolean" truevalue="--skipQuant" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	179 label="skipQuant" help="Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	180 <param name="dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	181 label="Dump equivalence class counts"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	182 help="Dump the equivalence class counts that were computed during quasi-mapping."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	183 <param name="dumpEqWeights" type="boolean" truevalue="--dumpEqWeights" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	184 label="Dump equivalence class counts including rich weights"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	185 help="Includes 'rich' equivlance class weights in the output when equivalence class information is being dumped to file."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	186 <param name="minAssignedFrags" type="integer" optional="True" label="Minimum assigned fragments"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	187 help="The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	188 <param name="biasSpeedSamp" type="integer" value="5" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	189 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	190 <param name="fldMax" type="integer" value="1000" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	191 label="The maximum fragment length to consider when building the empirical distribution."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	192 <param name="fldMean" type="integer" value="250" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	193 label="The mean used in the fragment length distribution prior"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	194 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	195 <param name="fldSD" type="integer" value="25" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	196 label="Standard deviation"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	197 help="The standard deviation used in the fragment length distribution prior."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	198 <param name="forgettingFactor" type="float" value="0.65000000000000002" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	199 label="The forgetting factor used in the online learning schedule."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	200 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]." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	201 <param name="initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	202 label="Initialization with uniform parameters"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	203 help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	204 <param name="maxReadOcc" type="integer" value="100" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	205 label="Maximal read mapping occurence"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	206 help="Reads mapping to more than this many places won't be considered."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	207 <param name="noLengthCorrection" type="boolean" truevalue="--noLengthCorrection" falsevalue=""
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	208 label="No length correction"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	209 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)"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	210 <param name="noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	211 label="Disable effective length correction"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	212 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	213 <param name="noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	214 label="Ignore fragment length distribution"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	215 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." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	216 <param name="noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	217 label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	218 help="This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	219 <param name="numBiasSamples" type="integer" value="2000000" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	220 label="Number of fragment mappings to use when learning the sequence-specific bias model."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	221 <param name="numAuxModelSamples" type="integer" value="5000000" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	222 label="The first numAuxModelSamples are used to train the auxiliary model parameters."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	223 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." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	224 <param name="numPreAuxModelSamples" type="integer" value="5000" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	225 label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	226 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." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	227 <param name="useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	228 label="Use the traditional EM algorithm for optimization in the batch passes."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	229 help=""/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	230 <param name="rangeFactorizationBins" type="integer" value="0" label="Range of factorization bins"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	231 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	232 <param name="numGibbsSamples" type="integer" value="0" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	233 label="Number of Gibbs sampling rounds to perform."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	234 help="" />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	235 <param name="noGammaDraw" type="boolean" truevalue="--noGammaDraw" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	236 label="No gamma draw"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	237 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"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	238 <param name="numBootstraps" type="integer" value="0" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	239 label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	240 help="" />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	241 <param name="bootstrapReproject" type="boolean" truevalue="--bootstrapReproject" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	242 label="Bootstrap reproject"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	243 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	244 <param name="thinningFactor" type="integer" value="16" optional="true" label="Thinning factor"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	245 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."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	246 <param name="perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	247 label="The prior will be interpreted as a transcript-level prior."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	248 help="either the default or the argument provided via --vbPrior" />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	249 <param name="sigDigits" type="integer" value="3"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	250 label="Significant Digits"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	251 help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	252 <param name="vbPrior" type="float" value="1.0000000000000001e-05" optional="True"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	253 label="The prior that will be used in the VBEM algorithm."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	254 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." />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	255 <param name="writeOrphanLinks" type="boolean" truevalue="--writeOrphanLinks" falsevalue="" checked="False" label="Write orphan links"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	256 help="Write the transcripts that are linked by orphaned reads."/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	257 <param name="writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	258 label="Write the names of un-mapped reads to the file unmapped_names.txt."
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	259 help=""/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	260 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	261 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	262 <xml name="quantmerge">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	263 <repeat name="quantfiles" title="Quant file and names">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	264 <param name="quants" type="data" format="tsv,tabular"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	265 label="Salmon quant tabular output files"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	266 <param name="names" type="text" label="One-word sample names" optional="True"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	267 </repeat>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	268 <param name="column" type="select" label="Columns"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	269 help="Name of columns that will be merged in the output file">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	270 <option value="len" selected="True">Length</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	271 <option value="elen">Effective Length</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	272 <option value="tpm">Transcripts per Million</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	273 <option value="numreads">NumReads</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	274 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	275 <param name="genes" type="boolean" truevalue="--genes" falsevalue="" checked="False"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	276 label="Genes" help="Use gene quantifications instead of transcript"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	277 <param name="missing" type="integer" label="Missing" optional="True" help="The value of missing values"/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	278 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	279 <xml name="citations">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	280 <citations>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	281 <citation type="doi">10.1186/s13059-019-1670-y</citation>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	282 <citation type="doi">10.1038/nmeth.4197</citation>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	283 </citations>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	284 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	285 <token name="@indexing@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	286 mkdir ./index &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	287 mkdir ./output &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	288 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	289 salmon index -i ./index
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	290 --kmerLen '${quant_type.refTranscriptSource.s_index.kmer}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	291 --gencode
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	292 --transcripts '${quant_type.refTranscriptSource.s_index.fasta}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	293 &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	294 #set $index_path = './index'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	295 #else
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	296 #set $index_path = $quant_type.refTranscriptSource.index.fields.path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	297 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	298 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	299 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	300 <token name="@salreads@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	301 #set compressed = 'no'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	302 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	303 #if $quant_type.input.single_or_paired.input_singles.ext == 'fasta':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	304 #set $ext = 'fasta'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	305 #else:
908a8d400fa2 "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.is_of_type("fastq.gz", "fastqsanger.gz"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	307 #set compressed = 'GZ'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	308 #else if $quant_type.input.single_or_paired.input_singles.is_of_type("fastq.bz2", "fastqsanger.bz2"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	309 #set compressed = 'BZ2'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	310 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	311 #set $ext = 'fastq'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	312 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	313 ln -s $quant_type.input.single_or_paired.input_singles ./single.$ext &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	314 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	315 #if $quant_type.input.single_or_paired.input_mate1.ext == 'fasta':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	316 #set $ext = 'fasta'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	317 #else:
908a8d400fa2 "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.is_of_type("fastq.gz", "fastqsanger.gz"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	319 #set compressed = 'GZ'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	320 #else if $quant_type.input.single_or_paired.input_mate1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	321 #set compressed = 'BZ2'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	322 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	323 #set $ext = 'fastq'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	324 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	325 ln -s $quant_type.input.single_or_paired.input_mate1 ./mate1.$ext &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	326 ln -s $quant_type.input.single_or_paired.input_mate2 ./mate2.$ext &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	327 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_collection':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	328 #if $quant_type.input.single_or_paired.input_1.forward.ext == 'fasta':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	329 #set $ext = 'fasta'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	330 #else:
908a8d400fa2 "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.is_of_type("fastq.gz", "fastqsanger.gz"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	332 #set compressed = 'GZ'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	333 #else if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastq.bz2", "fastqsanger.bz2"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	334 #set compressed = 'BZ2'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	335 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	336 #set $ext = 'fastq'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	337 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	338 ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	339 ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	340 #else if '$quant_type.input.single_or_paired.single_or_paired_opts' == 'paired_interleaved':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	341 #if $quant_type.input.single_or_paired.input_1.ext == 'fasta':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	342 #set $ext = 'fasta'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	343 #else:
908a8d400fa2 "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.is_of_type("fastq.gz", "fastqsanger.gz"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	345 #set compressed = 'GZ'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	346 #else if $quant_type.input.single_or_paired.input_1.is_of_type("fastq.bz2", "fastqsanger.bz2"):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	347 #set compressed = 'BZ2'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	348 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	349 #set $ext = 'fastq'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	350 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	351 ln -s '$quant_type.input.single_or_paired.input_1' ./mate1.$ext &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	352 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	353 #if $geneMap:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	354 ln -s '$geneMap' ./geneMap.${geneMap.ext} &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	355 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	356
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	357 salmon quant
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	358 --index $index_path
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	359 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	360 --libType ${quant_type.input.single_or_paired.strandedness}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	361 #if $compressed == 'GZ':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	362 --unmatedReads <(zcat < ./single.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	363 #else if $compressed == 'BZ2':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	364 --unmatedReads <(bzcat < ./single.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	365 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	366 --unmatedReads ./single.$ext
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	367 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	368 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	369 --libType '${quant_type.input.single_or_paired.orientation}${quant_type.input.single_or_paired.strandedness}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	370 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	371 #if $compressed == 'BZ2':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	372 --mates1 <(bzcat < ./mate1.$ext \| seqtk seq -1)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	373 --mates2 <(bzcat < ./mate1.$ext \| seqtk seq -2)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	374 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	375 --mates1 <(seqtk seq -1 ./mate1.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	376 --mates2 <(seqtk seq -2 ./mate1.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	377 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	378 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	379 #if $compressed == 'GZ':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	380 --mates1 <(zcat < ./mate1.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	381 --mates2 <(zcat < ./mate2.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	382 #else if $compressed == 'BZ2':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	383 --mates1 <(bzcat < ./mate1.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	384 --mates2 <(bzcat < ./mate2.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	385 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	386 --mates1 ./mate1.$ext
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	387 --mates2 ./mate2.$ext
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	388 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	389 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	390 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	391 --threads "\${GALAXY_SLOTS:-4}"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	392 ${quant_type.discardOrphansQuasi}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	393 ${quant_type.validmap.validateMappings}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	394 #if $quant_type.validmap.validateMappings:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	395 #if $quant_type.validmap.minScoreFraction:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	396 --minScoreFraction '${quant_type.validmap.minScoreFraction}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	397 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	398 #if $quant_type.validmap.maxMMPExtension:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	399 --maxMMPExtension '${quant_type.validmap.maxMMPExtension}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	400 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	401 #if $quant_type.validmap.matchScore:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	402 --ma '${$quant_type.validmap.matchScore}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	403 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	404 #if $quant_type.validmap.mismatchPenalty:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	405 --mp '${$quant_type.validmap.mismatchPenalty}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	406 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	407 #if $quant_type.validmap.gapOpenPenalty:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	408 --go '${$quant_type.validmap.gapOpenPenalty}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	409 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	410 #if $quant_type.validmap.gapExtensionPenalty:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	411 --ge '${$quant_type.validmap.gapExtensionPenalty}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	412 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	413 ${$quant_type.validmap.mimicBT2}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	414 ${$quant_type.validmap.mimicStrictBT2}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	415 ${$quant_type.validmap.hardFilter}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	416 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	417 #if $quant_type.consensusSlack:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	418 --consensusSlack '${quant_type.consensusSlack}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	419 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	420 ${quant_type.dovetail}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	421 ${quant_type.recoverOrphans}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	422 ${quant_type.writeMappings}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	423 ${quant_type.consistentHits}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	424 #if $quant_type.quasiCoverage:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	425 --quasiCoverage '${quant_type.quasiCoverage}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	426 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	427 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	428 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	429 <token name="@salalign@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	430 #if $geneMap:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	431 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	432 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	433 salmon quant
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	434 -t '${quant_type.transcript}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	435 -l '${quant_type.strandedness}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	436 -a '${quant_type.afile}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	437 --threads "\${GALAXY_SLOTS:-4}"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	438 ${quant_type.discardOrphans}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	439 ${quant_type.noErrorModel}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	440 #if $quant_type.numErrorBins:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	441 --numErrorBins '${quant_type.numErrorBins}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	442 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	443 ${quant_type.sampleOut}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	444 ${quant_type.sampleUnaligned}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	445 ${quant_type.gencode}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	446 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	447 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	448 <token name="@salquant@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	449 #if $geneMap:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	450 --geneMap ./geneMap.${geneMap.ext}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	451 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	452
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	453 ##Further basic options##
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	454
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	455 ${seqBias}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	456 ${gcBias}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	457 --incompatPrior '${incompatPrior}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	458 ${meta}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	459
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	460 ##Advanced options##
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	461
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	462 ${adv.skipQuant}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	463 ${adv.dumpEq}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	464 ${adv.dumpEqWeights}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	465 #if $adv.minAssignedFrags:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	466 --minAssignedFrags '${adv.minAssignedFrags}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	467 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	468 #if $adv.biasSpeedSamp:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	469 --biasSpeedSamp '${adv.biasSpeedSamp}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	470 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	471 #if $adv.fldMax:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	472 --fldMax '${adv.fldMax}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	473 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	474 #if $adv.fldMean:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	475 --fldMean '${adv.fldMean}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	476 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	477 #if $adv.fldSD:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	478 --fldSD '${adv.fldSD}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	479 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	480 #if $adv.forgettingFactor:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	481 --forgettingFactor '${adv.forgettingFactor}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	482 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	483 ${adv.initUniform}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	484 #if str($adv.maxReadOcc):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	485 --maxReadOcc '${adv.maxReadOcc}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	486 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	487 ${adv.noLengthCorrection}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	488 ${adv.noEffectiveLengthCorrection}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	489 ${adv.noFragLengthDist}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	490 ${adv.noBiasLengthThreshold}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	491 #if str($adv.numBiasSamples):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	492 --numBiasSamples '${adv.numBiasSamples}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	493 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	494 #if str($adv.numAuxModelSamples):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	495 --numAuxModelSamples '${adv.numAuxModelSamples}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	496 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	497 #if str($adv.numPreAuxModelSamples):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	498 --numPreAuxModelSamples '${adv.numPreAuxModelSamples}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	499 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	500 ${adv.useEM}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	501 #if $adv.rangeFactorizationBins:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	502 --rangeFactorizationBins '${adv.rangeFactorizationBins}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	503 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	504 #if str($adv.numGibbsSamples):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	505 --numGibbsSamples '${adv.numGibbsSamples}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	506 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	507 ${adv.noGammaDraw}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	508 #if str($adv.numBootstraps):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	509 --numBootstraps '${adv.numBootstraps}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	510 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	511 ${adv.bootstrapReproject}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	512 #if $adv.thinningFactor:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	513 --thinningFactor '${adv.thinningFactor}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	514 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	515 ${adv.perTranscriptPrior}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	516 --sigDigits '${adv.sigDigits}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	517 #if $adv.vbPrior:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	518 --vbPrior '${adv.vbPrior}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	519 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	520 ${adv.writeOrphanLinks}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	521 ${adv.writeUnmappedNames}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	522 -o ./output
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	523 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	524 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	525 <token name="@qmerge@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	526 #import re
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	527
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	528 #for $counter, $input_data in enumerate($quantfiles):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	529 rank_of_series=$counter
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	530 mkdir ${counter}.quantmerge &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	531 ln -s $input_data.quants ${counter}.quantmerge/quant.sf &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	532 #end for
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	533 salmon quantmerge
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	534 --quants *.quantmerge
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	535 --names
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	536 #for $counter, $input_data in enumerate($quantfiles):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	537 #if $input_data.names and re.sub(' ', '', '$input_data.names') != '':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	538 '${input_data.names}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	539 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	540 #set $identifier=re.sub('[^\w\-\s]', '_', str($input_data.quants.element_identifier))
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	541 "$identifier"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	542 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	543 #end for
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	544 --column '${column}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	545 ${genes}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	546 #if $missing:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	547 --missing '${missing}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	548 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	549 -o qmergeout.tab
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	550 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	551 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	552 <token name="@salmonhelp@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	553 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.
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	554
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	555 The salmon package contains 4 tools:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	556
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	557 * Index: creates a salmon index
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	558
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	559 * Quant: quantifies a sample (Reads or mapping-based)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	560
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	561 * Alevin: Single-cell analysis
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	562
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	563 * Quantmerge: Merges multiple quantifications into a single file
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	564
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	565 Galaxy divides these four into three separate tools in the IUC toolshed:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	566
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	567 * Salmon quant
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	568
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	569 * Salmon quantmerge
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	570
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	571 * Alevin
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	572 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	573 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	574 <token name="@alevinhelp@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	575 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:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	576
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	577 * Drop-seq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	578
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	579 * 10x-Chromium v1/2/3
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	580
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	581 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).
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	582
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	583 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.
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	584
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	585 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.
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	586 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	587 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	588 </macros>

Mercurial > repos > bgruening > alevin

annotate macros.xml @ 0:908a8d400fa2 draft