blobtoolkit: blobtoolkit.xml annotate

annotate blobtoolkit.xml @ 1:cbcbcb47b798 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955

author	bgruening
date	Mon, 20 Mar 2023 16:37:40 +0000
parents	73417c40e518
children	a4e7a0877d0c

rev	line source
0 73417c40e518 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">
73417c40e518 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>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	3 <macros>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	4 <import>macros.xml</import>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	5 </macros>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	6 <expand macro='requirements' />
73417c40e518 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[
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	8 #if $mode_conditional.selector == 'create'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	9 mkdir -p './Blobdir' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	10 mkdir -p './taxdump' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	11 ln -s '${mode_conditional.taxdump}' 'taxdump.tar' &&
73417c40e518 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' &&
73417c40e518 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' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	14 #if $mode_conditional.meta
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	15 ln -s '${mode_conditional.meta}' 'assembly.yaml' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	16 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	17 blobtools create
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	18 --fasta 'assembly.fasta'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	19 #if $mode_conditional.meta
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	20 --meta 'assembly.yaml'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	21 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	22 --taxid $mode_conditional.taxid
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	23 --taxdump './taxdump'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	24 './Blobdir'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	25 && cp -r './taxdump' './Blobdir/'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	26 && tar -zcf './Blobdir.tgz' './Blobdir'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	27
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	28 #else if $mode_conditional.selector == 'add'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	29 #if $mode_conditional.blobdir.is_of_type("tgz")
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	30 tar -zxf '${mode_conditional.blobdir}' -C './' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	31 #else
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	32 tar -xf '${mode_conditional.blobdir}' -C './' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	33 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	34 #if $mode_conditional.busco
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	35 ln -s '${mode_conditional.busco}' './busco_results.tab' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	36 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	37 #if $mode_conditional.blast_input.selector == 'enabled'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	38 ln -s '$mode_conditional.blast_input.hits' './blast_results.tab' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	39 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	40 #if $mode_conditional.cov
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	41 ln -s '$mode_conditional.cov' './input.bam' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	42 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	43 #if $mode_conditional.bed
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	44 mkdir -p './bed_files' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	45 #import re
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	46 #for $i, $input in enumerate($mode_conditional.bed):
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	47 #set $safename = re.sub('[^\w\-_]', '_', $input.element_identifier) + "." + str($i)
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	48 ln -sf '${input}' './bed_files/${safename}.bed' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	49 #end for
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	50 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	51 blobtools add
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	52 --threads \${GALAXY_SLOTS:-8}
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	53 --taxdump './Blobdir/taxdump'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	54 #if $mode_conditional.busco
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	55 --busco './busco_results.tab'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	56 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	57 #if $mode_conditional.blast_input.selector == 'enabled'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	58 --hits './blast_results.tab'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	59 #if $mode_conditional.blast_input.hits_cols
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	60 --hits-cols '${$mode_conditional.blast_input.hits_cols}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	61 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	62 --taxrule $mode_conditional.blast_input.taxrule
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	63 --evalue $mode_conditional.blast_input.evalue
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	64 --hit-count $mode_conditional.blast_input.hit_count
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	65 --bitscore $mode_conditional.blast_input.bitscore
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	66 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	67 #if $mode_conditional.bed
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	68 --beddir './bed_files'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	69 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	70 #if $mode_conditional.cov
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	71 --cov './input.bam'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	72 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	73 #if $mode_conditional.fasta
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	74 --fasta '${mode_conditional.fasta}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	75 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	76 #if $mode_conditional.trnascan
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	77 --trnascan '${mode_conditional.trnascan}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	78 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	79 #if $mode_conditional.text_input.selector == 'enabled'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	80 --text '${mode_conditional.text_input.text}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	81 --text-cols '${mode_conditional.text_input.text_cols}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	82 $mode_conditional.text_input.text_header
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	83 $mode_conditional.text_input.text_no_array
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	84 --text-delimiter $mode_conditional.text_input.text_delimiter
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	85 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	86 #if $mode_conditional.advanced_options.blobdb
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	87 --blobdb '${mode_conditional.advanced_options.blobdb}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	88 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	89 #if $mode_conditional.advanced_options.synonyms
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	90 --synonyms '${mode_conditional.advanced_options.synonyms}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	91 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	92 $mode_conditional.advanced_options.update_plot
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	93 #if $mode_conditional.advanced_options.pileup_args
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	94 --pileup-args '${mode_conditional.advanced_options.pileup_args}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	95 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	96 $mode_conditional.advanced_options.replace
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	97 './Blobdir'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	98 && tar -zcf './Blobdir.tgz' './Blobdir'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	99
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	100 #else if $mode_conditional.selector == 'filter'
1 cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	101 #if $mode_conditional.filter_options.list
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	102 echo $mode_conditional.filter_options.list > id_list.txt &&
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	103 #end if
0 73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	104 #if $mode_conditional.blobdir.is_of_type("tgz")
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	105 tar -zxf '${mode_conditional.blobdir}' -C './' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	106 #else
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	107 tar -xf '${mode_conditional.blobdir}' -C './' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	108 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	109 #if $mode_conditional.filter_options.fasta
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	110 ln -s '${mode_conditional.filter_options.fasta}' './input.fasta' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	111 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	112 #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled'
1 cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	113 ln -s '${mode_conditional.filter_options.fastq_filter.fastq}' './input.fastq' &&
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	114 ln -s '$mode_conditional.filter_options.fastq_filter.cov' './input.bam' &&
0 73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	115 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	116 blobtools filter
73417c40e518 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.param
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	118 --param $mode_conditional.filter_options.param
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	119 #end if
73417c40e518 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.json
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	121 --json $mode_conditional.filter_options.json
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	122 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	123 #if $mode_conditional.filter_options.list
1 cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	124 --list id_list.txt
0 73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	125 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	126 $mode_conditional.filter_options.invert
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	127 #if $mode_conditional.filter_options.fasta
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	128 --fasta './input.fasta'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	129 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	130 #if $mode_conditional.filter_options.fastq_filter.selector == 'enabled'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	131 --fastq './input.fastq'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	132 --cov './input.bam'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	133 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	134 #if $mode_conditional.filter_options.text_input.selector == 'enabled'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	135 --text '${mode_conditional.filter_options.text_input.text}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	136 --text-cols '${mode_conditional.filter_options.text_input.text_cols}'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	137 $mode_conditional.filter_options.text_input.text_header
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	138 --text-delimiter $mode_conditional.filter_options.text_input.text_delimiter
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	139 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	140 ./Blobdir
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	141 #if $mode_conditional.remove_options.remove_selector or $mode_conditional.remove_options.field
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	142 && blobtools remove
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	143 #for $param in $mode_conditional.remove_options.remove_selector
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	144 $param
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	145 #end for
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	146 #if $mode_conditional.remove_options.field
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	147 --field $mode_conditional.remove_options.field
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	148 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	149 ./Blobdir
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	150 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	151 && tar -zcf './Blobdir.tgz' './Blobdir'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	152
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	153 #else if $mode_conditional.selector == 'plots'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	154 #if $mode_conditional.blobdir.is_of_type("tgz")
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	155 tar -zxf '${mode_conditional.blobdir}' -C './' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	156 #else
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	157 tar -xf '${mode_conditional.blobdir}' -C './' &&
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	158 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	159 blobtools view
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	160 --format $mode_conditional.format
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	161 --view 'blob'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	162 ./Blobdir
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	163 && mv ./Blobdir.blob.circle* ./Blobdir.blob.circle
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	164 && blobtools view
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	165 --format $mode_conditional.format
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	166 --view 'cumulative'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	167 ./Blobdir
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	168 && mv ./Blobdir.cumulative* Blobdir.cumulative
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	169 && blobtools view
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	170 --format $mode_conditional.format
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	171 --view 'snail'
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	172 ./Blobdir
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	173 && mv ./Blobdir.snail* Blobdir.snail
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	174 #end if
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	175 ]]></command>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	176 <inputs>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	177 <conditional name="mode_conditional">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	178 <param name="selector" type="select" label="Select mode" help="Select a BlobToolKit module">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	179 <option value="create">Create a BlobToolKit dataset</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	180 <option value="add">Add data to a BlobToolKit dataset</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	181 <option value="filter">Edit a BlobToolKit dataset</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	182 <option value="plots">Generate plots</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	183 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	184 <when value="create">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	185 <param argument="--fasta" type="data" format="fasta" label="Genome assembly file" help="FASTA sequence file" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	186 <param argument="--meta" type="data" format="yaml" label="Metadata file" optional="true" help="Optional metadata dataset"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	187 <param argument="--taxid" type="integer" value="" label="NCBI taxonomy ID" help="Add ranks to metadata for a taxid"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	188 <param argument="--taxdump" type="data" format="tar,tgz,gz" label="NCBI taxdump directory" help="It should be compressed in tar.gz format"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	189 </when>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	190 <when value="add">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	191 <param name="blobdir" type="data" format="tgz" label="Blobdir.tgz file" help="This file should be generated by Blobtool create" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	192 <param argument="--busco" type="data" format="tsv,tabular,txt" optional="true" label="BUSCO full table file"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	193 <conditional name="blast_input">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	194 <param name="selector" type="select" label="BLAST/Diamond hits">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	195 <option value="enabled">Enabled</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	196 <option value="disabled" selected="true">Disabled</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	197 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	198 <when value="enabled">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	199 <param argument="--hits" type="data" format="tsv,tabular" optional="true" label="BLAST/Diamond hits dataset" help="Tabular BLAST/Diamond output file"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	200 <param argument="--taxrule" type="select" label="BLAST hits to taxa rule" help="Rule to use when assigning BLAST hits to taxa">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	201 <option value="bestsum">Bestsum</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	202 <option value="bestsumorder">Bestsumorder</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	203 <option value="bestdistsum">Bestdistsum</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	204 <option value="bestdistsumorder">Bestdistsumorder</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	205 <option value="blastp">Blastp</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	206 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	207 <param argument="--evalue" type="float" min="0" value="1" label="E-value cutoff"
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	208 help="The smaller the E-value, the better the match. Any hits with an evalue weaker than the value specified will be excluded"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	209 <param argument="--bitscore" type="float" min="0" value="1" label="Bitscore cutoff"
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	210 help="The higher the bit-score, the better the sequence similarity. Any hits with an bitscore lower the value specified will be excluded"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	211 <param argument="--hit-count" type="integer" min="1" value="10" label="Hits to a given taxon" optional="true"
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	212 help="By default the 10 highest scoring hits to a given taxon will be used when applying the --taxrule"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	213 <param argument="--hits-cols" type="text" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue" optional="true"
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	214 label="BLAST/Diamond file column order" help="More information in the help section">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	215 <sanitizer invalid_char="">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	216 <valid initial="string.letters,string.digits">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	217 <add value="=" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	218 <add value="," />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	219 </valid>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	220 </sanitizer>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	221 <validator type="regex">[0-9a-z=,]+</validator>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	222 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	223 </when>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	224 <when value="disabled"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	225 </conditional>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	226 <param argument="--bed" type="data" format="bed" multiple="true" optional="true" label="BED file of coverages per scaffold"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	227 <param argument="--cov" type="data" format="bam,sam,cram" optional="true" label="BAM/SAM/CRAM read alignment file"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	228 <param argument="--fasta" type="data" format="fasta" optional="true" label="FASTA sequence" help="FASTA sequence file" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	229 <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"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	230 <expand macro="macro_text_input">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	231 <param argument="--text-no-array" type="boolean" truevalue="--text-no-array" falsevalue="" checked="false" label="Prevent duplicated identifiers"
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	232 help="Prevent fields in files with duplicate identifiers being loaded as array fields" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	233 </expand>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	234 <section name="advanced_options" title="Advanced options">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	235 <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"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	236 <param argument="--synonyms" type="data" format="tsv" optional="true" label="Identifier and sinonyms" help="TSV file containing current identifiers and synonyms"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	237 <param argument="--update-plot" type="boolean" truevalue="--update-plot" falsevalue="" checked="false" label="Update plot" help="Flag to use new taxrule as default category" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	238 <param argument="--pileup-args" type="text" value="" optional="true" label="Samtools Pileup" help="Key/value pairs to pass to samtools pileup">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	239 <sanitizer invalid_char="">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	240 <valid initial="string.letters,string.digits">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	241 <add value="=" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	242 <add value="," />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	243 <add value="-" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	244 </valid>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	245 </sanitizer>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	246 <validator type="regex">[0-9a-zA-Z=,-]+</validator>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	247 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	248 <param argument="--replace" type="boolean" truevalue="--replace" falsevalue="" checked="false" label="Replace fields" help="Allow existing fields to be overwritten" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	249 </section>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	250 </when>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	251 <when value="filter">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	252 <param name="blobdir" type="data" format="tgz" label="Blobdir file" help="This file should be generated by the moudule create" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	253 <section name="filter_options" title="Filter mode options" expanded="true">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	254 <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
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	255 filter based on Variable or Category fields">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	256 <sanitizer invalid_char="">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	257 <valid initial="string.letters,string.digits">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	258 <add value="=" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	259 <add value="," />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	260 <add value="-" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	261 </valid>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	262 </sanitizer>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	263 <validator type="regex">[0-9a-zA-Z=,-]+</validator>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	264 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	265 <param argument="--list" type="text" value="" optional="true" label="List of identifiers" help="Space separated list of identifiers">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	266 <sanitizer invalid_char="">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	267 <valid initial="string.letters,string.digits">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	268 <add value=" " />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	269 <add value="-" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	270 <add value="_" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	271 </valid>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	272 </sanitizer>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	273 <validator type="regex">[0-9a-zA-Z _-]+</validator>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	274 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	275 <param argument="--json" type="data" format="json" optional="true" label="JSON format list file" help="JSON format list file as generated by BlobtoolKit Viewer"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	276 <param argument="--fasta" type="data" format="fasta" multiple="true" optional="true" label="Assembly to be filtered" help="FASTA format assembly file to be filtered"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	277 <conditional name="fastq_filter">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	278 <param name="selector" type="select" label="Filter FASTQ reads">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	279 <option value="disabled">Disabled</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	280 <option value="enabled">Enabled</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	281 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	282 <when value="disabled"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	283 <when value="enabled">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	284 <param argument="--fastq" type="data" format="fastq" optional="true" label="Reads to be filtered" help="FASTQ format read file to be filtered"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	285 <param argument="--cov" type="data" format="bam,sam,cram" optional="true" label="BAM/SAM/CRAM read alignment file" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	286 </when>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	287 </conditional>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	288 <expand macro="macro_text_input"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	289 <param argument="--summary-rank" type="text" value="phylum" label="Sumamry rank" help="Taxonomic level for summary">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	290 <sanitizer invalid_char="">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	291 <valid initial="string.letters"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	292 </sanitizer>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	293 <validator type="regex">[a-zA-Z]+</validator>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	294 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	295 <param argument="--invert" type="boolean" truevalue="--invert" falsevalue="" checked="false" label="Invert filter" help="Invert the filter (exclude matching records)"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	296 </section>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	297 <section name="remove_options" title="Remove mode options" expanded="true">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	298 <param name="remove_selector" type="select" multiple="true" display="checkboxes" label="Fields to remove">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	299 <option value="--all">Remove all fields except identifiers (--all)</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	300 <option value="--busco">Remove all BUSCO fields (--busco)</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	301 <option value="--cov">Remove all cov and read_cov fields (--cov)</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	302 <option value="--fasta">Remove gc, length and ncount fields (--fasta)</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	303 <option value="--hits">Remove all taxonomy fields (--hits)</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	304 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	305 <param argument="--field" type="text" value="" optional="true" label="Remove fields by ID">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	306 <sanitizer invalid_char="">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	307 <valid initial="string.letters,string.digits"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	308 </sanitizer>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	309 <validator type="regex">[0-9a-zA-Z]+</validator>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	310 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	311 </section>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	312 </when>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	313 <when value="plots">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	314 <param name="blobdir" type="data" format="tgz" label="Blobdir file" help="This file should be generated by the moudule create" />
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	315 <param argument="--format" type="select" label="Image format">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	316 <option value="png">PNG</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	317 <option value="svg">SVG</option>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	318 </param>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	319 <param argument="--param" type="text" optional="true" label="Query parameter" help="Query string parameter."/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	320 </when>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	321 </conditional>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	322 </inputs>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	323 <outputs>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	324 <data name="blobdir" format="tgz" from_work_dir="./Blobdir.tgz" label="${tool.name} on ${on_string}: Blobdir.tgz">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	325 <filter>mode_conditional['selector'] == 'create' or mode_conditional['selector'] == 'add' or mode_conditional['selector'] == 'filter'</filter>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	326 </data>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	327 <data name="plot_circle" format="png" from_work_dir="./Blobdir.blob.circle" label="${tool.name} on ${on_string}: blob plot">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	328 <filter>mode_conditional['selector'] == 'plots'</filter>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	329 <change_format>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	330 <when input="$mode_conditional.format" value="svg" format="svg"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	331 </change_format>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	332 </data>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	333 <data name="plot_cumulative" format="png" from_work_dir="./Blobdir.cumulative" label="${tool.name} on ${on_string}: cumulative plot">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	334 <filter>mode_conditional['selector'] == 'plots'</filter>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	335 <change_format>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	336 <when input="$mode_conditional.format" value="svg" format="svg"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	337 </change_format>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	338 </data>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	339 <data name="plot_snail" format="png" from_work_dir="./Blobdir.snail" label="${tool.name} on ${on_string}: snail plot">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	340 <filter>mode_conditional['selector'] == 'plots'</filter>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	341 <change_format>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	342 <when input="$mode_conditional.format" value="svg" format="svg"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	343 </change_format>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	344 </data>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	345 </outputs>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	346 <tests>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	347 <test expect_num_outputs="1">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	348 <conditional name="mode_conditional">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	349 <param name="selector" value="create"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	350 <param name="fasta" value="assembly.fasta.gz"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	351 <param name="meta" value="assembly.yaml"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	352 <param name="taxid" value="801"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	353 <param name="taxdump" value="small_taxdump.tar.gz"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	354 </conditional>
1 cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	355 <output name="blobdir" file="test01_blobdir.tar.gz" compare="sim_size" delta="1500"/>
0 73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	356 </test>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	357 <test expect_num_outputs="1">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	358 <conditional name="mode_conditional">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	359 <param name="selector" value="add"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	360 <param name="blobdir" value="test01_blobdir.tar.gz"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	361 <param name="busco" value="busco_full_table.tabular"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	362 <param name="cov" value="bam_file.bam"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	363 <param name="fasta" value="contig.fasta"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	364 <section name="advanced_options">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	365 <param name="update_plot" value="false"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	366 </section>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	367 <conditional name="blast_input">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	368 <param name="selector" value="enabled"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	369 <param name="hits" value="blast_results.tabular"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	370 <param name="taxrule" value="bestsum"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	371 <param name="evalue" value="1"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	372 <param name="bitscore" value="1"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	373 <param name="hit_count" value="10"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	374 <param name="hits_cols" value="1=qseqid,2=staxids,3=bitscore,5=sseqid,10=qstart,11=qend,14=evalue"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	375 </conditional>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	376 </conditional>
1 cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	377 <output name="blobdir" file="test02_blobdir.tar.gz" compare="sim_size" delta="1500"/>
0 73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	378 </test>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	379 <test expect_num_outputs="1">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	380 <conditional name="mode_conditional">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	381 <param name="selector" value="filter"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	382 <param name="blobdir" value="test02_blobdir.tar.gz"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	383 <section name="filter_options">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	384 <param name="fasta" value="contig.fasta"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	385 <param name="summary_rank" value="phylum"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	386 <param name="invert" value="false"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	387 </section>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	388 <section name="remove_options">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	389 <param name="remove_selector" value="--all"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	390 </section>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	391 </conditional>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	392 <output name="blobdir">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	393 <assert_contents>
1 cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	394 <has_size value="672500" delta="1000"/>
0 73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	395 </assert_contents>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	396 </output>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	397 </test>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	398 <test expect_num_outputs="3">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	399 <conditional name="mode_conditional">
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	400 <param name="selector" value="plots"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	401 <param name="blobdir" value="test02_blobdir.tar.gz"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	402 <param name="format" value="png"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	403 </conditional>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	404 <output name="plot_circle" file="test04_circle.png" ftype="png"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	405 <output name="plot_cumulative" file="test04_cumulative.png" ftype="png"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	406 <output name="plot_snail" file="test04_snail.png" ftype="png"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	407 </test>
1 cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	408 <test expect_num_outputs="1">
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	409 <conditional name="mode_conditional">
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	410 <param name="selector" value="filter"/>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	411 <param name="blobdir" value="test02_blobdir.tar.gz"/>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	412 <section name="filter_options">
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	413 <param name="list" value="801 802"/>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	414 <param name="fasta" value="contig.fasta"/>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	415 </section>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	416 <section name="remove_options">
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	417 <param name="remove_selector" value="--all"/>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	418 </section>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	419 </conditional>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	420 <output name="blobdir">
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	421 <assert_contents>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	422 <has_size value="672497" delta="1000"/>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	423 </assert_contents>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	424 </output>
cbcbcb47b798 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 797eb67eae4dfe502325c53f78824c5ba4033955 bgruening parents: 0 diff changeset	425 </test>
0 73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	426 </tests>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	427 <help><![CDATA[
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	428 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,
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	429 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.
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	430 ]]></help>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	431 <expand macro="citations"/>
73417c40e518 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/blobtoolkit commit 7c0db48ffd4dbee68fb2320fc5a064bc9c3219d9 bgruening parents: diff changeset	432 </tool>

Mercurial > repos > bgruening > blobtoolkit

annotate blobtoolkit.xml @ 1:cbcbcb47b798 draft