bigscape: bigscape.xml annotate

annotate bigscape.xml @ 0:ccaa79de86c2 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4

author	iuc
date	Sun, 11 Aug 2024 21:08:49 +0000
parents
children

rev	line source
0 ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	1 <tool id="bigscape" name="BiG-SCAPE" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	2 <description>Construct sequence similarity networks of BGCs and group them into GCF</description>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	3 <macros>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	4 <token name="@TOOL_VERSION@">1.1.9</token>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	5 <token name="@VERSION_SUFFIX@">2</token>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	6 </macros>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	7 <xrefs>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	8 <xref type="bio.tools">BiG-SCAPE</xref>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	9 </xrefs>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	10 <requirements>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">bigscape</requirement>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	12 </requirements>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	13 <command detect_errors="exit_code">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	14 <![CDATA[
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	15
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	16 #set $path_to_html = $html.files_path
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	17 mkdir -p '$path_to_html' result input &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	18 #for $files in $inputdir:
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	19 #set $filename = "region." + $files.element_identifier
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	20 ln -s '$files' './input/${filename}.gbk' &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	21 #end for
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	22
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	23 mkdir pfam &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	24 ln -s '$pfam_dir' './pfam/$pfam_dir.element_identifier' &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	25 hmmpress './pfam/Pfam-A.hmm' &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	26
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	27 #if $anchor.is_select == "yes":
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	28 ln -s '$anchorfile' '$anchorfile.element_identifier' &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	29 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	30 #if $list.is_select == "yes":
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	31 cat '$__tool_directory__/domain_includelist.txt' > save.txt &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	32 cat '$domain_includelist' > '$__tool_directory__/domain_includelist.txt' &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	33 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	34
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	35 bigscape
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	36 --inputdir input
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	37 #if $mibig.is_select == "yes"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	38 $mibig.mibig.value
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	39 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	40 --outputdir result
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	41 #if $use_label.is_select == "yes":
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	42 --label '${label}'
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	43 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	44 --pfam_dir pfam
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	45 --cores \${GALAXY_SLOTS:-8}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	46 ${verbose}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	47 ${log}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	48 ${include_singletons}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	49 --domain_overlap_cutoff ${domain_overlap_cutoff}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	50 --min_bgc_size ${min_big_size}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	51 ${mix}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	52 ${no_classify}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	53 #if $banned_classes.value:
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	54 --banned_classes
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	55 #for $banned in str($banned_classes).split( "," ):
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	56 '$banned'
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	57 #end for
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	58 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	59 --cutoffs #for $c in $cutoff# ${c.cutoffs} #end for#
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	60 ${clans_off}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	61 #if $clan_cutoff.is_select == "yes":
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	62 --clan_cutoff $clan_cutoff_val1 $clan_cutoff_val2
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	63 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	64 ${hybrids_off}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	65 --mode ${mode.value}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	66 #if $anchor.is_select == "yes":
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	67 --anchorfile '${anchorfile.element_identifier}'
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	68 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	69 ${force_hmmscan}
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	70 #if $list.is_select == "yes":
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	71 --domain_includelist
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	72 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	73 &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	74
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	75 cp './result/index.html' '$html' &&
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	76 cp -r './result/html_content' '$path_to_html'
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	77
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	78 #if $list.is_select == "yes":
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	79 && cat save.txt > '$__tool_directory__/domain_includelist.txt'
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	80 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	81
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	82 #if $log:
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	83 && cp log.txt '$logfile'
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	84 #end if
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	85 ]]>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	86 </command>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	87 <inputs>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	88 <param argument="--inputdir" format="genbank" multiple="true" type="data"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	89 label="Data files to include in the clustering"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	90 help="Add your .gbk files here. Do not wonder, in the filename 'region. will be added to ensure that every file will be included!" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	91 <conditional name="mibig">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	92 <param name="is_select" type="select" label="Include BGCs from MIBiG database?"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	93 help="Select yes and select which version of the database you want to use" >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	94 <option value="yes" selected="False">Yes</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	95 <option value="no" selected="True">No</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	96 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	97 <when value="yes">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	98 <param name="mibig" type="select" optional="false" label="Version from the MIBiG database"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	99 help="Select which version of the MIBiG databse you want to use." >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	100 <option value="--mibig">3.1</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	101 <option value="--mibig21">2.1</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	102 <option value="--mibig14">1.4</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	103 <option value="--mibig13">1.3</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	104 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	105 </when>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	106 <when value="no" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	107 </conditional>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	108 <conditional name="use_label" >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	109 <param name="is_select" type="select" label="Adding extra string to BiG-SCAPE runs?"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	110 help="Select yes if you want to add an extra string to the outputs">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	111 <option value="yes" selected="False">Yes</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	112 <option value="no" selected="True">No</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	113 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	114 <when value="yes">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	115 <param argument="--label" type="text" value="" optional="false" label="Adding extra string to BiG-SCAPE runs name"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	116 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).">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	117 <validator type="empty_field" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	118 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	119 </when>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	120 <when value="no" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	121 </conditional>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	122 <param argument="--pfam_dir" format="hmm3" type="data"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	123 label="Data file Pfam-A.hmm"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	124 help="Add Pfam-A.hmm.gz file here, please. Look at the help section where you can download it!" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	125 <param argument="--verbose" type="boolean" truevalue="--verbose" falsevalue="" checked="False"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	126 label="Print more detailed information about each step"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	127 help="Getting more information about the analysis if toggled is true." />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	128 <param name="log" type="boolean" truevalue="> log.txt" falsevalue="" checked="False"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	129 label="Extra log file as output"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	130 help="When using you will receive a log file for the printed output of the toll. Can be useful when using the option above!" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	131 <param argument="--include_singletons" type="boolean" truevalue="--include_singletons" falsevalue="" checked="False"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	132 label="Include BGCs with lower cutoff distance"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	133 help="With this option you can include BGCs who don't have a distance lower than the cutoff distance specified" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	134 <param argument="--domain_overlap_cutoff" type="float" value="0.1" min="0.0" max="1.0"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	135 label="Specify when domains are considered to overlap"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	136 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" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	137 <param argument="--min_big_size" type="integer" value="0"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	138 label="Minimum size of a BGC (bp)"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	139 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." />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	140 <param argument="--mix" type="boolean" truevalue="--mix" falsevalue="" checked="False"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	141 label="mix all classes in the analysis"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	142 help="BiG-SCAPE separates the analysis according to the BGC product by default. If used BiG-SCAPE will mix all classes and analyse them." />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	143 <param argument="--no_classify" type="boolean" truevalue="--no_classify" falsevalue="" checked="False"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	144 label="No classified output based on the BGC product"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	145 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!" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	146 <param argument="--banned_classes" type="select" optional="true" multiple="true" display="checkboxes"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	147 label="Excluded classes from classification in BiG-SCAPE"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	148 help="You can exclude any of these classes to not be classified. Multiple banned classes are possible." >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	149 <option value="PKSI" selected="False">PKSI</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	150 <option value="PKSother" selected="False">PKSother</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	151 <option value="NRPS" selected="False">NRPS</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	152 <option value="RiPPs" selected="False">RiPPs</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	153 <option value="Saccharides" selected="False">Saccharides</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	154 <option value="Terpene" selected="False">Terpene</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	155 <option value="PKS-NRP_Hybrids" selected="False">PKS-NRP_Hybrids</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	156 <option value="Others" selected="False">Others</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	157 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	158 <repeat name="cutoff" title="Cutoffs" default="1"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	159 help="Generate networks using multiple raw distance cutoff values. The default value here is 0.3.">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	160 <param argument="--cutoffs" type="float" value="0.3" min="0.1" max="1.0"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	161 label="GCF cutoff value"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	162 </repeat>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	163 <param argument="--clans-off" type="boolean" truevalue="--clans-off" falsevalue="" checked="False"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	164 label="Turn off cluster GCFs into GCCs"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	165 help="By default, BiG-SCAPE will perform a second layer of clustering to group GCFs into GCCs. Toggle to deactivate this." />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	166 <conditional name="clan_cutoff" >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	167 <param name="is_select" type="select" label="Change cutoff values for cluster GCF into GCC?"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	168 help="Select yes if you want to change cutoffs for cluster families into clans.">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	169 <option value="yes" selected="False">Yes</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	170 <option value="no" selected="True">No</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	171 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	172 <when value="yes">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	173 <param name="clan_cutoff_val1" type="float" value="0.3" min="0.1" max="1.0" label="GCF cutoff value"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	174 help="This value is for finding GCFs which will be used for clan calling. The default value is 0.3." />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	175 <param name="clan_cutoff_val2" type="float" value="0.7" min="0.1" max="1.0" label="GCC cutoff value"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	176 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!" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	177 </when>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	178 <when value="no" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	179 </conditional>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	180 <param argument="--hybrids-off" type="boolean" truevalue="--hybrids-off" falsevalue="" checked="False"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	181 label="Exclude hybrid predicted products"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	182 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." />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	183 <param argument="--mode" type="select"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	184 label="Alignment Mode"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	185 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!" >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	186 <option value="glocal">glocal</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	187 <option value="global">global</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	188 <option value="auto">auto</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	189 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	190 <conditional name="anchor">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	191 <param name="is_select" type="select" label="Change Anchorfile?"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	192 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!" >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	193 <option value="yes" selected="False">Yes</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	194 <option value="no" selected="True">No</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	195 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	196 <when value="yes">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	197 <param argument="--anchorfile" type="data" format="txt" optional="false"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	198 label="Using a different Anchorfile instead of default file"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	199 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!" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	200 </when>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	201 <when value="no" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	202 </conditional>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	203 <param argument="--force_hmmscan" type="boolean" truevalue="--force_hmmscan" falsevalue="" checked="False"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	204 label="Use hmmscan for the domain prediction"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	205 help="Even if BiG-SCAPE finds processed domtables files we can force the domain prediction with hmmscan. Toggle to force hmmscan!" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	206 <conditional name="list">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	207 <param name="is_select" type="select" label="Use a domain list to include domains?"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	208 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">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	209 <option value="yes" selected="False">Yes</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	210 <option value="no" selected="True">No</option>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	211 </param>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	212 <when value="yes">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	213 <param argument="--domain_includelist" type="data" format="txt" optional="false"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	214 label="Use a .txt file to include domains"
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	215 help="Upload a text file where the inputs are filtered based on the Pfam IDs/domains given in this file!" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	216 </when>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	217 <when value="no" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	218 </conditional>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	219 </inputs>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	220 <outputs>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	221 <data name="html" format="html" label="${tool.name}: HTML"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	222 <collection name="tsv_collection_1" type="list" format="tabular" label="${tool.name}: NETWORK ANNOTATIONS COLLECTION">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	223 <discover_datasets pattern="Network_Annotations_(?P<designation>.+)\.tsv" directory="result/network_files" recurse="true"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	224 </collection>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	225 <collection name="tsv_collection_2" type="list" format="tabular" label="${tool.name}: CLAN TABULAR FILES COLLECTION">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	226 <discover_datasets pattern="(?P<identifier_0>[^_]+)_clans_(?P<designation>.+)\.tsv" directory="result/network_files" recurse="true"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	227 <filter> clans_off == False </filter>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	228 </collection>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	229 <collection name="tsv_collection_3" type="list:list" format="tabular" label="${tool.name}: CLUSTERING TABULAR FILES COLLECTION">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	230 <discover_datasets pattern="(?P<identifier_0>[^_]+)_clustering_(?P<identifier_1>.+)\.tsv" directory="result/network_files" recurse="true"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	231 </collection>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	232 <collection name="newtwork_collection" type="list" format="network" label="${tool.name}: NETWORK FILES COLLECTION">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	233 <discover_datasets pattern="(?P<designation>.+)\.network" directory="result/network_files" recurse="true"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	234 </collection>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	235 <data name="logfile" format="txt" label="${tool.name}: LOG FILE">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	236 <filter>log == True</filter>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	237 </data>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	238 </outputs>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	239 <tests>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	240 <test expect_num_outputs="5">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	241 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	242 <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" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	243 </test>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	244 <test expect_num_outputs="6">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	245 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	246 <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" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	247 <param name="log" value="true" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	248 <repeat name="cutoff">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	249 <param name="cutoffs" value="1.0"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	250 </repeat>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	251 <output name="html" >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	252 <assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	253 <has_line line="<!DOCTYPE html>" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	254 </assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	255 </output>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	256 <output name="logfile">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	257 <assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	258 <has_line line=" - - Processing input files - -" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	259 </assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	260 </output>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	261 <output_collection name="tsv_collection_1" type="list">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	262 <element name="Full" >
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	263 <assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	264 <has_text text="Accession ID" n="1"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	265 </assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	266 </element>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	267 </output_collection>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	268 <output_collection name="tsv_collection_2" type="list">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	269 <element name="NRPS">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	270 <assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	271 <has_text text="Clan Number" n="1"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	272 </assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	273 </element>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	274 </output_collection>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	275 <output_collection name="tsv_collection_3" type="list:list">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	276 <element name="NRPS">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	277 <element name="c0.30">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	278 <assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	279 <has_text text="Family Number" n="1" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	280 </assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	281 </element>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	282 <element name="c1.00">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	283 <assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	284 <has_text text="Family Number" n="1" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	285 </assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	286 </element>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	287 </element>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	288 </output_collection>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	289 <output_collection name="newtwork_collection" type="list">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	290 <element name="NRPS_c0.30">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	291 <assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	292 <has_text text="Raw distance" n="1"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	293 </assert_contents>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	294 </element>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	295 </output_collection>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	296 </test>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	297 <test expect_num_outputs="5">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	298 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	299 <param name="inputdir" value="NC_012963.1.region001.no-genbank-suffix,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" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	300 <param name="log" value="true" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	301 <param name="clans_off" value="true" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	302 </test>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	303 <test expect_num_outputs="5">
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	304 <param name="pfam_dir" value="Pfam-A.hmm" ftype="hmm3"/>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	305 <param name="inputdir" value="NC_012963.1.region001.no-genbank-suffix,NC_010530.1.region005.gbk" ftype="genbank" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	306 <param name="log" value="true" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	307 <param name="clans_off" value="true" />
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	308 </test>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	309 </tests>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	310 <help>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	311 <![CDATA[
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	312 .. class:: infomark
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	313
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	314 What is BiG-SCAPE
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	315
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	316 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).
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	317
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	318 .. class:. infomark
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	319
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	320 What it does
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	321
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	322 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.
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	323
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	324 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.
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	325
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	326 Here is a grapic how BiG-SCAPE works:
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	327
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	328 .. image:: bigscape_corason.png
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	329 :alt: BiG-SCAPE + CORASON workflow
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	330
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	331 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>`_.
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	332
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	333 Input
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	334
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	335 BiG-SCAPE uses two kind of inputs:
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	336
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	337 - The genbank files from antiSMASH
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	338
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	339 .. class:: infomark
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	340
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	341 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!
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	342
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	343 - The Pfamm-A.hmm file
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	344
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	345 .. class:: infomark
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	346
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	347 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.
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	348
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	349 There are two additional inputs which can be used:
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	350
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	351 - An anchor_domains.txt file
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	352
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	353 .. class:: infomark:
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	354
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	355 Example (default file which will be used):
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	356
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	357 ::
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	358
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	359 PF00668 Condensation domain [NRPS]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	360 PF00501 AMP-binding enzyme [NRPS]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	361 PF00109 Beta-ketoacyl synthase N-terminal [PKS]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	362 PF02801 Beta-ketoacyl synthase C-terminal [PKS]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	363 PF01397 Terpene synthase, N-terminal domain (Terpene_synth) [Terpene]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	364 PF03936 Terpene synthase family, metal binding domain (Terpene_synth_C) [Terpene]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	365 PF00195 Chalcone and stilbene synthases, N-terminal domain (Cahl_sti_synt_N)
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	366 PF02797 Chalcone and stilbene synthases, C-terminal domain (Chal_sti_synt_C)
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	367 PF05147 Lanthionine synthetase C-like protein (LANC_like) [lantipeptide/RiPP]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	368 PF00494 Squalene/phytoene synthase (SQS_PSY) [Terpene]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	369 PF00432 Prenyltransferase and squalene oxidase repeat (Prenyltrans)
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	370 PF02624 YcaO cyclodehydratase, ATP-ad MG2+-binding (YcaO) [RiPP]
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	371
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	372 The first column contains the Pfam model ID while the second column is optionally for writing a comment. The columns are tab-separated!
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	373
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	374 - A domain_includelist.txt
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	375
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	376 .. class:: infomark
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	377
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	378 Example:
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	379
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	380 ::
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	381
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	382 PF00067 Cytochrome P450
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	383 PF01451 Any Comment
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	384
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	385 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!
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	386
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	387
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	388 Output
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	389
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	390 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.
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	391
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	392
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	393 Additionally information for the alignment Mode
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	394
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	395 - 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.
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	396
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	397 - global: The whole list of domains of each BGC are compared.
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	398
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	399 - 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.
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	400 ]]>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	401 </help>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	402 <citations>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	403 <citation type="doi">10.1038/s41589-019-0400-9</citation>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	404 </citations>
ccaa79de86c2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigscape/ commit 8a0f3092ca824856263328efe66941409f527ca4 iuc parents: diff changeset	405 </tool>

Mercurial > repos > iuc > bigscape

annotate bigscape.xml @ 0:ccaa79de86c2 draft default tip