blobtoolkit: blobtoolkit.xml annotate

annotate blobtoolkit.xml @ 2:53dd00a4ab68 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37

author	bgruening
date	Tue, 28 Mar 2023 15:17:19 +0000
parents	840822c1e84a
children	8c2167481e72

rev	line source
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	1 <tool id="blobtoolkit" name="BlobToolKit" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	2 <description>genome assembly QC</description>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	3 <macros>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	4 <import>macros.xml</import>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	5 </macros>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	6 <expand macro='requirements' />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	7 <command detect_errors="exit_code"><![CDATA[
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	8 #if $mode_conditional.selector == 'create'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	9 mkdir -p './Blobdir' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	10 mkdir -p './taxdump' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	11 ln -s '${mode_conditional.taxdump}' 'taxdump.tar' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	12 tar -xf 'taxdump.tar' -C './taxdump' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	13 ln -s '${mode_conditional.fasta}' 'assembly.fasta' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	14 #if $mode_conditional.meta
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	15 ln -s '${mode_conditional.meta}' 'assembly.yaml' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	16 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	17 blobtools create
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	18 --fasta 'assembly.fasta'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	19 #if $mode_conditional.meta
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	20 --meta 'assembly.yaml'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	21 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	22 --taxid $mode_conditional.taxid
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	23 --taxdump './taxdump'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	24 './Blobdir'
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	25 && tar -C ./Blobdir -zcvf Blobdir.tgz .
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	26 #else if $mode_conditional.selector == 'add'
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	27 mkdir -p './Blobdir' &&
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	28 mkdir -p './taxdump' &&
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	29 ln -s '${mode_conditional.taxdump}' 'taxdump.tar' &&
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	30 tar -xf 'taxdump.tar' -C './taxdump' &&
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	31 #if $mode_conditional.blobdir.is_of_type("tgz")
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	32 tar -zxf '${mode_conditional.blobdir}' -C './Blobdir' &&
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	33 #else
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	34 tar -xf '${mode_conditional.blobdir}' -C './Blobdir' &&
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	35 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	36 #if $mode_conditional.busco
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	37 ln -s '${mode_conditional.busco}' './busco_results.tab' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	38 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	39 #if $mode_conditional.blast_input.selector == 'enabled'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	40 ln -s '$mode_conditional.blast_input.hits' './blast_results.tab' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	41 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	42 #if $mode_conditional.cov
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	43 ln -s '$mode_conditional.cov' './input.bam' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	44 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	45 #if $mode_conditional.bed
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	46 mkdir -p './bed_files' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	47 #import re
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	48 #for $i, $input in enumerate($mode_conditional.bed):
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	49 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) + "." + str($i)
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	50 ln -sf '${input}' './bed_files/${safename}.bed' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	51 #end for
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	52 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	53 blobtools add
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	54 --threads \${GALAXY_SLOTS:-8}
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	55 --taxdump './taxdump'
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	56 #if $mode_conditional.busco
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	57 --busco './busco_results.tab'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	58 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	59 #if $mode_conditional.blast_input.selector == 'enabled'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	60 --hits './blast_results.tab'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	61 #if $mode_conditional.blast_input.hits_cols
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	62 --hits-cols '${$mode_conditional.blast_input.hits_cols}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	63 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	64 --taxrule $mode_conditional.blast_input.taxrule
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	65 --evalue $mode_conditional.blast_input.evalue
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	66 --hit-count $mode_conditional.blast_input.hit_count
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	67 --bitscore $mode_conditional.blast_input.bitscore
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	68 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	69 #if $mode_conditional.bed
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	70 --beddir './bed_files'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	71 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	72 #if $mode_conditional.cov
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	73 --cov './input.bam'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	74 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	75 #if $mode_conditional.fasta
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	76 --fasta '${mode_conditional.fasta}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	77 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	78 #if $mode_conditional.trnascan
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	79 --trnascan '${mode_conditional.trnascan}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	80 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	81 #if $mode_conditional.text_input.selector == 'enabled'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	82 --text '${mode_conditional.text_input.text}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	83 --text-cols '${mode_conditional.text_input.text_cols}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	84 $mode_conditional.text_input.text_header
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	85 $mode_conditional.text_input.text_no_array
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	86 --text-delimiter $mode_conditional.text_input.text_delimiter
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	87 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	88 #if $mode_conditional.advanced_options.blobdb
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	89 --blobdb '${mode_conditional.advanced_options.blobdb}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	90 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	91 #if $mode_conditional.advanced_options.synonyms
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	92 --synonyms '${mode_conditional.advanced_options.synonyms}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	93 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	94 $mode_conditional.advanced_options.update_plot
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	95 #if $mode_conditional.advanced_options.pileup_args
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	96 --pileup-args '${mode_conditional.advanced_options.pileup_args}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	97 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	98 $mode_conditional.advanced_options.replace
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	99 './Blobdir'
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	100 && tar -C ./Blobdir -zcvf Blobdir.tgz .
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	101
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	102 #else if $mode_conditional.selector == 'filter'
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	103 mkdir -p './Blobdir' &&
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	104 #if $mode_conditional.blobdir.is_of_type("tgz")
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	105 tar -zxf '${mode_conditional.blobdir}' -C './Blobdir' &&
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	106 #else
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	107 tar -xf '${mode_conditional.blobdir}' -C './Blobdir' &&
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	108 #end if
1 840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	109 #if $mode_conditional.filter_options.list
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	110 echo $mode_conditional.filter_options.list > id_list.txt &&
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	111 #end if
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	112 #if $mode_conditional.blobdir.is_of_type("tgz")
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	113 tar -zxf '${mode_conditional.blobdir}' -C './' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	114 #else
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	115 tar -xf '${mode_conditional.blobdir}' -C './' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	116 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	117 #if $mode_conditional.filter_options.fasta
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	118 ln -s '${mode_conditional.filter_options.fasta}' './input.fasta' &&
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	119 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	120 #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled'
1 840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	121 ln -s '${mode_conditional.filter_options.fastq_filter.fastq}' './input.fastq' &&
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	122 ln -s '$mode_conditional.filter_options.fastq_filter.cov' './input.bam' &&
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	123 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	124 blobtools filter
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	125 #if $mode_conditional.filter_options.param
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	126 --param $mode_conditional.filter_options.param
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	127 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	128 #if $mode_conditional.filter_options.json
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	129 --json $mode_conditional.filter_options.json
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	130 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	131 #if $mode_conditional.filter_options.list
1 840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	132 --list id_list.txt
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	133 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	134 $mode_conditional.filter_options.invert
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	135 #if $mode_conditional.filter_options.fasta
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	136 --fasta './input.fasta'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	137 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	138 #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	139 --fastq './input.fastq'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	140 --cov './input.bam'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	141 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	142 #if $mode_conditional.filter_options.text_input.selector == 'enabled'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	143 --text '${mode_conditional.filter_options.text_input.text}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	144 --text-cols '${mode_conditional.filter_options.text_input.text_cols}'
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	145 $mode_conditional.filter_options.text_input.text_header
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	146 --text-delimiter $mode_conditional.filter_options.text_input.text_delimiter
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	147 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	148 ./Blobdir
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	149 #if $mode_conditional.remove_options.remove_selector or $mode_conditional.remove_options.field
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	150 && blobtools remove
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	151 #for $param in $mode_conditional.remove_options.remove_selector
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	152 $param
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	153 #end for
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	154 #if $mode_conditional.remove_options.field
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	155 --field $mode_conditional.remove_options.field
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	156 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	157 ./Blobdir
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	158 #end if
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	159 && tar -C ./Blobdir -zcvf Blobdir.tgz .
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	160 #end if
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	161 ]]></command>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	162 <inputs>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	163 <conditional name="mode_conditional">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	164 <param name="selector" type="select" label="Select mode" help="Select a BlobToolKit module">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	165 <option value="create">Create a BlobToolKit dataset</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	166 <option value="add">Add data to a BlobToolKit dataset</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	167 <option value="filter">Edit a BlobToolKit dataset</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	168 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	169 <when value="create">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	170 <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	171 <param argument="--meta" type="data" format="yaml" label="Metadata file" optional="true" help="Optional metadata dataset"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	172 <param argument="--taxid" type="integer" value="" label="NCBI taxonomy ID" help="Add ranks to metadata for a taxid"/>
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	173 <expand macro="macro_taxdump"/>
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	174 </when>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	175 <when value="add">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	176 <param name="blobdir" type="data" format="tgz" label="Blobdir.tgz file" help="This file should be generated by Blobtool create" />
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	177 <expand macro="macro_taxdump"/>
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	178 <param argument="--busco" type="data" format="tsv,tabular,txt" optional="true" label="BUSCO full table file"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	179 <conditional name="blast_input">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	180 <param name="selector" type="select" label="BLAST/Diamond hits">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	181 <option value="enabled">Enabled</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	182 <option value="disabled" selected="true">Disabled</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	183 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	184 <when value="enabled">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	185 <param argument="--hits" type="data" format="tsv,tabular" optional="true" label="BLAST/Diamond hits dataset" help="Tabular BLAST/Diamond output file"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	186 <param argument="--taxrule" type="select" label="BLAST hits to taxa rule" help="Rule to use when assigning BLAST hits to taxa">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	187 <option value="bestsum">Bestsum</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	188 <option value="bestsumorder">Bestsumorder</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	189 <option value="bestdistsum">Bestdistsum</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	190 <option value="bestdistsumorder">Bestdistsumorder</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	191 <option value="blastp">Blastp</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	192 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	193 <param argument="--evalue" type="float" min="0" value="1" label="E-value cutoff"
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	194 help="The smaller the E-value, the better the match. Any hits with an evalue weaker than the value specified will be excluded"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	195 <param argument="--bitscore" type="float" min="0" value="1" label="Bitscore cutoff"
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	196 help="The higher the bit-score, the better the sequence similarity. Any hits with an bitscore lower the value specified will be excluded"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	197 <param argument="--hit-count" type="integer" min="1" value="10" label="Hits to a given taxon" optional="true"
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	198 help="By default the 10 highest scoring hits to a given taxon will be used when applying the --taxrule"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	199 <param argument="--hits-cols" type="text" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue" optional="true"
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	200 label="BLAST/Diamond file column order" help="More information in the help section">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	201 <sanitizer invalid_char="">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	202 <valid initial="string.letters,string.digits">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	203 <add value="=" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	204 <add value="," />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	205 </valid>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	206 </sanitizer>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	207 <validator type="regex">[0-9a-z=,]+</validator>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	208 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	209 </when>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	210 <when value="disabled"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	211 </conditional>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	212 <param argument="--bed" type="data" format="bed" multiple="true" optional="true" label="BED file of coverages per scaffold"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	213 <param argument="--cov" type="data" format="bam,sam,cram" optional="true" label="BAM/SAM/CRAM read alignment file"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	214 <param argument="--fasta" type="data" format="fasta" optional="true" label="FASTA sequence" help="FASTA sequence file" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	215 <param argument="--trnascan" type="data" format="tsv,tabular" optional="true" label="tRNAscan2-SE" help="tRNAscan-SE is employed for identifying and annotating tRNA genes in genomes"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	216 <expand macro="macro_text_input">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	217 <param argument="--text-no-array" type="boolean" truevalue="--text-no-array" falsevalue="" checked="false" label="Prevent duplicated identifiers"
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	218 help="Prevent fields in files with duplicate identifiers being loaded as array fields" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	219 </expand>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	220 <section name="advanced_options" title="Advanced options">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	221 <param argument="--blobdb" type="data" format="json" optional="true" label="Blobtools v1 database" help="This file should have been generated with the previous Blobtools tool version"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	222 <param argument="--synonyms" type="data" format="tsv" optional="true" label="Identifier and sinonyms" help="TSV file containing current identifiers and synonyms"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	223 <param argument="--update-plot" type="boolean" truevalue="--update-plot" falsevalue="" checked="false" label="Update plot" help="Flag to use new taxrule as default category" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	224 <param argument="--pileup-args" type="text" value="" optional="true" label="Samtools Pileup" help="Key/value pairs to pass to samtools pileup">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	225 <sanitizer invalid_char="">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	226 <valid initial="string.letters,string.digits">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	227 <add value="=" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	228 <add value="," />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	229 <add value="-" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	230 </valid>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	231 </sanitizer>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	232 <validator type="regex">[0-9a-zA-Z=,-]+</validator>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	233 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	234 <param argument="--replace" type="boolean" truevalue="--replace" falsevalue="" checked="false" label="Replace fields" help="Allow existing fields to be overwritten" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	235 </section>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	236 </when>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	237 <when value="filter">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	238 <param name="blobdir" type="data" format="tgz" label="Blobdir file" help="This file should be generated by the moudule create" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	239 <section name="filter_options" title="Filter mode options" expanded="true">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	240 <param argument="--param" type="text" value="" optional="true" label="Parameter value" help="String of type param=value. Individual param=value pairs can be specified to
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	241 filter based on Variable or Category fields">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	242 <sanitizer invalid_char="">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	243 <valid initial="string.letters,string.digits">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	244 <add value="=" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	245 <add value="," />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	246 <add value="-" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	247 </valid>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	248 </sanitizer>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	249 <validator type="regex">[0-9a-zA-Z=,-]+</validator>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	250 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	251 <param argument="--list" type="text" value="" optional="true" label="List of identifiers" help="Space separated list of identifiers">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	252 <sanitizer invalid_char="">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	253 <valid initial="string.letters,string.digits">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	254 <add value=" " />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	255 <add value="-" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	256 <add value="_" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	257 </valid>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	258 </sanitizer>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	259 <validator type="regex">[0-9a-zA-Z _-]+</validator>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	260 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	261 <param argument="--json" type="data" format="json" optional="true" label="JSON format list file" help="JSON format list file as generated by BlobtoolKit Viewer"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	262 <param argument="--fasta" type="data" format="fasta" multiple="true" optional="true" label="Assembly to be filtered" help="FASTA format assembly file to be filtered"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	263 <conditional name="fastq_filter">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	264 <param name="selector" type="select" label="Filter FASTQ reads">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	265 <option value="disabled">Disabled</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	266 <option value="enabled">Enabled</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	267 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	268 <when value="disabled"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	269 <when value="enabled">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	270 <param argument="--fastq" type="data" format="fastq" optional="true" label="Reads to be filtered" help="FASTQ format read file to be filtered"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	271 <param argument="--cov" type="data" format="bam,sam,cram" optional="true" label="BAM/SAM/CRAM read alignment file" />
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	272 </when>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	273 </conditional>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	274 <expand macro="macro_text_input"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	275 <param argument="--summary-rank" type="text" value="phylum" label="Sumamry rank" help="Taxonomic level for summary">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	276 <sanitizer invalid_char="">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	277 <valid initial="string.letters"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	278 </sanitizer>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	279 <validator type="regex">[a-zA-Z]+</validator>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	280 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	281 <param argument="--invert" type="boolean" truevalue="--invert" falsevalue="" checked="false" label="Invert filter" help="Invert the filter (exclude matching records)"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	282 </section>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	283 <section name="remove_options" title="Remove mode options" expanded="true">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	284 <param name="remove_selector" type="select" multiple="true" display="checkboxes" label="Fields to remove">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	285 <option value="--all">Remove all fields except identifiers (--all)</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	286 <option value="--busco">Remove all BUSCO fields (--busco)</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	287 <option value="--cov">Remove all cov and read_cov fields (--cov)</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	288 <option value="--fasta">Remove gc, length and ncount fields (--fasta)</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	289 <option value="--hits">Remove all taxonomy fields (--hits)</option>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	290 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	291 <param argument="--field" type="text" value="" optional="true" label="Remove fields by ID">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	292 <sanitizer invalid_char="">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	293 <valid initial="string.letters,string.digits"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	294 </sanitizer>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	295 <validator type="regex">[0-9a-zA-Z]+</validator>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	296 </param>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	297 </section>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	298 </when>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	299 </conditional>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	300 </inputs>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	301 <outputs>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	302 <data name="blobdir" format="tgz" from_work_dir="./Blobdir.tgz" label="${tool.name} on ${on_string}: Blobdir.tgz">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	303 <filter>mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter'</filter>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	304 </data>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	305 </outputs>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	306 <tests>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	307 <test expect_num_outputs="1">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	308 <conditional name="mode_conditional">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	309 <param name="selector" value="create"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	310 <param name="fasta" value="assembly.fasta.gz"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	311 <param name="meta" value="assembly.yaml"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	312 <param name="taxid" value="801"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	313 <param name="taxdump" value="small_taxdump.tar.gz"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	314 </conditional>
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	315 <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="100"/>
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	316 </test>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	317 <test expect_num_outputs="1">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	318 <conditional name="mode_conditional">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	319 <param name="selector" value="add"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	320 <param name="blobdir" value="test01_blobdir.tar.gz"/>
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	321 <param name="taxdump" value="small_taxdump.tar.gz"/>
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	322 <param name="busco" value="busco_full_table.tabular"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	323 <param name="cov" value="bam_file.bam"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	324 <param name="fasta" value="contig.fasta"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	325 <section name="advanced_options">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	326 <param name="update_plot" value="false"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	327 </section>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	328 <conditional name="blast_input">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	329 <param name="selector" value="enabled"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	330 <param name="hits" value="blast_results.tabular"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	331 <param name="taxrule" value="bestsum"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	332 <param name="evalue" value="1"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	333 <param name="bitscore" value="1"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	334 <param name="hit_count" value="10"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	335 <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	336 </conditional>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	337 </conditional>
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	338 <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="100"/>
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	339 </test>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	340 <test expect_num_outputs="1">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	341 <conditional name="mode_conditional">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	342 <param name="selector" value="filter"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	343 <param name="blobdir" value="test02_blobdir.tar.gz"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	344 <section name="filter_options">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	345 <param name="fasta" value="contig.fasta"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	346 <param name="summary_rank" value="phylum"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	347 <param name="invert" value="false"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	348 </section>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	349 <section name="remove_options">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	350 <param name="remove_selector" value="--all"/>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	351 </section>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	352 </conditional>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	353 <output name="blobdir">
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	354 <assert_contents>
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	355 <has_size value="620" delta="50"/>
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	356 </assert_contents>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	357 </output>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	358 </test>
1 840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	359 <test expect_num_outputs="1">
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	360 <conditional name="mode_conditional">
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	361 <param name="selector" value="filter"/>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	362 <param name="blobdir" value="test02_blobdir.tar.gz"/>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	363 <section name="filter_options">
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	364 <param name="list" value="801 802"/>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	365 <param name="fasta" value="contig.fasta"/>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	366 </section>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	367 <section name="remove_options">
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	368 <param name="remove_selector" value="--all"/>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	369 </section>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	370 </conditional>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	371 <output name="blobdir">
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	372 <assert_contents>
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	373 <has_size value="620" delta="50"/>
1 840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	374 </assert_contents>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	375 </output>
840822c1e84a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	376 </test>
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	377 </tests>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	378 <help><![CDATA[
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	379 BlobToolKit is a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. It can be used to process assembly,
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	380 read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility.
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	381
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	382 .. class:: infomark
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	383
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	384 NCBI taxdump directory
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	385
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	386 The taxdump database, provided by NCBI, includes the taxonomic lineage of taxa, information on type strains and material, and host information. The file new_taxdump.tar.gz can be downloaded from the taxonomy directory on the `FTP site <ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/>`_.
53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	387
0 7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	388 ]]></help>
7d9ee8cd14b8 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	389 <expand macro="citations"/>
2 53dd00a4ab68 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 5078c7010ec46fd01fec2057dd4486781c958c37 bgruening parents: 1 diff changeset	390 </tool>

Mercurial > repos > bgruening > blobtoolkit

annotate blobtoolkit.xml @ 2:53dd00a4ab68 draft