phabox_contamination: macros.xml annotate

annotate macros.xml @ 0:6c7718bc9849 draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd

author	ufz
date	Wed, 16 Apr 2025 09:42:58 +0000
parents
children

rev	line source
0 6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	1 <macros>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	2 <token name="@TOOL_VERSION@">2.1.11</token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	3 <token name="@VERSION_SUFFIX@">0</token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	4 <xml name="citations">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	5 <citations>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	6 <citation type="doi">10.1093/bioadv/vbad101</citation>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	7 <yield/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	8 </citations>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	9 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	10
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	11 <xml name="general">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	12 <param argument="--dbdir" type="select" label="Phabox2 database">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	13 <options from_data_table="phabox"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	14 </param>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	15 <param argument="--contigs" type="data" format="fasta" optional="false" label="Contig sequences"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	16 <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	17 <param argument="--len" type="integer" value="3000" min="0" label="Minimum contig length" help="Contigs with length smaller than this value will not proceed"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	18 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	19 <token name="@GENERAL@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	20 --dbdir '$dbdir.fields.path'
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	21 --outpth output/
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	22 --contigs '$contigs'
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	23 #if $proteins
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	24 --proteins '$proteins'
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	25 #end if
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	26 --midfolder intermediate/
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	27 --len $len
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	28 --threads "\${GALAXY_SLOTS:-1}"
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	29 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	30
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	31
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	32 <xml name="phamer">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	33 <section name="phamer" title="Options for virus identification" help="">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	34 <param argument="--reject" type="float" value="10" min="0" max="20" label="Minimum known proteins percentage" help="Reject sequences in which the percent proteins aligned to known phages is smaller than the value"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	35 </section>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	36 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	37 <token name="@PHAMER@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	38 --reject $phamer.reject
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	39 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	40
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	41
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	42 <xml name="network">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	43 <section name="network" title="Options for virus-virus connections" help="The options below are used to generate a network for virus-virus connections. The current parameters are optimized for the ICTV 2024 and are highly accurate for grouping genus-level vOTUs. When making changes, make sure you understand what they are.">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	44 <param argument="--aai" type="float" value="75" min="0" max="100" label="Average amino acids identity"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	45 <param argument="--share" type="float" value="15" min="0" max="100" label="Minimum shared number of proteins"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	46 <param argument="--pcov" type="float" value="80" min="0" max="100" label="Protein-based coverage"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	47 <!-- \-\-draw not recommended to be used according to CLI help -->
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	48 </section>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	49 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	50 <token name="@NETWORK@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	51 --aai $network.aai
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	52 --share $network.share
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	53 --pcov $network.pcov
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	54 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	55
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	56 <xml name="crispr">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	57 <section name="crispr" title="Options used to predict CRISPRs based on MAGs" help="">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	58 <param argument="--bfolder" type="data" format="fasta" optional="true" label="MAGS"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	59 <param argument="--prophage" type="integer" value="1000" min="0" max="100000" label="Minimum alignment length for estimate potential prophage"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	60 <param argument="--cpident" type="float" value="90" min="90" max="100" label="Alignment identity for CRISPRs"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	61 <param argument="--ccov" type="float" value="90" min="0" max="100" label="Alignment coverage for CRISPRs"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	62 <param argument="--blast" type="select" label="BLAST program for CRISPRs" help="blastn-short will lead to more sensitive results but require more time to execute the program">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	63 <option value="blastn">blastn</option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	64 <option value="blastn-short">blastn-short</option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	65 </param>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	66 <param argument="--magonly" type="boolean" truevalue="--magonly Y" falsevalue="--magonly N" label="Only predicting host based on the provided MAGs" help="Default is to predict the host based on the MAGs and the reference database"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	67 </section>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	68 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	69 <token name="@CRISPR_PRE@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	70 #if $crispr.bfolder
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	71 mkdir bfolder &&
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	72 #for b in $crispr.bfolder
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	73 #set bname = re.sub('[^\w\-_\.]', '_', $b.element_identifier)
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	74 ln -s '$b' '$bname' &&
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	75 #end for
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	76 #end if
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	77 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	78 <token name="@CRISPR@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	79 #if $crispr.bfolder
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	80 --bfolder bfolder
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	81 #end if
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	82 --prophage $crispr.prophage
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	83 --cpident $crispr.cpident
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	84 --ccov $crispr.ccov
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	85 --blast $crispr.blast
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	86 $magonly
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	87 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	88
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	89 <xml name="contamination">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	90 <section name="contamination" title="Options for contamination detection" help="">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	91 <param argument="--sensitive" type="boolean" truevalue="--sensitive Y" falsevalue="--sensitive N" label="Sensitive search for prokaryotic genes" help="Enabling this will lead to more sensitive results but require more time to execute the program"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	92 </section>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	93 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	94 <token name="@CONTAMINATION@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	95 $contamination.sensitive
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	96 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	97
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	98 <xml name="aai">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	99 <param argument="--aai" type="float" value="75" min="0" max="100" label="Average amino acids identity for AAI based genus grouping"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	100 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	101
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	102 <xml name="votu">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	103 <section name="votu" title="Options vOTU grouping" help="">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	104 <conditional name="mode_cond">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	105 <param argument="--mode" type="select" label="Clustering mode" >
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	106 <option value="ANI">ANI</option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	107 <option value="AAI">AAI</option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	108 </param>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	109 <when value="ANI">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	110 <param argument="--ani" type="float" value="95" min="0" max="100" label="Alignment identity for ANI-based clustering"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	111 <param argument="--tcov" type="float" value="85" min="0" max="100" label="Alignment coverage for ANI-based clustering"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	112 </when>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	113 <when value="AAI">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	114 <param argument="--aai" type="float" value="75" min="0" max="100" label="Average amino acids identity for AAI based genus grouping"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	115 <param argument="--pcov" type="float" value="80" min="0" max="100" label="Protein-level coverage for AAI based genus grouping"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	116 <param argument="--share" type="float" value="15" min="0" max="100" label="Minimum shared number of proteins for AAI based genus grouping"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	117 </when>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	118 </conditional>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	119 </section>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	120 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	121 <token name="@VOTU@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	122 --mode $votu.mode_cond.mode
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	123 #if $votu.mode_cond.mode == "AAI"
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	124 --aai $votu.mode_cond.aai
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	125 --pcov $votu.mode_cond.pcov
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	126 --share $votu.mode_cond.share
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	127 #else if $votu.mode_cond.mode == "ANI"
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	128 --ani $votu.mode_cond.ani
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	129 --tcov $votu.mode_cond.tcov
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	130 #end if
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	131 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	132
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	133 <xml name="tree">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	134 <section name="tree" title="Options for tree building" help="">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	135 <param argument="--marker" type="select" multiple="true" label="Markers used to generate tree" help="Using combinations of these markers can improve the accuracy of the tree. But will decrease the number of sequences in the tree. Numbers in parentheses give the percentage of prokaryotic viruses that have the corresponding protein.">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	136 <option value="endolysin">endolysin (91)</option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	137 <option value="holin">holin (75)</option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	138 <option value="head">marjor head (77)</option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	139 <option value="portal" selected="true">portal (84) </option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	140 <option value="terl" selected="true">terminase large subunit (92)</option>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	141 </param>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	142 <param argument="--mcov" type="float" value="50" min="0" max="100" label="Alignment coverage for matching marker genes"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	143 <param argument="--mpident" type="float" value="25" min="0" max="100" label="Alignment identitiy for matching marker genes"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	144 </section>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	145 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	146 <token name="@TREE@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	147 --marker
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	148 #for m in $tree.marker
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	149 $m
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	150 #end for
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	151 --mcov $tree.mcov
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	152 --mpident $tree.mpident
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	153 ## constructing the MSA and building the tree
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	154 ## (the program would use mafft and fasttree)
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	155 ## can be done more flexibly in Galaxy
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	156 ## (leavinh this here to ensure it won't be implemented)
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	157 ## --msa Y
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	158 ## --tree Y
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	159 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	160
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	161 <xml name="supp_out" tokens="task">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	162 <collection name="@TASK@_supp_out" type="list" label="${tool.name} on ${on_string}: @TASK@ supplement">
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	163 <discover_datasets pattern="(?P<designation>.+).fa" format="fasta" directory="output/final_prediction/@TASK@_supplementary"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	164 <discover_datasets pattern="(?P<designation>.+).tsv" format="tabular" directory="output/final_prediction/@TASK@_supplementary"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	165 <discover_datasets pattern="(?P<designation>.+).tab" format="tabular" directory="output/final_prediction/@TASK@_supplementary"/>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	166 <filter>supplements and "@TASK@" in supplements</filter>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	167 </collection>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	168 </xml>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	169
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	170 <token name="@COMMON_OUTPUT_DOC@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	171 A tabular dataset with the following columns:
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	172
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	173 - Accession: the accession or the name of the input contigs.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	174 - Length: the length of input contigs.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	175 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	176 <token name="@PHAMER_OUTPUT_DOC@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	177 - Pred: virus or non-virus.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	178 - Proportion: the proportion of the proteins that can be aligned to the virus database (from 0 to 1).
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	179 - PhaMerScore: the prediction score given by the deep learning model.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	180 - PhaMerConfidence: the confidence of prediction, determined by both Proportion and PhaMerScore (high-confidence, medium-confidence, low-confidence, lower than reject threshold (according to the --reject parameter, default: 0.1)).
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	181 For the virus with low-confidence or lower than reject threshold, we recommend you to run the contamination task to check their sequence quality.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	182 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	183 <token name="@PHAGCN_OUTPUT_DOC@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	184 - Lineage: the predicted taxonomy lineage (NCBI version) of the contigs. Each rank is separated by the ';'.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	185 - PhaGCNScore: the predicted score for each rank in the lineage. Each rank is separated by the ';'.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	186 - Genus: whether the contig has a genus level name ('-' means unknown).
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	187 - GenusCluster: if the Genus is '-', the program will assign a genus-level grouping result: group_idx (idx = 1, 2, 3, ...) or singleton. This can be viewed as genus-level OTUs based on the average shared protein identities between sequences.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	188 - Prokaryotic virus (Bacteriophages and Archaeal virus): Y/N
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	189 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	190 <token name="@PHATYP_OUTPUT_DOC@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	191 - TYPE: virulent or temperate (virus).
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	192 - PhaTYPScore: the prediction score given by the deep learning model.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	193 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	194 <token name="@CHERRY_OUTPUT_DOC@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	195 - Host: the predicted host (NCBI taxonomy) of the contigs. '-' means unknown host.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	196 - CHERRYScore: the predicted score from the model.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	197 - Method:
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	198 - CRISPR-based(MAG): CRISPRs alignment results from provided MAG (if any)
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	199 - CRISPR-based(DB): CRISPRs alignment results from database.
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	200 - AAI-based: predicting host based on virus-simil
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	201 - Host_NCBI_lineage
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	202 - Host_GTDB_lineage
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	203 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	204
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	205 <token name="@COMMON_INPUT_DOC@"><![CDATA[
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	206 Input
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	207
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	208 - Contig sequences in FASTA format
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	209 - Optionally own predicted protein sequences can be given (by default the tool will use prodigal and diamond blastp for the prediction)
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	210 ]]></token>
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	211
6c7718bc9849 planemo upload for repository https://github.com/Helmholtz-UFZ/ufz-galaxy-tools/blob/main/tools/phabox commit 52385539f64c4e46c2e8953588efa3ea01bb99fd ufz parents: diff changeset	212 </macros>

Mercurial > repos > ufz > phabox_contamination

annotate macros.xml @ 0:6c7718bc9849 draft default tip