lastz: lastz.xml annotate

annotate lastz.xml @ 13:bf107d23242b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94

author	iuc
date	Thu, 05 Feb 2026 12:52:06 +0000
parents	48d39ee9eb30
children

rev	line source
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	1 <tool id="lastz_wrapper_2" name="LASTZ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	2 <description>align long sequences</description>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	3 <macros>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	4 <import>lastz_macros.xml</import>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	5 </macros>
10 3e1ea2facca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 9 diff changeset	6 <expand macro="bio_tools"/>
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	7 <expand macro="requirements"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	8 <command detect_errors="exit_code"><![CDATA[
10 3e1ea2facca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 9 diff changeset	9 #if $lastz_32:
3e1ea2facca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 9 diff changeset	10 lastz_32
3e1ea2facca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 9 diff changeset	11 #else:
3e1ea2facca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 9 diff changeset	12 lastz
3e1ea2facca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 9 diff changeset	13 #end if
3e1ea2facca6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 9 diff changeset	14
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	15 @TARGET_INPUT_COMMAND_LINE@
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	16 ## If --self is set: perform self alignment and ignore the query
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	17 #if $where_to_look.self:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	18 '${where_to_look.self}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	19 #if $where_to_look.nomirror
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	20 '${where_to_look.nomirror}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	21 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	22 #else:
7 10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	23 @query_input@
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	24 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	25
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	26 ## WHERE TO LOOK --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	27
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	28 '${where_to_look.strand}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	29 #if str( $where_to_look.qhsplimit.qhsplimit_selector ) == "yes":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	30 #if $where_to_look.qhsplimit.qhsplimit_n:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	31 #if $where_to_look.qhsplimit.qhsplimit_nowarn:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	32 #if $where_to_look.qhsplimit.qhsplimit_keep:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	33 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_keep},${where_to_look.qhsplimit.qhsplimit_nowarn}:${where_to_look.qhsplimit.qhsplimit_n}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	34 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	35 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_nowarn}:${where_to_look.qhsplimit.qhsplimit_n}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	36 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	37 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	38 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_n}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	39 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	40 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	41 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	42
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	43 #if $where_to_look.qhspbest:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	44 '--queryhspbest=${where_to_look.qhspbest}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	45 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	46
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	47 #if str( $where_to_look.qdepth.qdepth_selector ) == "yes":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	48 #if $where_to_look.qdepth.qdepth_n:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	49 #if $where_to_look.qdepth.qdepth_nowarn and not $where_to_look.qdepth.qdepth_keep:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	50 '--querydepth=${where_to_look.qdepth.qdepth_nowarn}:${where_to_look.qdepth.qdepth_n}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	51 #elif not $where_to_look.qdepth.qdepth_nowarn and $where_to_look.qdepth.qdepth_keep:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	52 '--querydepth=${where_to_look.qdepth.qdepth_keep}:${where_to_look.qdepth.qdepth_n}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	53 #elif $where_to_look.qdepth.qdepth_nowarn and $where_to_look.qdepth.qdepth_keep:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	54 '--querydepth=${where_to_look.qdepth.qdepth_keep},${where_to_look.qdepth.qdepth_nowarn}:${where_to_look.qdepth.qdepth_n}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	55 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	56 '--querydepth=${where_to_look.qdepth.qdepth_n}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	57 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	58 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	59 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	60
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	61 ## SCORING --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	62
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	63 #if $scoring.score_file:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	64 '--scores=${scoring.score_file}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	65 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	66
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	67 #if str( $scoring.match.match_selector ) == "yes":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	68 #if $scoring.match.match_reward:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	69 #if $scoring.match.match_penalty:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	70 '--match=${scoring.match.match_reward},${scoring.match.match_penalty}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	71 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	72 '--match=${scoring.match.match_reward}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	73 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	74 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	75 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	76 #if str( $scoring.gap.gap_selector ) == "yes":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	77 #if $scoring.gap.gap_extend:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	78 #if $scoring.gap.gap_open:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	79 '--gap=${scoring.gap.gap_open},${scoring.gap.gap_extend}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	80 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	81 '--gap=${scoring.gap.gap_extend}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	82 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	83 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	84 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	85 #if $scoring.ambigN:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	86 '${scoring.ambigN}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	87 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	88 #if $scoring.ambigIUPAC:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	89 '${scoring.ambigIUPAC}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	90 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	91
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	92 ## SEEDING --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	93
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	94 #if str( $seeding.seed.seed_selector ) == "pre_set":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	95 '${seeding.seed.pre_set_seeds}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	96 #elif str( $seeding.seed.seed_selector ) == "len":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	97 '--seed=match${seeding.seed.seed_match}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	98 #elif str( $seeding.seed.seed_selector ) == "half_len":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	99 '--seed=half${seeding.seed.seed_half}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	100 #elif str( $seeding.seed.seed_selector ) == "pattern":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	101 '--seed=${seeding.seed.pattern}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	102 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	103 #if str( $seeding.transitions ) != "--transition":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	104 '${seeding.transitions}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	105 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	106 #if str( $seeding.seed_filer.seed_filer_selector ) == "yes":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	107 #if $seeding.seed_filer.filter_match:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	108 #if $seeding.seed_filer.filter_tr:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	109 '--filter=${seeding.seed_filer.filter_tr},${seeding.seed_filer.filter_match}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	110 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	111 '--filter=${seeding.seed_filer.filter_match}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	112 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	113 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	114 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	115
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	116 ## FINDING HSPs --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	117
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	118 #if $hsp.gfextend:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	119 '${hsp.gfextend}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	120 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	121 #if $hsp.nogfextend
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	122 '${hsp.nogfextend}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	123 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	124 #if str( $hsp.hsp_method.hsp_method_selector ) == "match":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	125
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	126 #if $hsp.hsp_method.exact:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	127 '--exact=${hsp.hsp_method.exact}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	128 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	129 #elif str( $hsp.hsp_method.hsp_method_selector ) == "mismatch":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	130
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	131 #if $hsp.hsp_method.mismatch_count and $hsp.hsp_method.mismatch_length:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	132 '--mismatch=${hsp.hsp_method.mismatch_count},${hsp.hsp_method.mismatch_length}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	133 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	134 #elif str( $hsp.hsp_method.hsp_method_selector ) == "x":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	135
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	136 #if $hsp.hsp_method.xdrop:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	137 '--xdrop=${hsp.hsp_method.xdrop}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	138 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	139
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	140 #if $hsp.hsp_method.hspthresh:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	141 '--hspthresh=${hsp.hsp_method.hspthresh}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	142 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	143
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	144 #if $hsp.hsp_method.hspthresh_top:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	145 '--hspthresh=top${hsp.hsp_method.hspthresh_top}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	146 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	147
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	148 #if $hsp.hsp_method.hspthresh_top_percent:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	149 '--hspthresh=top${hsp.hsp_method.hspthresh_top_percent}%'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	150 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	151 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	152 #if $hsp.entropy:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	153 '${hsp.entropy}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	154 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	155 #if $hsp.entropy_report:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	156 '${hsp.entropy_report}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	157 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	158 #if $hsp.noentropy:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	159 '${hsp.noentropy}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	160 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	161
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	162 ## CHAINING --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	163
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	164 #if $chaining.chain:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	165 '${chaining.chain}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	166 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	167 #if str( $chaining.chaning_penalties.chaning_penalties_selector ) == "yes":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	168 #if $chaining.chaning_penalties.diag and $chaining.chaning_penalties.anti:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	169 '--chain=${chaining.chaning_penalties.diag},${chaining.chaning_penalties.anti}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	170 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	171 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	172
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	173 ## GAPPED EXTENSION --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	174
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	175 #if $gap_ext.gapped:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	176 '${gap_ext.gapped}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	177 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	178 #if $gap_ext.nogapped:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	179 '${gap_ext.nogapped}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	180 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	181 #if $gap_ext.ydrop:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	182 '--ydrop=${gap_ext.ydrop}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	183 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	184 #if $gap_ext.noytrim:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	185 '${gap_ext.noytrim}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	186 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	187 #if $gap_ext.gappedthresh:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	188 '--gappedthresh=${gap_ext.gappedthresh}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	189 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	190 #if $gap_ext.allgappedbounds:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	191 '${gap_ext.allgappedbounds}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	192 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	193
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	194 ## FILTERING --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	195
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	196 #if $filters.identity.id_min:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	197 #if $filters.identity.id_max:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	198 '--filter=identity:${filters.identity.id_min}..${filters.identity.id_max}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	199 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	200 '--filter=identity:${filters.identity.id_min}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	201 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	202 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	203 #if $filters.continuity.cont_min:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	204 #if $filters.continuity.cont_max:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	205 '--filter=continuity:${filters.continuity.cont_min}..${filters.continuity.cont_max}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	206 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	207 '--filter=continuity:${filters.continuity.cont_min}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	208 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	209 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	210 #if $filters.coverage.cov_min:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	211 #if $filters.coverage.cov_max:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	212 '--filter=coverage:${filters.coverage.cov_min}..${filters.coverage.cov_max}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	213 #else:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	214 '--filter=coverage:${filters.coverage.cov_min}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	215 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	216 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	217 #if $filters.filter_nmatch:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	218 '--filter=nmatch:${filters.filter_nmatch}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	219 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	220 #if $filters.filter_nmatch_percent:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	221 '--filter=nmatch:${filters.filter_nmatch_percent}%'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	222 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	223 #if $filters.filter_nmismatch:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	224 '--filter=nmismatch:0..${filters.filter_nmismatch}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	225 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	226 #if $filters.filter_ngap:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	227 '--filter=ngap:0..${filters.filter_ngap}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	228 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	229 #if $filters.filter_cgap:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	230 '--filter=cgap:0..${filters.filter_cgap}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	231 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	232 #if $filters.notrivial:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	233 '${filters.notrivial}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	234 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	235
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	236 ## INTERPOLATION --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	237
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	238 #if $interpolation.inner:
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	239 '--inner=${interpolation.inner}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	240 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	241
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	242 ## HOUSEKEEPING ----------------------------------
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	243
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	244 --traceback=160M
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	245
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	246
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	247 ## OUTPUT FORMATS --------------------------------
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	248
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	249 #if str( $output_format.out.format ) == "bam":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	250 '--format=${output_format.out.bam_options}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	251 #elif str( $output_format.out.format ) == "general_def":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	252 --format=general-
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	253 #elif str( $output_format.out.format ) == "maf":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	254 '--format=${output_format.out.maf_type}'
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	255 #elif str( $output_format.out.format ) == "blastn":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	256 --format=BLASTN-
12 48d39ee9eb30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 11 diff changeset	257 #elif str( $output_format.out.format ) == "paf":
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	258 --format=PAF
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	259 #elif str( $output_format.out.format ) == "general_full":
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	260 '--format=general-:${output_format.out.fields}'
9 2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	261 #elif str( $output_format.out.format ) == "differences":
2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	262 '--format=differences'
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	263 #end if
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	264 --action:target=multiple
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	265 $output_format.rplot
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	266 #if str( $output_format.out.format ) == "bam":
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	267 \| samtools sort --no-PG -l 0 -T "\${TMPDIR:-.}" -O bam \| samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o '${output}'
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	268 #else:
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	269 > '${output}'
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	270 #end if
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	271 #if $output_format.rplot:
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	272 &&
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	273 Rscript $r_plot > /dev/null 2>&1
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	274 #end if
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	275
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	276 ]]>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	277 </command>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	278 <configfiles>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	279 <configfile name="r_plot">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	280 <![CDATA[
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	281 #!/usr/bin/env Rscript
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	282 ## Setup R error handling to go to stderr
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	283 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	284 ## Only produce image when 'plot.r' actually contains data
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	285 if(file.info('plot.r')\$size>0){
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	286 x <- read.table("plot.r", as.is=TRUE)
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	287 png("${out_plot}", width=640, height=640, res=72)
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	288 plot(x, type='l', xlab="target", ylab="query", main="plot")
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	289 dev.off()
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	290 }
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	291 ]]>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	292 </configfile>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	293 </configfiles>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	294 <inputs>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	295 <expand macro="target_input"/>
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	296 <param name="query" format="fasta,fastqsanger,fastqillumina,fasta.gz,fastq.gz,fastqsanger.gz,fastqillumina.gz,fastq.bz2,fastqsanger.bz2,fastqillumina.bz2" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	297 <param name="lastz_32" type="boolean" checked="false" label="Use lastz_32" help="It is highly recommended to use lastz_32 instead of lastz if the reference genome size is greater than 2G"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	298 <section name="where_to_look" expanded="False" title="Where to look">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	299 <param type="select" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	300 <option value="--strand=both" selected="True">Both</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	301 <option value="--strand=plus">Plus</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	302 <option value="--strand=minus">Minus</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	303 </param>
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	304 <param type="boolean" truevalue="--self" falsevalue="" checked="False" argument="--self" label="Perform a self-alignment: the target sequence is also the query." help="Computation is more efficient than it would be without this option, since only one of each mirror-image pair of alignment blocks is processed (the other, redundant one is skipped during processing, but re-created in the output). Also, the trivial self-alignment block along the main diagonal is omitted from the output. THIS OPTION CANNOT BE USED IF THE TARGET IS COMPRIZED OF MULTIPLE SEQUENCES"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	305 <param type="boolean" truevalue="--nomirror" falsevalue="" checked="False" label="Inhibit the re-creation of mirror-image alignments." argument="--nomirror" help="Output consists of only one copy of each meaningful alignment block in a self-alignment. This option is only applicable when the ‑‑self option is used."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	306 <conditional name="qhsplimit">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	307 <param name="qhsplimit_selector" type="select" label="Set HSP limit" argument="--queryhsplimit">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	308 <option value="yes">Yes</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	309 <option value="no" selected="true">No</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	310 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	311 <when value="yes">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	312 <param name="qhsplimit_n" optional="true" type="integer" value="" label="Discard queries that have more than N HSPs" help="Any queries that exceed this limit are reported as a warning (to stderr), and no alignments are reported. This is useful for mapping reads to a reference genome, when some reads align to too many places in the reference."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	313 <param name="qhsplimit_nowarn" type="boolean" truevalue="nowarn" checked="False" label=" Withhold warnings for queries that exceed the limit set above"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	314 <param name="qhsplimit_keep" type="boolean" truevalue="keep" checked="False" label="Keep queries that exceed the limit and supress warnings" help="For such a query, the first N HSPs found are passed along to downstream processing. Note that the HSPs reported are not the best N HSPs. They are simply the first N found; they very likely have a positional bias."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	315 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	316 <when value="no">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	317 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	318 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	319 </conditional>
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	320 <param name="qhspbest" type="integer" value="" optional="true" label="For queries that have more than N HSPs, discard any HSPs that score below the Nth best." help="This is useful for mapping reads to a reference genome, when some reads align to too many places in the reference."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	321 <conditional name="qdepth">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	322 <param name="qdepth_selector" type="select" label="Set ratio of aligned bases to query length" argument="--querydepth">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	323 <option value="yes">Yes</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	324 <option value="no" selected="true">No</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	325 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	326 <when value="yes">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	327 <param name="qdepth_n" optional="true" type="integer" value="" label="Stop processing gapped alignments for a query/strand if its ratio of aligned bases to query length exceeds" help="This is a real number that corresponds to a depth of coverage threshold. For example, a value of 5.0 would cause termination once a query/strand has an average of five alignments for every base in the query. The numerator is the number of matches or substitutions (but not gaps); the denominator is the length of the query sequence. The purpose of this option is one of saving time. It is useful for automatically terminating the processing of queries with high repeat content, for which other methods of dealing with repetitive content fail. Moreover, back-end filtering options are not considered. In other words, matches are counted for any alignment that meets the scoring threshold, regardless of whether that alignment would be reported. The justification is that we are trying to abort the processing of queries that have too many bounding alignments in the DP matrix, and back-end filtering occurs later in the process."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	328 <param name="qdepth_keep" type="boolean" truevalue="keep" checked="False" label="Warnings for queries that exceed the limit are witheld" help="Note that the alignments reported are not guaranteed to be the highest scoring alignments that would achieve the threshold. They are simply the first alignments found. In other words, the purpose of this option is one of saving time, not one of finding optimal alignments."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	329 <param name="qdepth_nowarn" type="boolean" truevalue="nowarn" checked="False" label="Same as above but any alignments discovered for this query/strand, before it exceeds the threshold, are reported."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	330 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	331 <when value="no">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	332 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	333 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	334 </conditional>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	335 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	336 <section name="scoring" expanded="false" title="Scoring">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	337 <param name="score_file" type="data" format="txt" optional="true" argument="--scores" label="Read the substitution scores and gap penalties (and possibly other options) from a scoring file (see help below for file fomat description)." help="This option cannot be used in conjunction with ‑‑match or inference."/> <!--TODO EDIT INFERENCE -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	338 <conditional name="match">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	339 <param name="match_selector" type="select" label="Set the score values for a match and mismatch" argument="--match" help="Note that specifying ‑‑match changes the defaults for some of the other options (e.g. the scoring penalties for gaps, and various extension thresholds), as described in respective sections of LASTZ manual. The regular defaults are chosen for compatibility with BLASTZ, but since BLASTZ doesn't support ‑‑match, LASTZ infers that you are not expecting BLASTZ compatibility for this run, so it is free to use improved defaults. THIS OPTION CANNOT BE USED WITH --scores">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	340 <option value="yes">Yes</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	341 <option value="no" selected="true">No</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	342 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	343 <when value="yes">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	344 <param name="match_reward" type="integer" value="" optional="true" label="Score value for a match"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	345 <param name="match_penalty" type="integer" value="" optional="true" label="Score value for a mismatch"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	346 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	347 <when value="no">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	348 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	349 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	350 </conditional>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	351 <conditional name="gap">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	352 <param name="gap_selector" type="select" label="Set the score penalties for opening and extending a gap" argument="--gap" help="These are specified as positive values; subtraction is implicitly assumed. Note that the first base in a gap incurs the sum of both penalties. This option is only valid if gapped extension is being performed, and cannot be used in conjunction with inference. These values specified on the command line override any corresponding values from a file provided with ‑‑scores.">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	353 <option value="yes">Yes</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	354 <option value="no" selected="true">No</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	355 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	356 <when value="yes">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	357 <param name="gap_open" type="integer" value="" optional="true" label="Gap opening penalty"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	358 <param name="gap_extend" type="integer" value="" optional="true" label="Gap extension penalty"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	359 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	360 <when value="no">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	361 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	362 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	363 </conditional>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	364 <param name="ambigN" type="boolean" truevalue="--ambiguous=n" checked="false" label="Treat each N in the input sequences as an ambiguous nucleotide" argument="--ambiguous=n" help="Substitutions with N are scored as zero, instead of using the fill_score value from the scoring file (which is -100 by default)."/>
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	365 <param name="ambigIUPAC" type="boolean" truevalue="--ambiguous=iupac" checked="true" label="Treat each of the IUPAC-IUB ambiguity codes (B, D, H, K, M, R, S, V, W, and Y, as well as N) in the input sequences as a completely ambiguous nucleotide." argument="--ambiguous=iupac" help="Substitutions with these characters are scored as zero, instead of using the fill_score value from the scoring file (which is -100 by default)."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	366 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	367 <section name="seeding" expanded="false" title="Seeding">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	368 <conditional name="seed">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	369 <param name="seed_selector" type="select" label="Select seed type">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	370 <option value="defaults" selected="true">Use defaults</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	371 <option value="pre_set">Use pre-set values</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	372 <option value="len">Set length</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	373 <option value="half_len">Set half length</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	374 <option value="pattern">Set pattern</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	375 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	376 <when value="defaults">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	377 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	378 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	379 <when value="pre_set">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	380 <param name="pre_set_seeds" type="select" label="Select seed pattern" help="Select between 12of19 seed (19-bp word with matches in 12 specific positions: 1110100110010101111) or 14of22 seed (22-bp word with matches in 14 specific positions: 1110101100110010101111). 0 = mismatch, 1 = match" argument="--seed=12of19,--seed=14of22">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	381 <option value="--seed=12of19">12of19</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	382 <option value="--seed=14of22">14of22</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	383 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	384 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	385 <when value="len">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	386 <param name="seed_match" type="integer" value="" optional="true" label="Set seed length" help="Seeds require a N-bp word with matches in all positions" argument="--seed=match" />
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	387 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	388 <when value="half_len">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	389 <param name="seed_half" type="integer" value="" optional="true" label="Set seed length" help="Seeds requires N-bp word with matches or transitions in all positions" argument="--seed=half" />
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	390 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	391 <when value="pattern">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	392 <param name="pattern" type="text" size="25" optional="true" argument="--seed=PATTERN" label="Specify an arbitrary pattern" help="Use 1s, 0s, and Ts for seed discovery (e.g., 1110100110010101111 where 1 = match, 0 = mismatch, T = transition)" />
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	393 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	394 </conditional>
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	395 <param name="transitions" type="select" label="Allow transitions" help="In each seed, specify how many match positions can be transition(s) instead">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	396 <option value="--transition" selected="true">One</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	397 <option value="--transition=2">Two</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	398 <option value="--notransition">None</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	399 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	400 <conditional name="seed_filer">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	401 <param name="seed_filer_selector" type="select" label="Filter seeds" argument="--filter">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	402 <option value="yes">Yes</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	403 <option value="no" selected="true">No</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	404 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	405 <when value="yes">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	406 <param name="filter_tr" type="integer" value="" optional="true" label="Number of transitions" help="Allowing no more than this number of transversions. If not specified, any number of transversions is allowed (they are not limited)" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	407 <param name="filter_match" type="integer" value="" optional="true" label="Number of matches" help="Require at least this many exact matches"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	408 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	409 <when value="no">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	410 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	411 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	412 </conditional>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	413 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	414 <section name="hsp" expanded="false" title="HSPs (Gap-free extension)">
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	415 <param type="boolean" truevalue="--gfextend" checked="false" argument="--gfextend" label="Perform gap-free extension of seeds to HSPs" help="This will take into account other papermeters in this section"/>
37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	416 <param type="boolean" truevalue="--nogfextend" argument="--nogfextend" label="Skip the gap-free extension stage" help="Instead, pass the seeds along to the next specified stage.It is not recommended to use --nogfextend without also using --nogapped."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	417 <conditional name="hsp_method">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	418 <param name="hsp_method_selector" type="select" label="Select HSP finding method">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	419 <option value="none" selected="true">None</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	420 <option value="match">Match extension</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	421 <option value="mismatch">Mismatch extension</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	422 <option value="x">X-drop extension</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	423 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	424 <when value="none">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	425 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	426 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	427 <when value="match">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	428 <param type="integer" value="" optional="true" argument="--exact" label="Find HSPs using the exact match extension method with the given length threshold" help="This is instead of using the x-drop method"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	429 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	430 <when value="mismatch">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	431 <param name="mismatch_count" type="integer" value="" optional="true" label="Specify number of mismatches"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	432 <param name="mismatch_length" type="integer" value="" min="1" max="50" optional="true" label="Specify length threshold" help="Find HSPs using the mismatch extension method with the given length threshold and allowing specified number of mismatches" argument="--mismatch"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	433 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	434 <when value="x">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	435 <param type="integer" value="" optional="true" argument="--xdrop" label="Find HSPs using the x-drop extension method with this threshold" help="The dropoff setting determines the endpoints of each gap-free segment: the extension of each seed is stopped when its cumulative score drops off by more than the given threshold from the maximum seen so far."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	436 <param type="integer" value="" optional="true" argument="--hspthresh" label="Set the score threshold for the x-drop extension method" help="HSPs scoring lower are discarded"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	437 <param name="hspthresh_top" type="integer" value="" optional="true" argument="--hspthresh=top" label="Set an adaptive score threshold for the x-drop extension method" help="HSPs scoring lower are discarded. The score threshold is chosen to limit the number of target sequence bases in HSPs to about this value (or possibly a little higher in case of ties, etc.)."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	438 <param name="hspthresh_top_percent" type="integer" value="" optional="true" argument="--hspthresh=top%" label="Set an adaptive score threshold for the x-drop extension method" help="HSPs scoring lower are discarded. The score threshold is chosen to limit the number of target sequence bases in HSPs to about this perentage value (or possibly a little higher in case of ties, etc.)."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	439 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	440 </conditional>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	441 <param name="entropy" type="boolean" truevalue="--entropy" checked="false" label="Adjust for entropy when qualifying HSPs in the x-drop extension method" help="Those that score just slightly above the HSP threshold are adjusted downward according to the entropy of their nucleotides, and any that then fall below the threshold are discarded."/>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	442 <param name="entropy_report" type="boolean" truevalue="--entropy=report" checked="false" label="Adjust for entropy when qualifying HSPs in the x-drop extension method, and report (to stderr) any HSPs that are discarded as a result." help="Reported HSPs are printed to stderr"/>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	443 <param name="noentropy" type="boolean" truevalue="--noentropy" checked="false" label="Don't adjust for entropy when qualifying HSPs"/>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	444 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	445 <section name="chaining" expanded="false" title="Chaining">
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	446 <param type="boolean" truevalue="--chain" checked="false" argument="--chain" label="Perform chaining of HSPs with no penalties"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	447 <conditional name="chaning_penalties">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	448 <param name="chaning_penalties_selector" type="select" argument="--chain=" label="Perform chaining with penalties">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	449 <option value="yes">Yes</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	450 <option value="no" selected="true">No</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	451 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	452 <when value="yes">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	453 <param name="diag" type="integer" value="" optional="true" label="Penalty for diagonal in dynamic programming matrix"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	454 <param name="anti" type="integer" value="" optional="true" label="Penalty for anti-diagonal in dynamic programming matrix" help="These are specified as positive values; subtraction from the score is implicitly assumed."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	455 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	456 <when value="no">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	457 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	458 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	459 </conditional>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	460 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	461 <section name="gap_ext" expanded="false" title="Gapped extension">
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	462 <param type="boolean" truevalue="--gapped" argument="--gapped" label="Perform gapped extension of HSPs" help="Extension of HSPs (or seeds, if gap-free extension is not performed), is performed after first reducing them to anchor points."/>
37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	463 <param type="boolean" truevalue="--nogapped" argument="--nogapped" label="Skip the gapped extension stage" help="This means that interpolation must also be skipped, since it is not allowed without gapped extension"/>
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	464 <param type="integer" value="" optional="true" argument="--ydrop" label="Set the threshold for terminating gapped extension" help="This restricts the endpoints of each local alignment by limiting the local region around each anchor in which extension is performed. The boundary of this region in the dynamic programming matrix is formed by the points where the cumulative score has dropped off by more than the given threshold from the maximum seen so far."/>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	465 <param type="boolean" truevalue="--noytrim" argument="--noytrim" label="If y-drop extension encounters the end of the sequence, extend the alignment to the end of the sequence rather than trimming it back to the location giving the maximum score" help="This is highly recommended when either the target or query sequences are short reads (say, less than 100 bases), to prevent y-drop mismatch shadow."/>
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	466 <param type="integer" value="" optional="true" argument="--gappedthresh" label="Set the threshold for gapped extension" help="Alignments scoring lower than that value are discarded. When used along with the x-drop method for gap-free extension, this value is generally set at least as high as the HSP threshold. Setting it lower has no effect, since at worst the HSP itself would always qualify (both extension stages use the same scoring matrix)."/>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	467 <param type="boolean" truevalue="--allgappedbounds" argument="--allgappedbounds" label="Revert to handling bounding alignments the way they were handled in BLASTZ."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	468 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	469 <section name="filters" expanded="false" title="Filtering">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	470 <section name="identity" expanded="true" title="Filter alignments by percent identity">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	471 <param name="id_min" type="integer" value="" min="0" max="100" optional="true" label="Minimum identity"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	472 <param name="id_max" type="integer" value="" min="0" max="100" optional="true" argument="--filter=identity" label="Maximum identity (optional)" help="0 ≤ min ≤ max ≤ 100 percent. Identity is the percentage of aligned bases that are matches. Alignment blocks outside the given range are discarded."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	473 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	474 <section name="continuity" expanded="false" title="Filter alignments by continuity">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	475 <param name="cont_min" type="integer" value="" min="0" max="100" optional="true" label="Minimum continuity"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	476 <param name="cont_max" type="integer" value="" min="0" max="100" optional="true" argument="--filter=continuity" label="Maximum continuity (optional)" help="0 ≤ min ≤ max ≤ 100 percent. Continuity is the percentage of alignment columns that are not gaps. Alignment blocks outside the given range are discarded."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	477 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	478 <section name="coverage" expanded="false" title="Filter alignments by coverage">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	479 <param name="cov_min" type="integer" value="" min="0" max="100" optional="true" label="Minimum coverage"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	480 <param name="cov_max" type="integer" value="" min="0" max="100" optional="true" argument="--filter=coverage" label="Maximum coverage (optional)" help=" 0 ≤ min ≤ max ≤ 100 percent. Coverage is the percentage of the entire target or query sequence (whichever is shorter) that is included in the alignment block. Blocks outside the given range are discarded."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	481 </section>
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	482 <param name="filter_nmatch" type="integer" value="" min="1" optional="true" argument="--filter=nmatch" label="Filter alignments by how many bases match" help="Requiring at least this number of matched bases, min > 0. Match count is the number of matched bases in the alignment."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	483 <param name="filter_nmatch_percent" type="integer" value="" min="1" optional="true" argument="--filter=nmatch%" label="Filter alignments by how many bases match expressed as percentage" help="e.g., percentage of the query length."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	484 <param name="filter_nmismatch" type="integer" value="" min="0" optional="true" argument="--filter=nmismatch:0.." label="Filter alignments by the number of mismatches" help="Allow no more than this number of mismatched bases. Mismatch count, or nmismatch, is the number of aligned bases in the alignment that are mismatches (substitutions)."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	485 <param name="filter_ngap" type="integer" value="" min="0" optional="true" argument="--filter=ngap:0.." label="Filter alignments by the number of gaps" help="Allow no more than this number of gaps. Gap count, or ngap, is the number of runs of gapped columns in the alignment (each run is counted as one gap)."/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	486 <param name="filter_cgap" type="integer" value="" min="0" optional="true" argument="--filter=cgap:0.." label="Filter alignments by the number of gap columns" help="Allow no more than this number of gaps. Gap column count, or cgap, is the number of gapped columns in the alignment (each column is counted as one gap)."/>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	487 <param type="boolean" truevalue="--notrivial" argument="--notrivial" label="Do not output a trivial self-alignment block if the target and query sequences are identical" help="Note that using ‑‑self automatically enables this option."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	488 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	489 <section name="interpolation" expanded="false" title="Interpolation">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	490 <param type="integer" value="" optional="true" argument="--inner" label="Perform additional alignment between the gapped alignment blocks, using (presumably) more sensitive alignment parameters" help="This value is used as the threshold for both the gap-free and gapped extension sub-stages; see the discussion of interpolation for more details. This option is only valid if gapped extension is performed."/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	491 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	492 <section name="output_format" expanded="false" title="Output">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	493 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	494 <param name="format" type="select" label="Specify the output format">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	495 <option value="bam" selected="true">BAM --format=sam)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	496 <option value="general_def">General default (--format=general)</option>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	497 <option value="general_full">Customized general (--format=general[:fields])</option>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	498 <option value="maf">MAF (--format=maf)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	499 <option value="blastn">blastn (--format=BLASTN)</option>
12 48d39ee9eb30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 11 diff changeset	500 <option value="paf">paf (--format=PAF)</option>
9 2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	501 <option value="differences">Differences (--format=differences)</option>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	502 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	503 <when value="bam">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	504 <param name="bam_options" type="select" argument="--format=sam, --format=softsam" label="Select a BAM flavor to output" help="Lastz actually outputs SAM data but Galaxy converts it into BAM to save space. For alignments that don't reach the end of a query, ‑‑format=sam uses 'hard clipping', while ‑‑format=softsam uses 'soft clipping'. See the section on 'clipped alignment' in the SAM specification for an explanation of what this means. The options ‑‑format=sam- and ‑‑format=softsam- suppress the SAM header lines. This makes them suitable for concatenating output from multiple runs. If you need to specify readgroup information: use AddOrEplaceReadGroups from Picard package">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	505 <option value="sam" selected="true">BAM</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	506 <option value="softsam">soft-clipped BAM</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	507 <option value="sam-">BAM without header</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	508 <option value="softsam-">soft-clipped BAM without header</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	509 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	510 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	511 <when value="general_def">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	512 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	513 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	514 <when value="general_full">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	515 <param name="fields" type="select" display="checkboxes" multiple="true" label="Select which fields to include" argument="--format=general-[:fields]">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	516 <option value="score" selected="true">score: Score of the alignment block</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	517 <option value="name1" selected="true">name1: Name of the target sequence</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	518 <option value="number1">number1: Number of the target sequence within the target file</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	519 <option value="strand1" selected="true">strand1: Target sequence strand </option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	520 <option value="size1" selected="true">size1: Size of the entire target sequence</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	521 <option value="start1">start1: Starting position of the alignment block in the target, origin-one</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	522 <option value="zstart1" selected="true">zstart1: Starting position of the alignment block in the target, origin-zero</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	523 <option value="end1" selected="true">end1: Ending position of the alignment block in the target</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	524 <option value="length1">length1: Length of the alignment block in the target (excluding gaps)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	525 <option value="text1">text1: Aligned characters in the target, including gap characters</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	526 <option value="qalign1">qalign1: The target quality sequence (if there is one) correpsonding to aligned characters</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	527 <option value="nucs1">nucs1: The entire target sequence</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	528 <option value="name2" selected="true">name2: Name of the query sequence</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	529 <option value="number2">number2: Number of the query sequence within the query file</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	530 <option value="strand2" selected="true">strand2: Query sequence strand</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	531 <option value="size2" selected="true">size2: Size of the entire query sequence</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	532 <option value="start2">start2: Starting position of the alignment block in the query, origin-one</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	533 <option value="zstart2" selected="true">zstart2: Starting position of the alignment block in the query, origin-one</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	534 <option value="end2" selected="true">end2: Ending position of the alignment block in the query</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	535 <option value="length2">length2: Length of the alignment block in the query (excluding gaps)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	536 <option value="text2">text2: Aligned characters in the query, including gap characters</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	537 <option value="qalign2">qalign2: The query quality sequence (if there is one) correpsonding to aligned characters</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	538 <option value="nucs2">nucs2: The entire query sequence</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	539 <option value="nmatch">nmatch: Match count</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	540 <option value="nmismatch">nmismatch: Mismatch count</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	541 <option value="ncolumn">ncolumn: Number of columns in the block. This includes matches, mismatches (substitutions), and gaps</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	542 <option value="npair">npair: Number of aligned bases in the block that are matches or mismatches (substitutions)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	543 <option value="ngap">ngap: Gap count, the number of gaps in the block, counting each run of gapped columns as a single gap</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	544 <option value="cgap">cgap: Gap column count, the number of gaps in the block, counting each gapped column as a separate gap</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	545 <option value="diff">diff: Differences between what would be written for text1 and text2</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	546 <option value="cigar">cigar: A CIGAR-like representation of the alignment’s path</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	547 <option value="cigarx">cigarx: Same as cigar, but uses a newer syntax that distinguishes matches from substitutions</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	548 <option value="identity" selected="true">identity: Fraction of aligned bases in the block that are matches </option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	549 <option value="idfrac">idfrac: Fraction of aligned bases in the block that are matches </option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	550 <option value="id%" selected="true">id% Fraction of aligned bases in the block that are matches (as %)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	551 <option value="blastid%">blastid%: Fraction of the alignment block that is matches, as would be reported by NCBI BLAST</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	552 <option value="continuity">continuity: Rate of non-gaps (non-indels) in the alignment block</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	553 <option value="confrac">confrac: Rate of non-gaps (non-indels) in the alignment block (as fraction)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	554 <option value="con%">con%: Rate of non-gaps (non-indels) in the alignment block (as %)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	555 <option value="coverage" selected="true">coverage: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	556 <option value="covfrac">covfrac: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as fraction)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	557 <option value="cov%" selected="true">cov%: Fraction of the entire input sequence (target or query, whichever is shorter) that is covered by the alignment block (as %)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	558 <option value="diagonal">diagonal: The diagonal of the start of the alignment block in the DP matrix, expressed as an identifying number start1-start2</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	559 <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	560 <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	561 <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	562 <sanitizer invalid_char="">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	563 <valid initial="string.letters,string.digits"><add value="%" /> </valid>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	564 </sanitizer>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	565 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	566 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	567 <when value="maf">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	568 <param name="maf_type" type="select" argument="--format=maf" label="Seleat MAF flavor" help="MAF is a multiple alignment format developed at UCSC">
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	569 <option value="maf">MAF</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	570 <option value="maf+">MAF with additional stats</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	571 <option value="maf-">MAF without header and comments</option>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	572 </param>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	573 </when>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	574 <when value="blastn">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	575 <!-- Do nothing -->
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	576 </when>
12 48d39ee9eb30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 11 diff changeset	577 <when value="paf">
48d39ee9eb30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 11 diff changeset	578 <!-- Do nothing -->
48d39ee9eb30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 11 diff changeset	579 </when>
9 2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	580 <when value="differences">
2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	581 <!-- Do nothing -->
2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	582 </when>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	583 </conditional>
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	584 <param name="rplot" type="boolean" truevalue="--rdotplot=plot.r" falsevalue="" checked="false" argument="--rdotplot" label="Create a dotplot representation of alignments?" help="The dotplot is only useful if query and target contain exactly one sequence each"/>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	585 </section>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	586 </inputs>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	587 <outputs>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	588 <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads">
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	589 <change_format>
12 48d39ee9eb30 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 11 diff changeset	590 <when input="output_format.out.format" value="paf" format="paf" />
9 2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	591 <when input="output_format.out.format" value="bam" format="bam" />
2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	592 <when input="output_format.out.format" value="maf" format="maf" />
2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	593 <when input="output_format.out.format" value="differences" format="interval" />
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	594 </change_format>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	595 </data>
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	596 <data format="png" name="out_plot" label="${tool.name} on ${on_string}: dot plot">
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	597 <filter>output_format['rplot']</filter>
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	598 </data>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	599 </outputs>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	600 <tests>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	601 <test expect_num_outputs="1">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	602 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	603 <param name="ref_source" value="cached" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	604 <param name="target_2bit" value="phiX174" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	605 </conditional>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	606 <param name="query" value="phiX_split.fasta" />
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	607 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	608 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	609 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	610 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	611 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	612 <param name="format" value="general_def" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	613 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	614 </section>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	615 <output name="output" value="test1.out" />
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	616 </test>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	617 <test expect_num_outputs="1">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	618 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	619 <param name="ref_source" value="history" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	620 <param name="target" value="phiX_split.fasta" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	621 </conditional>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	622 <param name="query" value="phiX.fasta" />
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	623 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	624 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	625 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	626 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	627 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	628 <param name="format" value="general_def" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	629 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	630 </section>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	631 <output name="output" value="test2.out" />
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	632 </test>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	633 <test expect_num_outputs="1">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	634 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	635 <param name="ref_source" value="history" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	636 <param name="target" value="phiX_split.fasta" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	637 </conditional>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	638 <param name="query" value="phiX.fasta" />
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	639 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	640 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	641 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	642 <section name="scoring">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	643 <param name="score_file" value="score_file.txt" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	644 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	645 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	646 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	647 <param name="format" value="general_def" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	648 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	649 </section>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	650 <output name="output" value="test3.out" />
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	651 </test>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	652 <test expect_num_outputs="1">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	653 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	654 <param name="ref_source" value="history" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	655 <param name="target" value="chrM_mouse.fa.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	656 </conditional>
7 10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	657 <param name="query" value="chrM_human.fa.gz" />
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	658 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	659 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	660 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	661 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	662 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	663 <param name="format" value="blastn" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	664 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	665 </section>
7 10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	666 <output name="output" value="test4.out" />
10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	667 </test>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	668 <test expect_num_outputs="1">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	669 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	670 <param name="ref_source" value="history" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	671 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	672 </conditional>
7 10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	673 <param name="query" ftype="fastq.bz2" value="chrM_mouse.fq.bz2" />
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	674 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	675 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	676 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	677 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	678 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	679 <param name="format" value="blastn" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	680 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	681 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	682 <output name="output" value="test5.out" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	683 </test>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	684 <test expect_num_outputs="1">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	685 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	686 <param name="ref_source" value="history" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	687 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	688 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	689 <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	690 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	691 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	692 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	693 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	694 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	695 <param name="format" value="blastn" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	696 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	697 </section>
7 10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	698 <output name="output" value="test5.out" />
10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	699 </test>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	700 <test expect_num_outputs="1">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	701 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	702 <param name="ref_source" value="history" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	703 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	704 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	705 <param name="query" ftype="fastq" value="chrM_mouse.fq" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	706 <param name="lastz_32" value="true" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	707 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	708 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	709 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	710 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	711 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	712 <param name="format" value="blastn" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	713 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	714 </section>
7 10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	715 <output name="output" value="test5.out" />
10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	716 </test>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	717 <test expect_num_outputs="1">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	718 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	719 <param name="ref_source" value="cached" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	720 <param name="target_2bit" value="phiX174" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	721 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	722 <param name="query" value="phiX_split.fasta" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	723 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	724 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	725 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	726 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	727 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	728 <param name="format" value="differences" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	729 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	730 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	731 <output name="output" value="test6.out" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	732 </test>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	733 <test expect_num_outputs="2">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	734 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	735 <param name="ref_source" value="history" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	736 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	737 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	738 <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	739 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	740 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	741 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	742 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	743 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	744 <param name="format" value="paf" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	745 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	746 <param name="rplot" value="true"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	747 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	748 <output name="output" value="test7.out" ftype="paf"/>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	749 <output name="out_plot" value="test7.png"/>
7 10aca14c2332 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 6 diff changeset	750 </test>
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	751 <test expect_num_outputs="1">
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	752 <conditional name="source">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	753 <param name="ref_source" value="history" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	754 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	755 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	756 <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	757 <section name="where_to_look">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	758 <param name="strand" value="--strand=both" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	759 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	760 <section name="output_format">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	761 <conditional name="out">
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	762 <param name="format" value="bam" />
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	763 </conditional>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	764 </section>
bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	765 <output name="output" value="test8.bam" ftype="bam"/>
9 2ff111fac1d7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 8 diff changeset	766 </test>
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	767 </tests>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	768
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	769 <help><![CDATA[
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	770
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	771 What is does
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	772
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	773 LASTZ is designed to preprocess one sequence or set of sequences (which we collectively call the TARGET) and then align several QUERY sequences to it. It was developed by `Bob Harris <http://www.bx.psu.edu/~rsharris/>`_ in the lab of Webb Miller at Penn State.
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	774
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	775 .. class:: infomark
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	776
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	777 Read documentation before proceeding. LASTZ is a complex tool with many parameter options. Fortunately, there is a `great manual <https://lastz.github.io/lastz/>`_ maintained by its author. Default parameters may be sufficient to obtain the initial idea about how similar your sequences are, but to produce reliable alignments you may need to tweak the parameters. Read the manual.
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	778
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	779 .. class:: warningmark
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	780
11 37b497aa133f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 10 diff changeset	781 Galaxy version of LASTZ sets --ambiguous=iupac as default (see Scoring section). This prevents LASTZ from erroring out if one of the DNA inputrs contains "non-standard" nucleotides.
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	782
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	783 About LASTZ parameters
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	784
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	785 Galaxy's version of LASTZ has nine parameter sections (Where to look, Scoring, Seeding, HSPs, Chaining, Gapped extension, Filtering, Interpolation, and Output). These sections closely follow parameter description in the `manual <https://lastz.github.io/lastz/#syntax>`_.
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	786
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	787 Defaults
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	788
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	789 here are defaults for some of the most important parameters::
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	790
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	791 --seed=<pattern> set seed pattern (12of19, 14of22, or general pattern)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	792 (default is 1110100110010101111)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	793 SEE "Seeding" SECTION -> "Select seed type"
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	794
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	795 --[no]transition allow (or don't) one transition in a seed hit
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	796 (by default a transition is allowed)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	797 SEE "Seeding" SECTION -> "Allow transitions"
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	798
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	799 --[no]chain perform chaining
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	800 (by default no chaining is performed)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	801 SEE "Chaining" SECTION
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	802
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	803 --[no]gapped perform gapped alignment (instead of gap-free)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	804 (by default gapped alignment is performed)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	805 SEE "Gapped extension" SECTION
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	806
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	807 --strand=both search both strands
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	808 --strand=plus search + strand only (matching strand of query spec)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	809 (by default both strands are searched)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	810 SEE "Where to look" SECTION
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	811
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	812 --scores=<file> read substitution and gap scores from a file
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	813 SEE "Scoring" SECTION
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	814
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	815 --xdrop=<score> set x-drop threshold (default is 10sub[A][A])
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	816 SEE "HSPs" SECTION
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	817
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	818 --ydrop=<score> set y-drop threshold (default is open+300extend)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	819 SEE "Gapped extension" SECTION
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	820
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	821 --hspthresh=<score> set threshold for high scoring pairs (default is 3000)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	822 ungapped extensions scoring lower are discarded
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	823 <score> can also be a percentage or base count
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	824 SEE "HSPs" SECTION
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	825
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	826 --gappedthresh=<score> set threshold for gapped alignments
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	827 gapped extensions scoring lower are discarded
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	828 <score> can also be a percentage or base count
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	829 (default is to use same value as --hspthresh)
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	830 SEE "Gapped extension" SECTION
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	831
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	832
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	833 Substitution matrix
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	834
13 bf107d23242b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 04ec440aef00477a46c89fdb9b74e9bade5ffd94 iuc parents: 12 diff changeset	835 By default the HOXD70 substitution scores are used (from `Chiaromonte et al. 2002 <https://doi.org/10.1142/9789812799623_0012>`_)::
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	836
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	837 bad_score = X:-1000 # used for sub['X'][] and sub[]['X']
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	838 fill_score = -100 # used when sub[][] is not defined
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	839 gap_open_penalty = 400
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	840 gap_extend_penalty = 30
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	841
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	842 A C G T
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	843 A 91 -114 -31 -123
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	844 C -114 100 -125 -31
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	845 G -31 -125 100 -114
e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	846 T -123 -31 -114 91
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	847
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	848 Matrix can be supplied as an input to Read the substitution scores parameter in Scoring section. Substitution matrix can be inferred from your data using another LASTZ-based tool (LASTZ_D: Infer substitution scores).
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	849
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	850 Output
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	851
8 e7f19d6a9af8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 7 diff changeset	852 This version of LASTZ produces one output by default: a BAM alignment file. Other formats as well as a Dot Plot can be configured in Output section. This incarnation of LASTZ produces outputs without comment line starting with '#'. To learn identity of each column, consult `formats section of LASTZ manual <https://lastz.github.io/lastz/#formats>`_.
5 bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	853
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	854 ]]>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	855 </help>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	856 <expand macro="citations"/>
bd84ff27bc16 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a0a0480a8df511d23ed6101a489ca06337f5ed56 devteam parents: diff changeset	857 </tool>

Mercurial > repos > devteam > lastz

annotate lastz.xml @ 13:bf107d23242b draft default tip