salmonquantmerge: macros.xml annotate

annotate macros.xml @ 10:42628a3010d4 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1

author	bgruening
date	Fri, 31 Oct 2025 19:16:59 +0000
parents	58b9ef13fcca
children

rev	line source
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	1 <macros>
8 3c3cf3ff1a91 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26cff0d523671ac1e56ba7ef4965861b387727e8 bgruening parents: 7 diff changeset	2 <token name="@TOOL_VERSION@">1.10.1</token>
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	3 <token name="@VERSION_SUFFIX@">4</token>
4 362ba03406b4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 3 diff changeset	4 <token name="@IDX_VERSION@">q7</token>
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	5 <token name="@PROFILE_VERSION@">24.1</token>
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	6 <xml name="xrefs">
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	7 <xrefs>
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	8 <xref type="bio.tools">salmon</xref>
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	9 </xrefs>
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	10 </xml>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	11 <xml name="requirements">
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	12 <requirements>
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	13 <requirement type="package" version="@TOOL_VERSION@">salmon</requirement>
3 c30842f419ce "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>
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	15 <requirement type="package" version="1.16.1">samtools</requirement>
2 7c618ec039b8 "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>
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	17 <requirement type="package" version="1.5.2">pandas</requirement>
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	18 <requirement type="package" version="3.0.0">graphviz</requirement>
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	19 <requirement type="package" version="1.9.3">scipy</requirement>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	20 </requirements>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	21 </xml>
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	22 <xml name="version_command">
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	23 <version_command><![CDATA[salmon --no-version-check --version \| cut -d" " -f2]]></version_command>
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	24 </xml>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	25 <xml name="orient">
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	26 <param argument="--libType" name="orientation" type="select" label="Relative orientation of reads within a pair">
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	27 <option value="M">Mates are oriented in the same direction (M = matching)</option>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	28 <option value="O">Mates are oriented away from each other (O = outward)</option>
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	29 <option value="I" selected="true">Mates are oriented toward each other (I = inward)</option>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	30 </param>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	31 </xml>
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	32 <xml name="stranded">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	33 <conditional name="libtype" >
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	34 <param argument="--libType" name="strandedness" type="select" label="Specify the strandedness of the reads" help="--libtype">
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	35 <option value="A" selected="true">Infer automatically (A)</option>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	36 <option value="U">Not stranded (U)</option>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	37 <option value="SF">read comes from the forward strand (SF)</option>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	38 <option value="SR">read comes from the reverse strand (SR)</option>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	39 </param>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	40 <yield/>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	41 </conditional>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	42 </xml>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	43 <xml name="stranded_se">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	44 <expand macro="stranded">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	45 <when value="A"/>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	46 <when value="U"/>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	47 <when value="SF"/>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	48 <when value="SR"/>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	49 </expand>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	50 </xml>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	51 <xml name="stranded_pe">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	52 <expand macro="stranded">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	53 <when value="A">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	54 </when>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	55 <when value="U">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	56 <expand macro="orient"/>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	57 </when>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	58 <when value="SF">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	59 <expand macro="orient"/>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	60 </when>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	61 <when value="SR">
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	62 <expand macro="orient"/>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	63 </when>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	64 </expand>
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	65 </xml>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	66 <xml name="index">
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	67 <conditional name="refTranscriptSource">
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	68 <param name="TranscriptSource" type="select" label="Select a reference transcriptome from your history or use a built-in index?"
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	69 help="Built-ins were indexed using default options">
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	70 <option value="indexed">Use a built-in index</option>
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	71 <option value="history" selected="true">Use one from the history</option>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	72 </param>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	73 <when value="indexed">
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	74 <param argument="--index" type="select" label="Select a reference transcriptome" help="If your transcriptome of interest is not listed, contact your Galaxy admin">
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	75 <options from_data_table="salmon_indexes_versioned">
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	76 <filter type="sort_by" column="2"/>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	77 <filter type="static_value" column="4" value="@IDX_VERSION@" />
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	78 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	79 </options>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	80 </param>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	81 </when> <!-- build-in -->
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	82 <when value="history">
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	83 <section name="s_index" title="Salmon index" expanded="true">
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	84 <param argument="--transcripts" name="fasta" type="data" format="fasta" label="Transcripts FASTA file"/>
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	85 <param argument="--genome" type="data" format="fasta" optional="true" label="Reference genome"
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	86 help="The reference genome is required for generating a decoy-away index. The decoy sequences are regions of the target genome
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	87 that are sequence similar to annotated transcripts. These are the regions of the genome most likely to cause mismapping." />
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	88 <param argument="--kmerLen" name="kmer" type="integer" value="31" label="Kmer length"/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	89 </section>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	90 </when>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	91 </conditional>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	92 </xml>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	93 <xml name="reads">
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	94 <section name="input" title="Data input" expanded="true">
0 864924030095 "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">
864924030095 "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?">
864924030095 "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>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	98 <option value="paired_collection">Paired-end Dataset Collection</option>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	99 </param>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	100 <when value="single">
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	101 <param argument="--unmatedReads" name="input_singles" type="data" format="fasta,fastqsanger,fastqsanger.gz,fastqsanger.bz2" label="FASTQ/FASTA file" help="FASTQ file." />
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	102 <expand macro="stranded_se"/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	103 </when>
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	104 <when value="paired_collection">
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	105 <param name="input_1" format="fasta,fastqsanger,fastqsanger.gz,fastqsanger.bz2" type="data_collection" collection_type="paired" label="FASTQ Paired Dataset" help="(--mates1,--mates2)" />
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	106 <expand macro="stranded_pe"/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	107 </when>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	108 </conditional>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	109 </section>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	110 <!--Salmon quant type select: reads-based or alignment-based-->
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	111 <param argument="--discardOrphansQuasi" type="boolean" truevalue="--discardOrphansQuasi" falsevalue="" checked="false" label="Discard orphan quasi" 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."/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	112 <conditional name="validmap">
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	113 <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.">
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	114 <option value="--validateMappings">True</option>
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	115 <option value="" selected="true">False</option>
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	116 </param>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	117 <when value="--validateMappings">
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	118 <param argument="--minScoreFraction" type="float" value="0.65" label="Min Score Fraction" 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].">
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	119 <validator type="in_range" min="0" exclude_max="1"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	120 </param>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	121 <param argument="--ma" name="matchScore" type="integer" value="2" label="Match Score" help="The value given to a match between read and reference nucleotides in an alignment."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	122 <param argument="--mp" name="mismatchPenalty" type="integer" value="-4" label="Mismatch Penalty" help="The value given to a mis-match between read and reference nucleotides in an alignment. This will be cast to a negative value."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	123 <param argument="--go" name="gapOpenPenalty" type="integer" value="6" label="Gap Open Penalty" help="The value given to a gap opening in an alignment."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	124 <param argument="--ge" name="gapExtensionPenalty" type="integer" value="2" label="Gap Extension Penalty" help="The value given to a gap extension in an alignment."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	125 <param argument="--mimicBT2" type="boolean" truevalue="--mimicBT2" falsevalue="" checked="false" label="Mimic Bowtie 2" 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 "/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	126 <param argument="--mimicStrictBT2" type="boolean" truevalue="--mimicStrictBT2" falsevalue="" checked="false" label="Mimic Strict Bowtie 2" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	127 <param argument="--hardFilter" type="boolean" truevalue="--hardFilter" falsevalue="" checked="false" label="Hard Filter" 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."/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	128 </when>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	129 <when value=""/>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	130 </conditional>
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	131 <param argument="--consensusSlack" type="float" value="0.349999994" label="Consensus Slack" 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.">
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	132 <validator type="in_range" min="0" exclude_max="1"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	133 </param>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	134 <param name="dovetail" argument="--allowDovetail" label="Allow Dovetail" type="boolean" truevalue="--allowDovetail" falsevalue="" checked="false" help="Allow dovetail mappings"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	135 <param argument="--recoverOrphans" label="Recover Orphans" type="boolean" truevalue="--recoverOrphans" falsevalue="" checked="false" 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."/>
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	136 <conditional name="bam_options">
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	137 <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">
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	138 <option value="--writeMappings=./output/samout.sam">Enabled</option>
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	139 <option value="" selected="true">Disabled</option>
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	140 </param>
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	141 <when value="--writeMappings=./output/samout.sam">
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	142 <param argument="--writeQualities" type="boolean" truevalue="--writeQualities" falsevalue="" checked="false" label="Write qualities" help="If this flag is provided, then the output SAM file will contain quality strings as well as read sequences." />
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	143 </when>
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	144 <when value=""/>
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	145 </conditional>
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	146 <param argument="--consistentHits" type="boolean" truevalue="--consistentHits" falsevalue="" checked="false" label="Consistent Hits" help="Force hits gathered during quasi-mapping to be 'consistent' (i.e. co-linear and approximately the right distance apart)."/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	147 </xml>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	148 <xml name="align">
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	149 <param argument="--alignments" name="afile" type="data" format="qname_input_sorted.bam,qname_sorted.bam" label="Alignment file"/>
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	150 <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"/>
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	151 <param argument="--targets" name="transcript" type="data" format="fasta,fasta.gz" label="Transcript file"/>
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	152 <expand macro="stranded_se"/>
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	153 <param argument="--discardOrphans" type="boolean" truevalue="--discardOrphans" falsevalue="" checked="false" label="Discard orphans" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	154 <param argument="--noErrorModel" type="boolean" truevalue="--noErrorModel" falsevalue="" checked="false" label="No Error Model" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	155 <param argument="--numErrorBins" type="integer" value="6" min="0" label="Number of Error Bins" 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)."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	156 <param argument="--sampleOut" type="boolean" truevalue="--sampleOut" falsevalue="" checked="false" label="Sample out" 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"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	157 <param argument="--sampleUnaligned" type="boolean" truevalue="--sampleUnaligned" falsevalue="" checked="false" label="Sample unaligned" help="In addition to sampling the aligned reads, also write the un-aligned reads to 'postSample.bam'."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	158 <param argument="--gencode" type="boolean" truevalue="--gencode" falsevalue="" checked="false" label="Gencode" 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."/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	159 </xml>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	160 <xml name="quantboth">
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	161 <param argument="--geneMap" type="data" format="tabular,gff,gtf" optional="true" label="File containing a mapping of transcripts to genes" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	162 <param argument="--seqBias" type="boolean" truevalue="--seqBias" falsevalue="" checked="false" label="Perform sequence-specific bias correction"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	163 <param argument="--gcBias" type="boolean" truevalue="--gcBias" falsevalue="" checked="false" label="Perform fragment GC bias correction"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	164 <param argument="--incompatPrior" type="float" min="0" max="1" value="0" 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"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	165 <param argument="--meta" type="boolean" truevalue="--meta" falsevalue="" checked="false" label="Meta" 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."/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	166 <!--Salmon quant advanced options: available to both kinds of quant-->
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	167 <section name="adv" title="Additional Options">
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	168 <param argument="--skipQuant" type="boolean" truevalue="--skipQuant" falsevalue="" checked="false" label="skipQuant" help="Skip performing the actual transcript quantification (including any Gibbs sampling or bootstrapping)."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	169 <param argument="--dumpEq" type="boolean" truevalue="--dumpEq" falsevalue="" checked="false" label="Dump equivalence class counts" help="Dump the equivalence class counts that were computed during quasi-mapping."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	170 <param argument="--dumpEqWeights" type="boolean" truevalue="--dumpEqWeights" falsevalue="" checked="false" label="Dump equivalence class counts including rich weights" help="Includes 'rich' equivlance class weights in the output when equivalence class information is being dumped to file."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	171 <param argument="--minAssignedFrags" type="integer" min="0" value="10" label="Minimum assigned fragments" help="The minimum number of fragments that must be assigned to the transcriptome for quantification to proceed."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	172 <param argument="--biasSpeedSamp" type="integer" value="5" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	173 <param argument="--fldMax" type="integer" min="0" value="1000" label="The maximum fragment length to consider when building the empirical distribution."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	174 <param argument="--fldMean" type="integer" min="0" value="250" label="The mean used in the fragment length distribution prior" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	175 <param argument="--fldSD" type="integer" min="0" value="25" label="Standard deviation" help="The standard deviation used in the fragment length distribution prior."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	176 <param argument="--forgettingFactor" type="float" value="0.65000000000000002" label="The forgetting factor used in the online learning schedule." 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].">
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	177 <validator type="in_range" min="0.5" exclude_max="1"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	178 </param>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	179 <param argument="--initUniform" type="boolean" truevalue="--initUniform" falsevalue="" checked="false" label="Initialization with uniform parameters" help="initialize the offline inference with uniform parameters, rather than seeding with online parameters." />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	180 <param argument="--maxReadOcc" type="integer" min="0" value="200" label="Maximal read mapping occurence" help="Reads mapping to more than this many places won't be considered."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	181 <param argument="--noLengthCorrection" type="boolean" truevalue="--noLengthCorrection" falsevalue="" label="No length correction" 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)"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	182 <param argument="--noEffectiveLengthCorrection" type="boolean" truevalue="--noEffectiveLengthCorrection" falsevalue="" checked="false" label="Disable effective length correction" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	183 <param argument="--noFragLengthDist" type="boolean" truevalue="--noFragLengthDist" falsevalue="" checked="false" label="Ignore fragment length distribution" 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." />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	184 <param argument="--noBiasLengthThreshold" type="boolean" truevalue="--noBiasLengthThreshold" falsevalue="" checked="false" label="[experimental] : If this option is enabled, then no (lower) threshold will be set on how short bias correction can make effecctive lengths." help="This can increase the precision of bias correction, but harm robustness. The default correction applies a threshold." />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	185 <param argument="--numBiasSamples" type="integer" min="0" value="2000000" label="Number of fragment mappings to use when learning the sequence-specific bias model."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	186 <param argument="--numAuxModelSamples" type="integer" min="0" value="5000000" label="The first numAuxModelSamples are used to train the auxiliary model parameters." 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." />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	187 <param argument="--numPreAuxModelSamples" type="integer" min="0" value="5000" label="The first numPreAuxModelSamples will have their assignment likelihoods and contributions to the transcript abundances computed without applying any auxiliary models." 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." />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	188 <param argument="--useEM" type="boolean" truevalue="--useEM" falsevalue="" checked="false" label="Use the traditional EM algorithm for optimization in the batch passes." help=""/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	189 <param argument="--rangeFactorizationBins" type="integer" value="4" label="Range of factorization bins" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	190 <param argument="--numGibbsSamples" type="integer" min="0" value="0" label="Number of Gibbs sampling rounds to perform." help="" />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	191 <param argument="--noGammaDraw" type="boolean" truevalue="--noGammaDraw" falsevalue="" checked="false" label="No gamma draw" 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"/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	192 <param argument="--numBootstraps" type="integer" min="0" value="0" label="Number of bootstrap samples to generate. Note: This is mutually exclusive with Gibbs sampling." help="" />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	193 <param argument="--bootstrapReproject" type="boolean" truevalue="--bootstrapReproject" falsevalue="" checked="false" label="Bootstrap reproject" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	194 <param argument="--thinningFactor" type="integer" min="0" value="16" label="Thinning factor" 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."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	195 <param argument="--perTranscriptPrior" type="boolean" truevalue="--perTranscriptPrior" falsevalue="" checked="false" label="The prior will be interpreted as a transcript-level prior." help="either the default or the argument provided via --vbPrior" />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	196 <param argument="--sigDigits" type="integer" min="0" value="3" label="Significant Digits" help="The number of significant digits to write when outputting the EffectiveLength and NumReads columns."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	197 <param argument="--vbPrior" type="float" value="0.01" label="The prior that will be used in the VBEM algorithm." 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." />
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	198 <param argument="--writeOrphanLinks" type="boolean" truevalue="--writeOrphanLinks" falsevalue="" checked="false" label="Write orphan links" help="Write the transcripts that are linked by orphaned reads."/>
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	199 <param argument="--writeUnmappedNames" type="boolean" truevalue="--writeUnmappedNames" falsevalue="" checked="false" label="Write the names of un-mapped reads to the file unmapped_names.txt." help=""/>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	200 </section>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	201 </xml>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	202 <xml name="citations">
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	203 <citations>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	204 <citation type="doi">10.1186/s13059-019-1670-y</citation>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	205 <citation type="doi">10.1038/nmeth.4197</citation>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	206 </citations>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	207 </xml>
3 c30842f419ce "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 30fe16f7d786e4b0c43b8333853fc56c59f6c664" bgruening parents: 2 diff changeset	208 <token name="@bam_sort@"><![CDATA[samtools sort -@ \${GALAXY_SLOTS} --output-fmt=BAM -o ./output/bamout.bam]]></token>
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	209 <token name="@indexing@"><![CDATA[
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	210 mkdir ./index &&
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	211 mkdir ./output &&
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	212 #if $TRANSCRIPTSOURCE_CONDITIONAL.TranscriptSource != "indexed":
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	213 #if $TRANSCRIPTSOURCE_CONDITIONAL.s_index.genome
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	214 cat '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.genome}' \| grep "^>" \| cut -d " " -f 1 > 'decoys.txt' &&
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	215 sed -i.bak -e 's/>//g' 'decoys.txt' &&
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	216 cat '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.fasta}' '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.genome}' > 'input_index.fasta' &&
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	217 #else
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	218 ln -s '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.fasta}' 'input_index.fasta' &&
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	219 #end if
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	220 salmon --no-version-check index -i ./index
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	221 --kmerLen '${TRANSCRIPTSOURCE_CONDITIONAL.s_index.kmer}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	222 --gencode
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	223 --threads "\$SLOTS"
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	224 --transcripts 'input_index.fasta'
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	225 #if $TRANSCRIPTSOURCE_CONDITIONAL.s_index.genome
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	226 --decoy 'decoys.txt'
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	227 #end if
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	228 &&
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	229 #set $index_path = './index'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	230 #else
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	231 #set $index_path = $TRANSCRIPTSOURCE_CONDITIONAL.index.fields.path
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	232 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	233 ]]>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	234 </token>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	235 <token name="@salreads@"><![CDATA[
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	236 #set compressed = 'no'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	237 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	238 #if $quant_type.input.single_or_paired.input_singles.ext == 'fasta':
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	239 #set $ext = 'fasta'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	240 #else:
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	241 #if $quant_type.input.single_or_paired.input_singles.is_of_type("fastqsanger.gz"):
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	242 #set compressed = 'GZ'
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	243 #else if $quant_type.input.single_or_paired.input_singles.is_of_type("fastqsanger.bz2"):
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	244 #set compressed = 'BZ2'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	245 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	246 #set $ext = 'fastq'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	247 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	248 ln -s $quant_type.input.single_or_paired.input_singles ./single.$ext &&
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	249 #else if $quant_type.input.single_or_paired.single_or_paired_opts == 'paired_collection':
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	250 #if $quant_type.input.single_or_paired.input_1.forward.ext == 'fasta':
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	251 #set $ext = 'fasta'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	252 #else:
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	253 #if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastqsanger.gz"):
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	254 #set compressed = 'GZ'
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	255 #else if $quant_type.input.single_or_paired.input_1.forward.is_of_type("fastqsanger.bz2"):
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	256 #set compressed = 'BZ2'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	257 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	258 #set $ext = 'fastq'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	259 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	260 ln -s '${quant_type.input.single_or_paired.input_1.forward}' ./mate1.$ext &&
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	261 ln -s '${quant_type.input.single_or_paired.input_1.reverse}' ./mate2.$ext &&
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	262 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	263 #if $geneMap:
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	264 ln -s '$geneMap' ./geneMap.${geneMap.ext} &&
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	265 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	266
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	267 salmon --no-version-check quant
4 362ba03406b4 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 4c71464b5f5047e0745067c115c37a5d06867649" bgruening parents: 3 diff changeset	268 --index '$index_path'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	269 #if $quant_type.input.single_or_paired.single_or_paired_opts == 'single':
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	270 --libType ${quant_type.input.single_or_paired.libtype.strandedness}
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	271 #if $compressed == 'GZ':
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	272 --unmatedReads <(zcat < ./single.$ext)
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	273 #else if $compressed == 'BZ2':
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	274 --unmatedReads <(bzcat < ./single.$ext)
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	275 #else:
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	276 --unmatedReads ./single.$ext
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	277 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	278 #else:
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	279 --libType
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	280 #if $quant_type.input.single_or_paired.libtype.strandedness == 'A'
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	281 A
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	282 #else
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	283 ${quant_type.input.single_or_paired.libtype.orientation}${quant_type.input.single_or_paired.libtype.strandedness}
510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	284 #end if
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	285 #if $compressed == 'GZ':
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	286 --mates1 <(zcat < ./mate1.$ext)
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	287 --mates2 <(zcat < ./mate2.$ext)
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	288 #else if $compressed == 'BZ2':
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	289 --mates1 <(bzcat < ./mate1.$ext)
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	290 --mates2 <(bzcat < ./mate2.$ext)
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	291 #else:
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	292 --mates1 ./mate1.$ext
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	293 --mates2 ./mate2.$ext
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	294 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	295 #end if
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	296 --threads "\$SLOTS"
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	297 ${quant_type.discardOrphansQuasi}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	298 ${quant_type.validmap.validateMappings}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	299 #if $quant_type.validmap.validateMappings:
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	300 --minScoreFraction '${quant_type.validmap.minScoreFraction}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	301 --ma '${$quant_type.validmap.matchScore}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	302 --mp '${$quant_type.validmap.mismatchPenalty}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	303 --go '${$quant_type.validmap.gapOpenPenalty}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	304 --ge '${$quant_type.validmap.gapExtensionPenalty}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	305 ${$quant_type.validmap.mimicBT2}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	306 ${$quant_type.validmap.mimicStrictBT2}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	307 ${$quant_type.validmap.hardFilter}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	308 #end if
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	309 --consensusSlack '${quant_type.consensusSlack}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	310 ${quant_type.dovetail}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	311 ${quant_type.recoverOrphans}
7 923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	312 ${quant_type.bam_options.writeMappings}
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	313 #if $quant_type.bam_options.writeMappings:
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	314 ${quant_type.bam_options.writeQualities}
923b40fc4442 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 363aead8810baedaff299537616cebdab36a8664 bgruening parents: 6 diff changeset	315 #end if
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	316 ${quant_type.consistentHits}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	317 ]]>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	318 </token>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	319 <token name="@salalign@"><![CDATA[
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	320 #if $geneMap:
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	321 ln -s "$geneMap" ./geneMap.${geneMap.ext} &&
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	322 #end if
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	323 salmon --no-version-check quant
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	324 --targets '${quant_type.transcript}'
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	325 --libType '${quant_type.libtype.strandedness}'
58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	326 --alignments '${quant_type.afile}'
6 510af1a0f9c8 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 26e9f1627e91a4be6bdc7e71cd44f1ea1701ee6f" bgruening parents: 4 diff changeset	327 $quant_type.ont
9 58b9ef13fcca planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 1971e35a365a91ae36c990b374a552a46196e888 bgruening parents: 8 diff changeset	328 --threads "\$SLOTS"
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	329 ${quant_type.discardOrphans}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	330 ${quant_type.noErrorModel}
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	331 --numErrorBins '${quant_type.numErrorBins}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	332 ${quant_type.sampleOut}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	333 ${quant_type.sampleUnaligned}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	334 ${quant_type.gencode}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	335 ]]>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	336 </token>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	337 <token name="@salquant@"><![CDATA[
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	338 #if $geneMap:
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	339 --geneMap ./geneMap.${geneMap.ext}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	340 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	341
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	342 ##Further basic options##
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	343
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	344 ${seqBias}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	345 ${gcBias}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	346 --incompatPrior '${incompatPrior}'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	347 ${meta}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	348
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	349 ##Advanced options##
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	350
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	351 ${adv.skipQuant}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	352 ${adv.dumpEq}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	353 ${adv.dumpEqWeights}
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	354 --minAssignedFrags '${adv.minAssignedFrags}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	355 --biasSpeedSamp '${adv.biasSpeedSamp}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	356 --fldMax '${adv.fldMax}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	357 --fldMean '${adv.fldMean}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	358 --fldSD '${adv.fldSD}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	359 --forgettingFactor '${adv.forgettingFactor}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	360 ${adv.initUniform}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	361 #if str($adv.maxReadOcc):
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	362 --maxReadOcc '${adv.maxReadOcc}'
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	363 #end if
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	364 ${adv.noLengthCorrection}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	365 ${adv.noEffectiveLengthCorrection}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	366 ${adv.noFragLengthDist}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	367 ${adv.noBiasLengthThreshold}
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	368 --numBiasSamples '${adv.numBiasSamples}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	369 --numAuxModelSamples '${adv.numAuxModelSamples}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	370 --numPreAuxModelSamples '${adv.numPreAuxModelSamples}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	371 ${adv.useEM}
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	372 --rangeFactorizationBins '${adv.rangeFactorizationBins}'
42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	373 --numGibbsSamples '${adv.numGibbsSamples}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	374 ${adv.noGammaDraw}
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	375 --numBootstraps '${adv.numBootstraps}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	376 ${adv.bootstrapReproject}
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	377 --thinningFactor '${adv.thinningFactor}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	378 ${adv.perTranscriptPrior}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	379 --sigDigits '${adv.sigDigits}'
10 42628a3010d4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 3b330b885fde7c730c5d121f6b37e1d99d3721e1 bgruening parents: 9 diff changeset	380 --vbPrior '${adv.vbPrior}'
0 864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	381 ${adv.writeOrphanLinks}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	382 ${adv.writeUnmappedNames}
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	383 -o ./output
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	384 ]]>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	385 </token>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	386
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	387 <token name="@salmonhelp@"><![CDATA[
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	388 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.
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	389
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	390 The salmon package contains 4 tools:
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	391
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	392 * Index: creates a salmon index
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	393
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	394 * Quant: quantifies a sample (Reads or mapping-based)
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	395
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	396 * Alevin: Single-cell analysis
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	397
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	398 * Quantmerge: Merges multiple quantifications into a single file
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	399
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	400 Galaxy divides these four into three separate tools in the IUC toolshed:
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	401
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	402 * Salmon quant
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	403
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	404 * Salmon quantmerge
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	405
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	406 * Alevin
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	407 ]]>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	408 </token>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	409 <token name="@alevinhelp@"><![CDATA[
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	410 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:
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	411
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	412 * Drop-seq
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	413
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	414 * 10x-Chromium v1/2/3
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	415
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	416 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).
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	417
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	418 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.
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	419
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	420 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.
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	421 ]]>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	422 </token>
864924030095 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/salmon commit 8f432498890670fd03a197bd3d1aa2638d1ff2b3" bgruening parents: diff changeset	423 </macros>

Mercurial > repos > bgruening > salmonquantmerge

annotate macros.xml @ 10:42628a3010d4 draft default tip