bigscape: bigscape.xml annotate

annotate bigscape.xml @ 0:a9e5d237d7d4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23

author	iuc
date	Sun, 25 Feb 2024 10:51:27 +0000
parents
children	353b2de0eabf

rev	line source
0 a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	1 <tool id="bigscape" name="BiG-SCAPE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	2 <description>Construct sequence similarity networks of BGCs and group them into GCF</description>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	3 <macros>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	4 <token name="@TOOL_VERSION@">1.1.9</token>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	5 <token name="@VERSION_SUFFIX@">0</token>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	6 </macros>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	7 <requirements>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	8 <requirement type="package" version="@TOOL_VERSION@">bigscape</requirement>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	9 </requirements>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	10 <command detect_errors="exit_code">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	11 <![CDATA[
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	12
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	13 #set $path_to_html = $html.files_path
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	14 mkdir -p '$path_to_html' result input &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	15 #for $files in $inputdir:
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	16 #set $filename = "region." + $files.element_identifier
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	17 ln -s '$files' './input/$filename' &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	18 #end for
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	19
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	20 mkdir pfam &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	21 ln -s '$pfam_dir' './pfam/$pfam_dir.element_identifier' &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	22 hmmpress './pfam/Pfam-A.hmm' &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	23
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	24 #if $anchor.is_select == "yes":
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	25 ln -s '$anchorfile' '$anchorfile.element_identifier' &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	26 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	27 #if $list.is_select == "yes":
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	28 cat '$__tool_directory__/domain_includelist.txt' > save.txt &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	29 cat '$domain_includelist' > '$__tool_directory__/domain_includelist.txt' &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	30 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	31
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	32 bigscape
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	33 --inputdir input
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	34 #if $mibig.is_select == "yes"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	35 $mibig.mibig.value
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	36 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	37 --outputdir result
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	38 #if $use_label.is_select == "yes":
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	39 --label '${label}'
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	40 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	41 --pfam_dir pfam
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	42 --cores \${GALAXY_SLOTS:-8}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	43 ${verbose}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	44 ${log}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	45 ${include_singletons}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	46 --domain_overlap_cutoff ${domain_overlap_cutoff}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	47 --min_bgc_size ${min_big_size}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	48 ${mix}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	49 ${no_classify}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	50 #if $banned_classes.value:
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	51 --banned_classes
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	52 #for $banned in str($banned_classes).split( "," ):
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	53 '$banned'
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	54 #end for
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	55 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	56 --cutoffs #for $c in $cutoff# ${c.cutoffs} #end for#
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	57 ${clans_off}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	58 #if $clan_cutoff.is_select == "yes":
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	59 --clan_cutoff $clan_cutoff_val1 $clan_cutoff_val2
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	60 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	61 ${hybrids_off}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	62 --mode ${mode.value}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	63 #if $anchor.is_select == "yes":
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	64 --anchorfile '${anchorfile.element_identifier}'
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	65 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	66 ${force_hmmscan}
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	67 #if $list.is_select == "yes":
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	68 --domain_includelist
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	69 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	70 &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	71
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	72 cp './result/index.html' '$html' &&
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	73 cp -r './result/html_content' '$path_to_html'
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	74
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	75 #if $list.is_select == "yes":
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	76 && cat save.txt > '$__tool_directory__/domain_includelist.txt'
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	77 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	78
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	79 #if $log:
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	80 && cp log.txt '$logfile'
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	81 #end if
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	82 ]]>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	83 </command>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	84 <inputs>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	85 <param argument="--inputdir" format="genbank" multiple="true" type="data"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	86 label="Data files to include in the clustering"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	87 help="Add your .gbk files here. Do not wonder, in the filename 'region. will be added to ensure that every file will be included!" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	88 <conditional name="mibig">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	89 <param name="is_select" type="select" label="Include BGCs from MIBiG database?"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	90 help="Select yes and select which version of the database you want to use" >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	91 <option value="yes" selected="False">Yes</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	92 <option value="no" selected="True">No</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	93 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	94 <when value="yes">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	95 <param name="mibig" type="select" optional="false" label="Version from the MIBiG database"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	96 help="Select which version of the MIBiG databse you want to use." >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	97 <option value="--mibig">3.1</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	98 <option value="--mibig21">2.1</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	99 <option value="--mibig14">1.4</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	100 <option value="--mibig13">1.3</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	101 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	102 </when>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	103 <when value="no" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	104 </conditional>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	105 <conditional name="use_label" >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	106 <param name="is_select" type="select" label="Adding extra string to BiG-SCAPE runs?"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	107 help="Select yes if you want to add an extra string to the outputs">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	108 <option value="yes" selected="False">Yes</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	109 <option value="no" selected="True">No</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	110 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	111 <when value="yes">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	112 <param argument="--label" type="text" value="" optional="false" label="Adding extra string to BiG-SCAPE runs name"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	113 help="By default the BiG-SCAPE runs are named as (YYYY-MM-DD_HH-MM-SS_[extra]) where extra means the mode and if activated (hybrids).">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	114 <validator type="empty_field" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	115 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	116 </when>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	117 <when value="no" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	118 </conditional>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	119 <param argument="--pfam_dir" format="hmm3" type="data"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	120 label="Data file Pfam-A.hmm"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	121 help="Add Pfam-A.hmm.gz file here, please. Look at the help section where you can download it!" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	122 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="False"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	123 label="Print more detailed information about each step"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	124 help="Getting more information about the analysis if toggled is true." />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	125 <param name="log" type="boolean" truevalue="> log.txt" falsevalue="" checked="False"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	126 label="Extra log file as output"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	127 help="When using you will receive a log file for the printed output of the toll. Can be useful when using the option above!" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	128 <param argument="--include_singletons" type="boolean" truevalue="--include_singletons" falsevalue="" checked="False"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	129 label="Include BGCs with lower cutoff distance"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	130 help="With this option you can include BGCs who don't have a distance lower than the cutoff distance specified" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	131 <param argument="--domain_overlap_cutoff" type="float" value="0.1" min="0.0" max="1.0"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	132 label="Specify when domains are considered to overlap"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	133 help="When using this option you can specify at which percentage domains are considered to overlap. The domain with the best score is kept. The default value is 0.1" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	134 <param argument="--min_big_size" type="integer" value="0"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	135 label="Minimum size of a BGC (bp)"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	136 help="Minimum size of a BGC to be included in the analysis. The Default value is 0 base pairs. This also includes the sum of all loci in a multi-record GenBank file." />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	137 <param argument="--mix" type="boolean" truevalue="--mix" falsevalue="" checked="False"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	138 label="mix all classes in the analysis"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	139 help="BiG-SCAPE separates the analysis according to the BGC product by default. If used BiG-SCAPE will mix all classes and analyse them." />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	140 <param argument="--no_classify" type="boolean" truevalue="--no_classify" falsevalue="" checked="False"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	141 label="No classified output based on the BGC product"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	142 help="By default, BiG-SCAPE classifies the output based on the BGC product. If toggled it will deactivate it. Note: when (--mix) is not activated, BiG-SCAPE will not create any network file!" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	143 <param argument="--banned_classes" type="select" optional="true" multiple="true" display="checkboxes"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	144 label="Excluded classes from classification in BiG-SCAPE"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	145 help="You can exclude any of these classes to not be classified. Multiple banned classes are possible." >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	146 <option value="PKSI" selected="False">PKSI</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	147 <option value="PKSother" selected="False">PKSother</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	148 <option value="NRPS" selected="False">NRPS</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	149 <option value="RIPPs" selected="False">RIPPs</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	150 <option value="Saccharides" selected="False">Saccharides</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	151 <option value="Terpene" selected="False">Terpene</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	152 <option value="PKS-NRP_Hybrids" selected="False">PKS-NRP_Hybrids</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	153 <option value="Others" selected="False">Others</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	154 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	155 <repeat name="cutoff" title="Cutoffs" default="1"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	156 help="Generate networks using multiple raw distance cutoff values. The default value here is 0.3.">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	157 <param argument="--cutoffs" type="float" value="0.3" min="0.1" max="1.0"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	158 label="GCF cutoff value"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	159 </repeat>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	160 <param argument="--clans-off" type="boolean" truevalue="--clans-off" falsevalue="" checked="False"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	161 label="Turn off cluster GCFs into GCCs"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	162 help="By default, BiG-SCAPE will perform a second layer of clustering to group GCFs into GCCs. Toggle to deactivate this." />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	163 <conditional name="clan_cutoff" >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	164 <param name="is_select" type="select" label="Change cutoff values for cluster GCF into GCC?"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	165 help="Select yes if you want to change cutoffs for cluster families into clans.">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	166 <option value="yes" selected="False">Yes</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	167 <option value="no" selected="True">No</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	168 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	169 <when value="yes">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	170 <param name="clan_cutoff_val1" type="float" value="0.3" min="0.1" max="1.0" label="GCF cutoff value"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	171 help="This value is for finding GCFs which will be used for clan calling. The default value is 0.3." />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	172 <param name="clan_cutoff_val2" type="float" value="0.7" min="0.1" max="1.0" label="GCC cutoff value"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	173 help="This value is for clustering families into clans. The default value is 0.7. Every pair of GCFs linked with a distance of this value or less will be taken into account!" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	174 </when>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	175 <when value="no" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	176 </conditional>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	177 <param argument="--hybrids-off" type="boolean" truevalue="--hybrids-off" falsevalue="" checked="False"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	178 label="Exclude hybrid predicted products"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	179 help="By default, BGCs with hybrid predicted products from the PKS/NRPS Hybrids and Others classes will be included in each subclass. Since the same cluster can appear in different classes you can turn this off here." />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	180 <param argument="--mode" type="select"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	181 label="Alignment Mode"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	182 help="Here you can choose between 3 Alignment Mode which is used in comparing each pair of gene clusters. For more information look into the help section!" >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	183 <option value="glocal">glocal</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	184 <option value="global">global</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	185 <option value="auto">auto</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	186 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	187 <conditional name="anchor">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	188 <param name="is_select" type="select" label="Change Anchorfile?"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	189 help="Select yes if you want to use an Anchorfile. BiG-SCAPE has a default file which is always used and only these domains are counted in the result. Look in the help section to see what are the default domains!" >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	190 <option value="yes" selected="False">Yes</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	191 <option value="no" selected="True">No</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	192 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	193 <when value="yes">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	194 <param argument="--anchorfile" type="data" format="txt" optional="false"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	195 label="Using a different Anchorfile instead of default file"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	196 help="Use a custom Anchorfile (in .txt format) to give certain domains a special weight in the DSS index. This file is important because otherwise certain domains (given from Pfam IDs) will not be listed in the results!" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	197 </when>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	198 <when value="no" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	199 </conditional>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	200 <param argument="--force_hmmscan" type="boolean" truevalue="--force_hmmscan" falsevalue="" checked="False"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	201 label="Use hmmscan for the domain prediction"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	202 help="Even if BiG-SCAPE finds processed domtables files we can force the domain prediction with hmmscan. Toggle to force hmmscan!" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	203 <conditional name="list">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	204 <param name="is_select" type="select" label="Use a domain list to include domains?"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	205 help="Select yes if you want to use a list to filter the input to certain domains. Look in the help section how this list should look like">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	206 <option value="yes" selected="False">Yes</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	207 <option value="no" selected="True">No</option>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	208 </param>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	209 <when value="yes">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	210 <param argument="--domain_includelist" type="data" format="txt" optional="false"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	211 label="Use a .txt file to include domains"
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	212 help="Upload a text file where the inputs are filtered based on the Pfam IDs/domains given in this file!" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	213 </when>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	214 <when value="no" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	215 </conditional>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	216 </inputs>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	217 <outputs>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	218 <data name="html" format="html" label="${tool.name}: HTML"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	219 <collection name="tsv_collection_1" type="list" format="tabular" label="${tool.name}: NETWORK ANNOTATIONS COLLECTION">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	220 <discover_datasets pattern="Network_Annotations_(?P<designation>.+)\.tsv" directory="result/network_files" recurse="true"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	221 </collection>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	222 <collection name="tsv_collection_2" type="list" format="tabular" label="${tool.name}: CLAN TABULAR FILES COLLECTION">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	223 <discover_datasets pattern="(?P<identifier_0>[^_]+)_clans_(?P<designation>.+)\.tsv" directory="result/network_files" recurse="true"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	224 <filter> clans_off == False </filter>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	225 </collection>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	226 <collection name="tsv_collection_3" type="list:list" format="tabular" label="${tool.name}: CLUSTERING TABULAR FILES COLLECTION">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	227 <discover_datasets pattern="(?P<identifier_0>[^_]+)_clustering_(?P<identifier_1>.+)\.tsv" directory="result/network_files" recurse="true"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	228 </collection>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	229 <collection name="newtwork_collection" type="list" format="network" label="${tool.name}: NETWORK FILES COLLECTION">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	230 <discover_datasets pattern="(?P<designation>.+)\.network" directory="result/network_files" recurse="true"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	231 </collection>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	232 <data name="logfile" format="txt" label="${tool.name}: LOG FILE">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	233 <filter>log == True</filter>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	234 </data>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	235 </outputs>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	236 <tests>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	237 <test expect_num_outputs="5">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	238 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	239 <param name="inputdir" value="NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	240 </test>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	241 <test expect_num_outputs="6">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	242 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	243 <param name="inputdir" value="NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	244 <param name="log" value="true" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	245 <repeat name="cutoff">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	246 <param name="cutoffs" value="1.0"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	247 </repeat>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	248 <output name="html" >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	249 <assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	250 <has_line line="<!DOCTYPE html>" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	251 </assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	252 </output>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	253 <output name="logfile">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	254 <assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	255 <has_line line=" - - Processing input files - -" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	256 </assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	257 </output>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	258 <output_collection name="tsv_collection_1" type="list">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	259 <element name="Full" >
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	260 <assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	261 <has_text text="Accession ID" n="1"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	262 </assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	263 </element>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	264 </output_collection>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	265 <output_collection name="tsv_collection_2" type="list">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	266 <element name="NRPS">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	267 <assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	268 <has_text text="Clan Number" n="1"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	269 </assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	270 </element>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	271 </output_collection>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	272 <output_collection name="tsv_collection_3" type="list:list">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	273 <element name="NRPS">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	274 <element name="c0.30">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	275 <assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	276 <has_text text="Family Number" n="1" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	277 </assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	278 </element>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	279 <element name="c1.00">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	280 <assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	281 <has_text text="Family Number" n="1" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	282 </assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	283 </element>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	284 </element>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	285 </output_collection>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	286 <output_collection name="newtwork_collection" type="list">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	287 <element name="NRPS_c0.30">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	288 <assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	289 <has_text text="Raw distance" n="1"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	290 </assert_contents>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	291 </element>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	292 </output_collection>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	293 </test>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	294 <test expect_num_outputs="5">
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	295 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	296 <param name="inputdir" value="NC_010530.1.region005.gbk,NC_012963.1.region001.gbk,NW_009799099.1.region003.gbk,NW_021940918.1.region003.gbk,NW_009799102.1.region001.gbk,NW_022985561.1.region002.gbk,NW_022985549.1.region005.gbk,NW_022985575.1.region001.gbk" ftype="genbank" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	297 <param name="log" value="true" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	298 <param name="clans_off" value="true" />
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	299 </test>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	300 </tests>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	301 <help>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	302 <![CDATA[
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	303 .. class:: infomark
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	304
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	305 What is BiG-SCAPE
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	306
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	307 BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs).
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	308
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	309 .. class:. infomark
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	310
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	311 What it does
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	312
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	313 BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	314
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	315 In principle, BiG-SCAPE can also be used on any other gene clusters, such as pathogenicity islands, secretion system-encoding gene clusters, or even whole viral genomes.
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	316
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	317 Here is a grapic how BiG-SCAPE works:
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	318
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	319 .. image:: bigscape_corason.png
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	320 :alt: BiG-SCAPE + CORASON workflow
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	321
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	322 For more information you can visit `BiG-SCAPE on GitHub <https://github.com/medema-group/BiG-SCAPE>`_ or go on the `combine website <https://bigscape-corason.secondarymetabolites.org/index.html>`_.
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	323
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	324 Input
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	325
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	326 BiG-SCAPE uses two kind of inputs:
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	327
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	328 - The genbank files from antiSMASH
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	329
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	330 .. class:: infomark
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	331
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	332 Note: By default, BiG-SCAPE includes any Genbank file where the filename contains either region or cluster. To ensure every file will be included we add 'region.' in in the file name!
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	333
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	334 - The Pfamm-A.hmm file
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	335
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	336 .. class:: infomark
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	337
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	338 Note: You can download `Pfam-A.hmm.gz <https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz>`_ here and then unzip it or you can use the command: $ wget https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz && gunzip Pfam-A.hmm.gz in e.g. VSC.
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	339
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	340 There are two additional inputs which can be used:
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	341
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	342 - An anchor_domains.txt file
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	343
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	344 .. class:: infomark:
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	345
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	346 Example (default file which will be used):
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	347
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	348 ::
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	349
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	350 PF00668 Condensation domain [NRPS]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	351 PF00501 AMP-binding enzyme [NRPS]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	352 PF00109 Beta-ketoacyl synthase N-terminal [PKS]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	353 PF02801 Beta-ketoacyl synthase C-terminal [PKS]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	354 PF01397 Terpene synthase, N-terminal domain (Terpene_synth) [Terpene]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	355 PF03936 Terpene synthase family, metal binding domain (Terpene_synth_C) [Terpene]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	356 PF00195 Chalcone and stilbene synthases, N-terminal domain (Cahl_sti_synt_N)
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	357 PF02797 Chalcone and stilbene synthases, C-terminal domain (Chal_sti_synt_C)
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	358 PF05147 Lanthionine synthetase C-like protein (LANC_like) [lantipeptide/RiPP]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	359 PF00494 Squalene/phytoene synthase (SQS_PSY) [Terpene]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	360 PF00432 Prenyltransferase and squalene oxidase repeat (Prenyltrans)
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	361 PF02624 YcaO cyclodehydratase, ATP-ad MG2+-binding (YcaO) [RiPP]
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	362
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	363 The first column contains the Pfam model ID while the second column is optionally for writing a comment. The columns are tab-separated!
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	364
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	365 - A domain_includelist.txt
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	366
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	367 .. class:: infomark
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	368
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	369 Example:
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	370
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	371 ::
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	372
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	373 PF00067 Cytochrome P450
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	374 PF01451 Any Comment
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	375
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	376 The first column contains the Pfam model ID while the second column is optionally for writing a comment. The columns are tab-separated and any line that starts with a # will be ignored!
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	377
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	378
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	379 Output
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	380
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	381 BiG-SCAPE will produce one HTML Output together with a dataset with different tabular files depending on the input. When the log file option is set it will create another output, where all prints made from this tool are stored.
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	382
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	383
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	384 Additionally information for the alignment Mode
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	385
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	386 - glocal: This is the default mode. Here the subset of the domains used to calculate distance is redefined by finding the longest slice of common domain content per gene in both BGCs, and then expanding each slice.
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	387
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	388 - global: The whole list of domains of each BGC are compared.
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	389
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	390 - auto: Use glocal mode when at least one of the BGCs in each pair has the contig_edge annotation from antiSMASH. Otherwise global will be used.
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	391 ]]>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	392 </help>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	393 <citations>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	394 <citation type="doi">10.1038/s41589-019-0400-9</citation>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	395 </citations>
a9e5d237d7d4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 1c7a35c3aabb33682b263cb3a8dbeaf605469c23 iuc parents: diff changeset	396 </tool>

Mercurial > repos > iuc > bigscape

annotate bigscape.xml @ 0:a9e5d237d7d4 draft