alevin: macros.xml annotate

annotate macros.xml @ 14:c9944a2600f1 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a

author	bgruening
date	Mon, 18 Mar 2024 09:36:09 +0000
parents	e32b215b7c04
children

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>
13 e32b215b7c04 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26cff0d523671ac1e56ba7ef4965861b387727e8 bgruening parents: 12 diff changeset	2 <token name="@TOOL_VERSION@">1.10.1</token>
14 c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	3 <token name="@VERSION_SUFFIX@">2</token>
6 53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 5 diff changeset	4 <token name="@IDX_VERSION@">q7</token>
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	5 <token name="@PROFILE_VERSION@">20.01</token>
14 c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	6 <xml name="xrefs">
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	7 <xrefs>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	8 <xref type="bio.tools">salmon</xref>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	9 </xrefs>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	10 </xml>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	11 <xml name="requirements">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	12 <requirements>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	13 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
5 e572598580c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664" bgruening parents: 2 diff changeset	14 <requirement type="package" version="1.3">seqtk</requirement>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	15 <requirement type="package" version="1.16.1">samtools</requirement>
2 e53f19161c59 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit c17bc974bf9bbaa1fc1e47ea72162fd244f0e612" bgruening parents: 1 diff changeset	16 <requirement type="package" version="0.2.0">vpolo</requirement>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	17 <requirement type="package" version="1.5.2">pandas</requirement>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	18 <requirement type="package" version="3.0.0">graphviz</requirement>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	19 <requirement type="package" version="1.9.3">scipy</requirement>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	20 </requirements>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	21 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	22 <xml name="orient">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	23 <param name="orientation" type="select" label="Relative orientation of reads within a pair">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	24 <option value="M">Mates are oriented in the same direction (M = matching)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	25 <option value="O">Mates are oriented away from each other (O = outward)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	26 <option value="I" selected="True">Mates are oriented toward each other (I = inward)</option>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	27 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	28 </xml>
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	29 <xml name="stranded">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	30 <conditional name="libtype" >
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	31 <param name="strandedness" type="select" label="Specify the strandedness of the reads" help="--libtype">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	32 <option value="A" selected="true">Infer automatically (A)</option>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	33 <option value="U">Not stranded (U)</option>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	34 <option value="SF">read comes from the forward strand (SF)</option>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	35 <option value="SR">read comes from the reverse strand (SR)</option>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	36 </param>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	37 <yield/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	38 </conditional>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	39 </xml>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	40 <xml name="stranded_se">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	41 <expand macro="stranded">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	42 <when value="A"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	43 <when value="U"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	44 <when value="SF"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	45 <when value="SR"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	46 </expand>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	47 </xml>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	48 <xml name="stranded_pe">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	49 <expand macro="stranded">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	50 <when value="A">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	51 </when>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	52 <when value="U">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	53 <expand macro="orient"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	54 </when>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	55 <when value="SF">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	56 <expand macro="orient"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	57 </when>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	58 <when value="SR">
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	59 <expand macro="orient"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	60 </when>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	61 </expand>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	62 </xml>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	63 <xml name="index">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	64 <conditional name="refTranscriptSource">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	65 <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	66 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	67 <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	68 <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	69 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	70 <when value="indexed">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	71 <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	72 <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	73 <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	74 <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	75 <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	76 </options>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	77 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	78 </when> <!-- build-in -->
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	79 <when value="history">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	80 <section name="s_index" title="Salmon index" expanded="true">
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	81 <param name="fasta" type="data" format="fasta" label="Transcripts FASTA file"/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	82 <param name="genome" type="data" format="fasta" optional="true" label="Reference genome"
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	83 help="The reference genome is required for generating a decoy-away index. The decoy sequences are regions of the target genome
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	84 that are sequence similar to annotated transcripts. These are the regions of the genome most likely to cause mismapping." />
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	85 <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	86 <param name="phash" type="boolean" label="Perfect Hash" truevalue="--perfectHash" falsevalue="" checked="false"
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	87 help="Build the index using a perfect hash rather than a dense hash. This will require less memory (especially during quantification),
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	88 but will take longer to construct"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	89 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	90 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	91 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	92 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	93 <xml name="reads">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	94 <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	95 <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	96 <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	97 <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	98 <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	99 <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	100 <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	101 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	102 <when value="single">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	103 <param name="input_singles" type="data" format="fastq,fasta,fastq.gz,fastq.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	104 <expand macro="stranded_se"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	105 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	106 <when value="paired">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	107 <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	108 <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." />
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	109 <expand macro="stranded_pe"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	110 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	111 <when value="paired_collection">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	112 <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"" />
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	113 <expand macro="stranded_pe"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	114 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	115 <when value="paired_interleaved">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	116 <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"/>
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	117 <expand macro="stranded_pe"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	118 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	119 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	120 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	121 <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	122 <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	123 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	124 <!--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	125 <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	126 label="Discard orphan quasi"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	127 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	128 <conditional name="validmap">
14 c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	129 <param name="validateMappings" type="select" label="Validate mappings" 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.">
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	130 <option value="--validateMappings">True</option>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	131 <option value="" selected="true">False</option>
c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	132 </param>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	133 <when value="--validateMappings">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	134 <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	135 label="Min Score Fraction"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	136 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	137 <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	138 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	139 <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	140 label="Match Score"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	141 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	142 <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	143 label="Mismatch Penalty"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	144 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	145 <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	146 label="Gap Open Penalty"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	147 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	148 <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	149 label="Gap Extension Penalty"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	150 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	151 <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	152 label="Mimic Bowtie 2"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	153 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	154 <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	155 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	156 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	157 <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	158 label="Hard Filter"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	159 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	160 </when>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	161 <when value=""/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	162 </conditional>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	163 <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	164 label="Consensus Slack"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	165 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	166 <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	167 <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	168 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."/>
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	169 <conditional name="bam_options">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	170 <param argument="--writeMappings" type="select" label="Write Mappings to BAM File" 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">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	171 <option value="--writeMappings=./output/samout.sam">Enabled</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	172 <option value="" selected="true">Disabled</option>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	173 </param>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	174 <when value="--writeMappings=./output/samout.sam">
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	175 <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	176 provided, then the output SAM file will contain quality strings as well as read sequences." />
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	177 </when>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	178 <when value=""/>
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	179 </conditional>
12 f2000bc73102 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 11 diff changeset	180 <param name="consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="False"
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	181 label="Consistent Hits"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	182 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	183 <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	184 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	185 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	186 <xml name="align">
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	187 <param name="afile" type="data" format="qname_input_sorted.bam,qname_sorted.bam" label="Alignment file"/>
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	188 <param argument="--ont" type="boolean" truevalue="--ont" falsevalue="" label="Is this Alignment file a Oxford Nanopore Technologies (ONT) dataset ?" help="Select this for both cDNA and direct RNA ONT datasets. Enables an alignment error model designed to work with long-read alignments and disables the length effect in the generative model when computing the conditional probability of observing a fragment given that it arises from a specific transcript. This is because in long-read sequencing, we do not expect to observe (i.e. sequence) multiple fragments from the same molecule, and thus we do not expect the transcript length to directly affect the observed fragment count directly"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	189 <param name="transcript" type="data" format="fasta,fa" label="Transcript file"/>
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	190 <expand macro="stranded_se"/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	191 <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	192 label="Discard orphans"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	193 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	194 <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	195 label="No Error Model"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	196 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	197 <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	198 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	199 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	200 <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	201 label="Sample out"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	202 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	203 <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	204 label="Sample unaligned"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	205 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	206 <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	207 label="Gencode"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	208 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	209 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	210 <xml name="quantboth">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	211 <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	212 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	213 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	214 <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	215 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	216 <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	217 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	218 <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	219 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	220 <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	221 label="Meta"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	222 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	223 <!--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	224 <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	225 <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	226 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	227 <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	228 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	229 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	230 <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	231 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	232 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	233 <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	234 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	235 <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	236 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	237 <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	238 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	239 <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	240 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	241 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	242 <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	243 label="Standard deviation"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	244 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	245 <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	246 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	247 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	248 <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	249 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	250 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	251 <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	252 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	253 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	254 <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	255 label="No length correction"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	256 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	257 <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	258 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	259 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	260 <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	261 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	262 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	263 <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	264 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	265 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	266 <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	267 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	268 <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	269 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	270 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	271 <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	272 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	273 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	274 <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	275 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	276 help=""/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	277 <param name="rangeFactorizationBins" type="integer" value="0" label="Range of factorization bins"
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	278 help="Factorizes the likelihood used in quantification by adopting a new notion of 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."/>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	279 <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	280 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	281 help="" />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	282 <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	283 label="No gamma draw"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	284 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	285 <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	286 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	287 help="" />
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	288 <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	289 label="Bootstrap reproject"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	290 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	291 <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	292 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	293 <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	294 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	295 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	296 <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	297 label="Significant Digits"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	298 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	299 <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	300 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	301 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	302 <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	303 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	304 <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	305 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	306 help=""/>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	307 </section>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	308 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	309 <xml name="quantmerge">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	310 <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	311 <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	312 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	313 <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	314 </repeat>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	315 <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	316 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	317 <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	318 <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	319 <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	320 <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	321 </param>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	322 <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	323 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	324 <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	325 </xml>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	326 <xml name="citations">
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	327 <citations>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	328 <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	329 <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	330 </citations>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	331 </xml>
5 e572598580c2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664" bgruening parents: 2 diff changeset	332 <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	333 <token name="@indexing@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	334 mkdir ./index &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	335 mkdir ./output &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	336 #if $quant_type.refTranscriptSource.TranscriptSource != "indexed":
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	337 #if $quant_type.refTranscriptSource.s_index.genome
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	338 cat '${quant_type.refTranscriptSource.s_index.genome}' \| grep "^>" \| cut -d " " -f 1 > 'decoys.txt' &&
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	339 sed -i.bak -e 's/>//g' 'decoys.txt' &&
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	340 cat '${quant_type.refTranscriptSource.s_index.fasta}' '${quant_type.refTranscriptSource.s_index.genome}' > 'input_index.fasta' &&
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	341 #else
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	342 ln -s '${quant_type.refTranscriptSource.s_index.fasta}' 'input_index.fasta' &&
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	343 #end if
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	344 salmon index -i ./index
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	345 --kmerLen '${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	346 --gencode
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	347 --threads "\${GALAXY_SLOTS:-4}"
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	348 --transcripts 'input_index.fasta'
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	349 #if $quant_type.refTranscriptSource.s_index.genome
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	350 --decoy 'decoys.txt'
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	351 #end if
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	352 &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	353 #set $index_path = './index'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	354 #else
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	355 #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	356 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	357 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	358 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	359 <token name="@salreads@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	360 #set compressed = 'no'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	361 #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	362 #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	363 #set $ext = 'fasta'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	364 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	365 #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	366 #set compressed = 'GZ'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	367 #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	368 #set compressed = 'BZ2'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	369 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	370 #set $ext = 'fastq'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	371 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	372 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	373 #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	374 #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	375 #set $ext = 'fasta'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	376 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	377 #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	378 #set compressed = 'GZ'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	379 #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	380 #set compressed = 'BZ2'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	381 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	382 #set $ext = 'fastq'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	383 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	384 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	385 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	386 #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	387 #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	388 #set $ext = 'fasta'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	389 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	390 #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	391 #set compressed = 'GZ'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	392 #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	393 #set compressed = 'BZ2'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	394 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	395 #set $ext = 'fastq'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	396 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	397 ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	398 ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
14 c9944a2600f1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 20eabb7209eb447bc66450e955291143694b419a bgruening parents: 13 diff changeset	399 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_interleaved':
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	400 #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	401 #set $ext = 'fasta'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	402 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	403 #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	404 #set compressed = 'GZ'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	405 #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	406 #set compressed = 'BZ2'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	407 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	408 #set $ext = 'fastq'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	409 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	410 ln -s '$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	411 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	412 #if $geneMap:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	413 ln -s '$geneMap' ./geneMap.${geneMap.ext} &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	414 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	415
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	416 salmon quant
6 53d74155bb52 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 5 diff changeset	417 --index '$index_path'
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	418 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	419 --libType ${quant_type.input.single_or_paired.libtype.strandedness}
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	420 #if $compressed == 'GZ':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	421 --unmatedReads <(zcat < ./single.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	422 #else if $compressed == 'BZ2':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	423 --unmatedReads <(bzcat < ./single.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	424 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	425 --unmatedReads ./single.$ext
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 #else:
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	428 --libType
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	429 #if $quant_type.input.single_or_paired.libtype.strandedness == 'A'
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	430 A
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	431 #else
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	432 ${quant_type.input.single_or_paired.libtype.orientation}${quant_type.input.single_or_paired.libtype.strandedness}
e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	433 #end if
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	434 #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	435 #if $compressed == 'BZ2':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	436 --mates1 <(bzcat < ./mate1.$ext \| seqtk seq -1)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	437 --mates2 <(bzcat < ./mate1.$ext \| seqtk seq -2)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	438 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	439 --mates1 <(seqtk seq -1 ./mate1.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	440 --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	441 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	442 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	443 #if $compressed == 'GZ':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	444 --mates1 <(zcat < ./mate1.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	445 --mates2 <(zcat < ./mate2.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	446 #else if $compressed == 'BZ2':
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	447 --mates1 <(bzcat < ./mate1.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	448 --mates2 <(bzcat < ./mate2.$ext)
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	449 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	450 --mates1 ./mate1.$ext
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	451 --mates2 ./mate2.$ext
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	452 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	453 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	454 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	455 --threads "\${GALAXY_SLOTS:-4}"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	456 ${quant_type.discardOrphansQuasi}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	457 ${quant_type.validmap.validateMappings}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	458 #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	459 #if $quant_type.validmap.minScoreFraction:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	460 --minScoreFraction '${quant_type.validmap.minScoreFraction}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	461 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	462 #if $quant_type.validmap.maxMMPExtension:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	463 --maxMMPExtension '${quant_type.validmap.maxMMPExtension}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	464 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	465 #if $quant_type.validmap.matchScore:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	466 --ma '${$quant_type.validmap.matchScore}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	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 $quant_type.validmap.mismatchPenalty:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	469 --mp '${$quant_type.validmap.mismatchPenalty}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	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 $quant_type.validmap.gapOpenPenalty:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	472 --go '${$quant_type.validmap.gapOpenPenalty}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	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 $quant_type.validmap.gapExtensionPenalty:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	475 --ge '${$quant_type.validmap.gapExtensionPenalty}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	476 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	477 ${$quant_type.validmap.mimicBT2}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	478 ${$quant_type.validmap.mimicStrictBT2}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	479 ${$quant_type.validmap.hardFilter}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	480 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	481 #if $quant_type.consensusSlack:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	482 --consensusSlack '${quant_type.consensusSlack}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	483 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	484 ${quant_type.dovetail}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	485 ${quant_type.recoverOrphans}
11 e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	486 ${quant_type.bam_options.writeMappings}
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	487 #if $quant_type.bam_options.writeMappings:
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	488 ${quant_type.bam_options.writeQualities}
e661a3269313 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 10ccc47885ce71e602d66e157bd475f1facbd042 bgruening parents: 10 diff changeset	489 #end if
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	490 ${quant_type.consistentHits}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	491 #if $quant_type.quasiCoverage:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	492 --quasiCoverage '${quant_type.quasiCoverage}'
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 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	495 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	496 <token name="@salalign@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	497 #if $geneMap:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	498 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	499 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	500 salmon quant
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	501 -t '${quant_type.transcript}'
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	502 -l '${quant_type.libtype.strandedness}'
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	503 -a '${quant_type.afile}'
10 e4c01dcece8b "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 6 diff changeset	504 $quant_type.ont
0 908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	505 --threads "\${GALAXY_SLOTS:-4}"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	506 ${quant_type.discardOrphans}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	507 ${quant_type.noErrorModel}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	508 #if $quant_type.numErrorBins:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	509 --numErrorBins '${quant_type.numErrorBins}'
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 ${quant_type.sampleOut}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	512 ${quant_type.sampleUnaligned}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	513 ${quant_type.gencode}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	514 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	515 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	516 <token name="@salquant@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	517 #if $geneMap:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	518 --geneMap ./geneMap.${geneMap.ext}
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
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	521 ##Further basic options##
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	522
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	523 ${seqBias}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	524 ${gcBias}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	525 --incompatPrior '${incompatPrior}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	526 ${meta}
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 ##Advanced options##
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	529
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	530 ${adv.skipQuant}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	531 ${adv.dumpEq}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	532 ${adv.dumpEqWeights}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	533 #if $adv.minAssignedFrags:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	534 --minAssignedFrags '${adv.minAssignedFrags}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	535 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	536 #if $adv.biasSpeedSamp:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	537 --biasSpeedSamp '${adv.biasSpeedSamp}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	538 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	539 #if $adv.fldMax:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	540 --fldMax '${adv.fldMax}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	541 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	542 #if $adv.fldMean:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	543 --fldMean '${adv.fldMean}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	544 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	545 #if $adv.fldSD:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	546 --fldSD '${adv.fldSD}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	547 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	548 #if $adv.forgettingFactor:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	549 --forgettingFactor '${adv.forgettingFactor}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	550 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	551 ${adv.initUniform}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	552 #if str($adv.maxReadOcc):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	553 --maxReadOcc '${adv.maxReadOcc}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	554 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	555 ${adv.noLengthCorrection}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	556 ${adv.noEffectiveLengthCorrection}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	557 ${adv.noFragLengthDist}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	558 ${adv.noBiasLengthThreshold}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	559 #if str($adv.numBiasSamples):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	560 --numBiasSamples '${adv.numBiasSamples}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	561 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	562 #if str($adv.numAuxModelSamples):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	563 --numAuxModelSamples '${adv.numAuxModelSamples}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	564 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	565 #if str($adv.numPreAuxModelSamples):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	566 --numPreAuxModelSamples '${adv.numPreAuxModelSamples}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	567 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	568 ${adv.useEM}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	569 #if $adv.rangeFactorizationBins:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	570 --rangeFactorizationBins '${adv.rangeFactorizationBins}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	571 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	572 #if str($adv.numGibbsSamples):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	573 --numGibbsSamples '${adv.numGibbsSamples}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	574 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	575 ${adv.noGammaDraw}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	576 #if str($adv.numBootstraps):
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	577 --numBootstraps '${adv.numBootstraps}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	578 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	579 ${adv.bootstrapReproject}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	580 #if $adv.thinningFactor:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	581 --thinningFactor '${adv.thinningFactor}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	582 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	583 ${adv.perTranscriptPrior}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	584 --sigDigits '${adv.sigDigits}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	585 #if $adv.vbPrior:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	586 --vbPrior '${adv.vbPrior}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	587 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	588 ${adv.writeOrphanLinks}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	589 ${adv.writeUnmappedNames}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	590 -o ./output
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	591 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	592 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	593 <token name="@qmerge@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	594 #import re
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	595
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	596 #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	597 rank_of_series=$counter
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	598 mkdir ${counter}.quantmerge &&
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	599 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	600 #end for
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	601 salmon quantmerge
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	602 --quants *.quantmerge
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	603 --names
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	604 #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	605 #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	606 '${input_data.names}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	607 #else:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	608 #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	609 "$identifier"
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	610 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	611 #end for
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	612 --column '${column}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	613 ${genes}
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	614 #if $missing:
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	615 --missing '${missing}'
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	616 #end if
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	617 -o qmergeout.tab
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	618 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	619 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	620 <token name="@salmonhelp@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	621 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	622
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	623 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	624
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	625 * 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	626
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	627 * 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	628
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	629 * Alevin: Single-cell analysis
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	630
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	631 * 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	632
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	633 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	634
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	635 * Salmon quant
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	636
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	637 * Salmon quantmerge
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	638
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	639 * Alevin
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	640 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	641 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	642 <token name="@alevinhelp@"><![CDATA[
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	643 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	644
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	645 * Drop-seq
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	646
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	647 * 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	648
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	649 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	650
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	651 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	652
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	653 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	654 ]]>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	655 </token>
908a8d400fa2 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	656 </macros>

Mercurial > repos > bgruening > alevin

annotate macros.xml @ 14:c9944a2600f1 draft