lastz: lastz.xml annotate

annotate lastz.xml @ 9:15b1af922236 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595

author	iuc
date	Thu, 22 Jan 2026 18:27:59 +0000
parents	da6f44d06921
children

rev	line source
7 86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	1 <tool id="lastz_wrapper_2" name="LASTZ" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	2 <description>: align long sequences</description>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	3 <macros>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	4 <import>lastz_macros.xml</import>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	5 </macros>
7 86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	6 <expand macro="bio_tools"/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	7 <requirements>
7 86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	8 <requirement type="package" version="@TOOL_VERSION@">lastz</requirement>
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	9 <requirement type="package" version="1.14">samtools</requirement>
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	10 <requirement type="package" version="3.6.3">r-base</requirement>
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	11 <requirement type="package" version="1.0.8">bzip2</requirement>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	12 </requirements>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	13 <command detect_errors="exit_code"><![CDATA[
7 86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	14 #if $lastz_32:
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	15 lastz_32
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	16 #else:
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	17 lastz
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	18 #end if
86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	19
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	20 @TARGET_INPUT_COMMAND_LINE@
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	21 ## If --self is set: perform self alignment and ignore the query
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	22 #if $where_to_look.self:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	23 '${where_to_look.self}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	24 #if $where_to_look.nomirror
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	25 '${where_to_look.nomirror}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	26 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	27 #else:
3 c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	28 @query_input@
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	29 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	30
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	31 ## WHERE TO LOOK --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	32
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	33 '${where_to_look.strand}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	34 #if str( $where_to_look.qhsplimit.qhsplimit_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	35 #if $where_to_look.qhsplimit.qhsplimit_n:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	36 #if $where_to_look.qhsplimit.qhsplimit_nowarn:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	37 #if $where_to_look.qhsplimit.qhsplimit_keep:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	38 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_keep},${where_to_look.qhsplimit.qhsplimit_nowarn}:${where_to_look.qhsplimit.qhsplimit_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	39 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	40 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_nowarn}:${where_to_look.qhsplimit.qhsplimit_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	41 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	42 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	43 '--queryhsplimit=${where_to_look.qhsplimit.qhsplimit_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	44 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	45 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	46 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	47
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	48 #if $where_to_look.qhspbest:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	49 '--queryhspbest=${where_to_look.qhspbest}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	50 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	51
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	52 #if str( $where_to_look.qdepth.qdepth_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	53 #if $where_to_look.qdepth.qdepth_n:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	54 #if $where_to_look.qdepth.qdepth_nowarn and not $where_to_look.qdepth.qdepth_keep:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	55 '--querydepth=${where_to_look.qdepth.qdepth_nowarn}:${where_to_look.qdepth.qdepth_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	56 #elif not $where_to_look.qdepth.qdepth_nowarn and $where_to_look.qdepth.qdepth_keep:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	57 '--querydepth=${where_to_look.qdepth.qdepth_keep}:${where_to_look.qdepth.qdepth_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	58 #elif $where_to_look.qdepth.qdepth_nowarn and $where_to_look.qdepth.qdepth_keep:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	59 '--querydepth=${where_to_look.qdepth.qdepth_keep},${where_to_look.qdepth.qdepth_nowarn}:${where_to_look.qdepth.qdepth_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	60 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	61 '--querydepth=${where_to_look.qdepth.qdepth_n}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	62 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	63 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	64 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	65
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	66 ## SCORING --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	67
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	68 #if $scoring.score_file:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	69 '--scores=${scoring.score_file}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	70 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	71
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	72 #if str( $scoring.match.match_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	73 #if $scoring.match.match_reward:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	74 #if $scoring.match.match_penalty:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	75 '--match=${scoring.match.match_reward},${scoring.match.match_penalty}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	76 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	77 '--match=${scoring.match.match_reward}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	78 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	79 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	80 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	81 #if str( $scoring.gap.gap_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	82 #if $scoring.gap.gap_extend:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	83 #if $scoring.gap.gap_open:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	84 '--gap=${scoring.gap.gap_open},${scoring.gap.gap_extend}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	85 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	86 '--gap=${scoring.gap.gap_extend}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	87 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	88 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	89 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	90 #if $scoring.ambigN:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	91 '${scoring.ambigN}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	92 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	93 #if $scoring.ambigIUPAC:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	94 '${scoring.ambigIUPAC}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	95 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	96
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	97 ## SEEDING --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	98
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	99 #if str( $seeding.seed.seed_selector ) == "pre_set":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	100 '${seeding.seed.pre_set_seeds}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	101 #elif str( $seeding.seed.seed_selector ) == "len":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	102 '--seed=match${seeding.seed.seed_match}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	103 #elif str( $seeding.seed.seed_selector ) == "half_len":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	104 '--seed=half${seeding.seed.seed_half}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	105 #elif str( $seeding.seed.seed_selector ) == "pattern":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	106 '--seed=${seeding.seed.pattern}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	107 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	108 #if str( $seeding.transitions ) != "--transition":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	109 '${seeding.transitions}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	110 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	111 #if str( $seeding.seed_filer.seed_filer_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	112 #if $seeding.seed_filer.filter_match:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	113 #if $seeding.seed_filer.filter_tr:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	114 '--filter=${seeding.seed_filer.filter_tr},${seeding.seed_filer.filter_match}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	115 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	116 '--filter=${seeding.seed_filer.filter_match}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	117 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	118 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	119 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	120
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	121 ## FINDING HSPs --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	122
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	123 #if $hsp.gfextend:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	124 '${hsp.gfextend}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	125 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	126 #if $hsp.nogfextend
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	127 '${hsp.nogfextend}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	128 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	129 #if str( $hsp.hsp_method.hsp_method_selector ) == "match":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	130
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	131 #if $hsp.hsp_method.exact:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	132 '--exact=${hsp.hsp_method.exact}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	133 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	134 #elif str( $hsp.hsp_method.hsp_method_selector ) == "mismatch":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	135
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	136 #if $hsp.hsp_method.mismatch_count and $hsp.hsp_method.mismatch_length:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	137 '--mismatch=${hsp.hsp_method.mismatch_count},${hsp.hsp_method.mismatch_length}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	138 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	139 #elif str( $hsp.hsp_method.hsp_method_selector ) == "x":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	140
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	141 #if $hsp.hsp_method.xdrop:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	142 '--xdrop=${hsp.hsp_method.xdrop}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	143 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	144
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	145 #if $hsp.hsp_method.hspthresh:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	146 '--hspthresh=${hsp.hsp_method.hspthresh}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	147 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	148
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	149 #if $hsp.hsp_method.hspthresh_top:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	150 '--hspthresh=top${hsp.hsp_method.hspthresh_top}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	151 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	152
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	153 #if $hsp.hsp_method.hspthresh_top_percent:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	154 '--hspthresh=top${hsp.hsp_method.hspthresh_top_percent}%'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	155 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	156 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	157 #if $hsp.entropy:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	158 '${hsp.entropy}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	159 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	160 #if $hsp.entropy_report:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	161 '${hsp.entropy_report}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	162 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	163 #if $hsp.noentropy:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	164 '${hsp.noentropy}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	165 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	166
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	167 ## CHAINING --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	168
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	169 #if $chaining.chain:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	170 '${chaining.chain}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	171 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	172 #if str( $chaining.chaning_penalties.chaning_penalties_selector ) == "yes":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	173 #if $chaining.chaning_penalties.diag and $chaining.chaning_penalties.anti:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	174 '--chain=${chaining.chaning_penalties.diag},${chaining.chaning_penalties.anti}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	175 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	176 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	177
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	178 ## GAPPED EXTENSION --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	179
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	180 #if $gap_ext.gapped:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	181 '${gap_ext.gapped}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	182 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	183 #if $gap_ext.nogapped:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	184 '${gap_ext.nogapped}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	185 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	186 #if $gap_ext.ydrop:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	187 '--ydrop=${gap_ext.ydrop}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	188 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	189 #if $gap_ext.noytrim:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	190 '${gap_ext.noytrim}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	191 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	192 #if $gap_ext.gappedthresh:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	193 '--gappedthresh=${gap_ext.gappedthresh}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	194 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	195 #if $gap_ext.allgappedbounds:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	196 '${gap_ext.allgappedbounds}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	197 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	198
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	199 ## FILTERING --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	200
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	201 #if $filters.identity.id_min:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	202 #if $filters.identity.id_max:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	203 '--filter=identity:${filters.identity.id_min}..${filters.identity.id_max}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	204 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	205 '--filter=identity:${filters.identity.id_min}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	206 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	207 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	208 #if $filters.continuity.cont_min:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	209 #if $filters.continuity.cont_max:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	210 '--filter=continuity:${filters.continuity.cont_min}..${filters.continuity.cont_max}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	211 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	212 '--filter=continuity:${filters.continuity.cont_min}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	213 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	214 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	215 #if $filters.coverage.cov_min:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	216 #if $filters.coverage.cov_max:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	217 '--filter=coverage:${filters.coverage.cov_min}..${filters.coverage.cov_max}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	218 #else:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	219 '--filter=coverage:${filters.coverage.cov_min}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	220 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	221 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	222 #if $filters.filter_nmatch:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	223 '--filter=nmatch:${filters.filter_nmatch}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	224 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	225 #if $filters.filter_nmatch_percent:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	226 '--filter=nmatch:${filters.filter_nmatch_percent}%'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	227 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	228 #if $filters.filter_nmismatch:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	229 '--filter=nmismatch:0..${filters.filter_nmismatch}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	230 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	231 #if $filters.filter_ngap:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	232 '--filter=ngap:0..${filters.filter_ngap}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	233 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	234 #if $filters.filter_cgap:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	235 '--filter=cgap:0..${filters.filter_cgap}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	236 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	237 #if $filters.notrivial:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	238 '${filters.notrivial}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	239 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	240
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	241 ## INTERPOLATION --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	242
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	243 #if $interpolation.inner:
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	244 '--inner=${interpolation.inner}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	245 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	246
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	247 ## HOUSEKEEPING ----------------------------------
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	248
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	249 --traceback=160M
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	250
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	251
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	252 ## OUTPUT FORMATS --------------------------------
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	253
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	254 #if str( $output_format.out.format ) == "bam":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	255 '--format=${output_format.out.bam_options}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	256 #elif str( $output_format.out.format ) == "general_def":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	257 --format=general-
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	258 #elif str( $output_format.out.format ) == "maf":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	259 '--format=${output_format.out.maf_type}'
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	260 #elif str( $output_format.out.format ) == "blastn":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	261 --format=BLASTN-
9 15b1af922236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 8 diff changeset	262 #elif str( $output_format.out.format ) == "paf":
15b1af922236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 8 diff changeset	263 --format=PAF-
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	264 #elif str( $output_format.out.format ) == "general_full":
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	265 '--format=general-:${output_format.out.fields}'
5 ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	266 #elif str( $output_format.out.format ) == "differences":
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	267 '--format=differences'
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	268 #end if
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	269 --action:target=multiple
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	270 $output_format.rplot
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	271 #if str( $output_format.out.format ) == "bam":
5 ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	272 \| samtools sort -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '${output}'
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	273 #else:
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	274 > '${output}'
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	275 #end if
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	276 #if $output_format.rplot:
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	277 &&
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	278 Rscript $r_plot > /dev/null 2>&1
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	279 #end if
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	280
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	281 ]]>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	282 </command>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	283 <configfiles>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	284 <configfile name="r_plot">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	285 <![CDATA[
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	286 #!/usr/bin/env Rscript
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	287 ## Setup R error handling to go to stderr
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	288 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	289 ## Only produce image when 'plot.r' actually contains data
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	290 if(file.info('plot.r')\$size>0){
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	291 x <- read.table("plot.r", as.is=TRUE)
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	292 png("${out_plot}", width=640, height=640, res=72)
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	293 plot(x, type='l', xlab="target", ylab="query", main="plot")
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	294 dev.off()
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	295 }
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	296 ]]>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	297 </configfile>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	298 </configfiles>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	299 <inputs>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	300 <expand macro="target_input"/>
3 c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	301 <param name="query" format="fasta,fastq,fasta.gz,fastq.gz,fastq.bz2" type="data" label="Select QUERY sequence(s)" help="These are the sequences that you are aligning against TARGET"/>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	302 <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"/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	303 <section name="where_to_look" expanded="False" title="Where to look">
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	304 <param type="select" display="radio" label="which strand to search" argument="--strand" help="Search both strands or choose plus or minus">
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	305 <option value="--strand=both" selected="True">Both</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	306 <option value="--strand=plus">Plus</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	307 <option value="--strand=minus">Minus</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	308 </param>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	309 <param type="boolean" display="radio" 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"/>
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	310 <param type="boolean" display="radio" 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."/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	311 <conditional name="qhsplimit">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	312 <param name="qhsplimit_selector" type="select" display="radio" label="Set HSP limit" argument="--queryhsplimit">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	313 <option value="yes">Yes</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	314 <option value="no" selected="true">No</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	315 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	316 <when value="yes">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	317 <param name="qhsplimit_n" optional="true" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	318 <param name="qhsplimit_nowarn" type="boolean" truevalue="nowarn" display="radio" checked="False" label=" Withhold warnings for queries that exceed the limit set above"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	319 <param name="qhsplimit_keep" type="boolean" truevalue="keep" display="radio" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	320 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	321 <when value="no">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	322 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	323 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	324 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	325 <param name="qhspbest" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	326 <conditional name="qdepth">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	327 <param name="qdepth_selector" type="select" display="radio" label="Set ratio of aligned bases to query length" argument="--querydepth">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	328 <option value="yes">Yes</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	329 <option value="no" selected="true">No</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	330 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	331 <when value="yes">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	332 <param name="qdepth_n" optional="true" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	333 <param name="qdepth_keep" type="boolean" truevalue="keep" display="radio" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	334 <param name="qdepth_nowarn" type="boolean" truevalue="nowarn" display="radio" checked="False" label="Same as above but any alignments discovered for this query/strand, before it exceeds the threshold, are reported."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	335 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	336 <when value="no">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	337 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	338 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	339 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	340 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	341 <section name="scoring" expanded="false" title="Scoring">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	342 <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 -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	343 <conditional name="match">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	344 <param name="match_selector" type="select" display="radio" 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">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	345 <option value="yes">Yes</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	346 <option value="no" selected="true">No</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	347 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	348 <when value="yes">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	349 <param name="match_reward" type="integer" optional="true" label="Score value for a match"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	350 <param name="match_penalty" type="integer" optional="true" label="Score value for a mismatch"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	351 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	352 <when value="no">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	353 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	354 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	355 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	356 <conditional name="gap">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	357 <param name="gap_selector" type="select" display="radio" 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.">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	358 <option value="yes">Yes</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	359 <option value="no" selected="true">No</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	360 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	361 <when value="yes">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	362 <param name="gap_open" type="integer" optional="true" label="Gap opening penalty"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	363 <param name="gap_extend" type="integer" optional="true" label="Gap extension penalty"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	364 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	365 <when value="no">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	366 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	367 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	368 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	369 <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)."/>
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	370 <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)."/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	371 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	372 <section name="seeding" expanded="false" title="Seeding">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	373 <conditional name="seed">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	374 <param name="seed_selector" type="select" display="radio" label="Select seed type">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	375 <option value="defaults" selected="true">Use defaults</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	376 <option value="pre_set">Use pre-set values</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	377 <option value="len">Set length</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	378 <option value="half_len">Set half length</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	379 <option value="pattern">Set pattern</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	380 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	381 <when value="defaults">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	382 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	383 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	384 <when value="pre_set">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	385 <param name="pre_set_seeds" type="select" display="radio" 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">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	386 <option value="--seed=12of19">12of19</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	387 <option value="--seed=14of22">14of22</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	388 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	389 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	390 <when value="len">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	391 <param name="seed_match" type="integer" optional="true" label="Set seed length" help="Seeds require a N-bp word with matches in all positions" argument="--seed=match" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	392 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	393 <when value="half_len">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	394 <param name="seed_half" type="integer" optional="true" label="Set seed length" help="Seeds requires N-bp word with matches or transitions in all positions" argument="--seed=half" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	395 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	396 <when value="pattern">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	397 <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)" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	398 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	399 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	400 <param name="transitions" type="select" display="radio" label="Allow transitions" help="In each seed, specify how many match positions can be transition(s) instead">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	401 <option value="--transition" selected="true">One</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	402 <option value="--transition=2">Two</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	403 <option value="--notransition">None</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	404 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	405 <conditional name="seed_filer">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	406 <param name="seed_filer_selector" type="select" display="radio" label="Filter seeds" argument="--filter">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	407 <option value="yes">Yes</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	408 <option value="no" selected="true">No</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	409 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	410 <when value="yes">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	411 <param name="filter_tr" type="integer" 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)" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	412 <param name="filter_match" type="integer" optional="true" label="Number of matches" help="Require at least this many exact matches"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	413 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	414 <when value="no">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	415 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	416 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	417 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	418 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	419 <section name="hsp" expanded="false" title="HSPs (Gap-free extension)">
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	420 <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"/>
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	421 <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."/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	422 <conditional name="hsp_method">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	423 <param name="hsp_method_selector" type="select" display="radio" label="Select HSP finding method">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	424 <option value="none" selected="true">None</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	425 <option value="match">Match extension</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	426 <option value="mismatch">Mismatch extension</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	427 <option value="x">X-drop extension</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	428 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	429 <when value="none">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	430 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	431 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	432 <when value="match">
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	433 <param type="integer" 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"/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	434 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	435 <when value="mismatch">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	436 <param name="mismatch_count" type="integer" optional="true" label="Specify number of mismatches"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	437 <param name="mismatch_length" type="integer" 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"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	438 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	439 <when value="x">
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	440 <param type="integer" 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."/>
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	441 <param type="integer" optional="true" argument="--hspthresh" label="Set the score threshold for the x-drop extension method" help="HSPs scoring lower are discarded"/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	442 <param name="hspthresh_top" type="integer" 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.)."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	443 <param name="hspthresh_top_percent" type="integer" 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.)."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	444 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	445 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	446 <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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	447 <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"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	448 <param name="noentropy" type="boolean" truevalue="--noentropy" checked="false" label="Don't adjust for entropy when qualifying HSPs"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	449 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	450 <section name="chaining" expanded="false" title="Chaining">
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	451 <param type="boolean" truevalue="--chain" checked="false" argument="--chain" label="Perform chaining of HSPs with no penalties"/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	452 <conditional name="chaning_penalties">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	453 <param name="chaning_penalties_selector" type="select" display="radio" argument="--chain=" label="Perform chaining with penalties">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	454 <option value="yes">Yes</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	455 <option value="no" selected="true">No</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	456 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	457 <when value="yes">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	458 <param name="diag" type="integer" optional="true" label="Penalty for diagonal in dynamic programming matrix"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	459 <param name="anti" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	460 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	461 <when value="no">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	462 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	463 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	464 </conditional>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	465 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	466 <section name="gap_ext" expanded="false" title="Gapped extension">
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	467 <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."/>
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	468 <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"/>
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	469 <param type="integer" 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."/>
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	470 <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."/>
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	471 <param type="integer" 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)."/>
da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	472 <param type="boolean" truevalue="--allgappedbounds" argument="--allgappedbounds" label="Revert to handling bounding alignments the way they were handled in BLASTZ."/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	473 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	474 <section name="filters" expanded="false" title="Filtering">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	475 <section name="identity" expanded="true" title="Filter alignments by percent identity">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	476 <param name="id_min" type="integer" min="0" max="100" optional="true" label="Minimum identity"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	477 <param name="id_max" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	478 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	479 <section name="continuity" expanded="false" title="Filter alignments by continuity">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	480 <param name="cont_min" type="integer" min="0" max="100" optional="true" label="Minimum continuity"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	481 <param name="cont_max" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	482 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	483 <section name="coverage" expanded="false" title="Filter alignments by coverage">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	484 <param name="cov_min" type="integer" min="0" max="100" optional="true" label="Minimum coverage"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	485 <param name="cov_max" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	486 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	487 <param name="filter_nmatch" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	488 <param name="filter_nmatch_percent" type="integer" 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."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	489 <param name="filter_nmismatch" type="integer" 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)."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	490 <param name="filter_ngap" type="integer" 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)."/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	491 <param name="filter_cgap" type="integer" 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)."/>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	492 <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."/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	493 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	494 <section name="interpolation" expanded="false" title="Interpolation">
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	495 <param type="integer" 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."/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	496 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	497 <section name="output_format" expanded="false" title="Output">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	498 <conditional name="out">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	499 <param name="format" type="select" display="radio" label="Specify the output format">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	500 <option value="bam" selected="true">BAM --format=sam)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	501 <option value="general_def">General default (--format=general)</option>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	502 <option value="general_full">Customized general (--format=general[:fields])</option>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	503 <option value="maf">MAF (--format=maf)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	504 <option value="blastn">blastn (--format=BLASTN)</option>
9 15b1af922236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 8 diff changeset	505 <option value="paf">paf (--format=PAF)</option>
5 ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	506 <option value="differences">Differences (--format=differences)</option>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	507 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	508 <when value="bam">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	509 <param name="bam_options" type="select" display="radio" 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">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	510 <option value="sam" selected="true">BAM</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	511 <option value="softsam">soft-clipped BAM</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	512 <option value="sam-">BAM without header</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	513 <option value="softsam-">soft-clipped BAM without header</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	514 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	515 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	516 <when value="general_def">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	517 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	518 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	519 <when value="general_full">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	520 <param name="fields" type="select" display="checkboxes" multiple="true" label="Select which fields to include" argument="--format=general-[:fields]">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	521 <option value="score" selected="true">score: Score of the alignment block</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	522 <option value="name1" selected="true">name1: Name of the target sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	523 <option value="number1">number1: Number of the target sequence within the target file</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	524 <option value="strand1" selected="true">strand1: Target sequence strand </option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	525 <option value="size1" selected="true">size1: Size of the entire target sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	526 <option value="start1">start1: Starting position of the alignment block in the target, origin-one</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	527 <option value="zstart1" selected="true">zstart1: Starting position of the alignment block in the target, origin-zero</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	528 <option value="end1" selected="true">end1: Ending position of the alignment block in the target</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	529 <option value="length1">length1: Length of the alignment block in the target (excluding gaps)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	530 <option value="text1">text1: Aligned characters in the target, including gap characters</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	531 <option value="qalign1">qalign1: The target quality sequence (if there is one) correpsonding to aligned characters</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	532 <option value="nucs1">nucs1: The entire target sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	533 <option value="name2" selected="true">name2: Name of the query sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	534 <option value="number2">number2: Number of the query sequence within the query file</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	535 <option value="strand2" selected="true">strand2: Query sequence strand</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	536 <option value="size2" selected="true">size2: Size of the entire query sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	537 <option value="start2">start2: Starting position of the alignment block in the query, origin-one</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	538 <option value="zstart2" selected="true">zstart2: Starting position of the alignment block in the query, origin-one</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	539 <option value="end2" selected="true">end2: Ending position of the alignment block in the query</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	540 <option value="length2">length2: Length of the alignment block in the query (excluding gaps)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	541 <option value="text2">text2: Aligned characters in the query, including gap characters</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	542 <option value="qalign2">qalign2: The query quality sequence (if there is one) correpsonding to aligned characters</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	543 <option value="nucs2">nucs2: The entire query sequence</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	544 <option value="nmatch">nmatch: Match count</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	545 <option value="nmismatch">nmismatch: Mismatch count</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	546 <option value="ncolumn">ncolumn: Number of columns in the block. This includes matches, mismatches (substitutions), and gaps</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	547 <option value="npair">npair: Number of aligned bases in the block that are matches or mismatches (substitutions)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	548 <option value="ngap">ngap: Gap count, the number of gaps in the block, counting each run of gapped columns as a single gap</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	549 <option value="cgap">cgap: Gap column count, the number of gaps in the block, counting each gapped column as a separate gap</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	550 <option value="diff">diff: Differences between what would be written for text1 and text2</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	551 <option value="cigar">cigar: A CIGAR-like representation of the alignment’s path</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	552 <option value="cigarx">cigarx: Same as cigar, but uses a newer syntax that distinguishes matches from substitutions</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	553 <option value="identity" selected="true">identity: Fraction of aligned bases in the block that are matches </option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	554 <option value="idfrac">idfrac: Fraction of aligned bases in the block that are matches </option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	555 <option value="id%" selected="true">id% Fraction of aligned bases in the block that are matches (as %)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	556 <option value="blastid%">blastid%: Fraction of the alignment block that is matches, as would be reported by NCBI BLAST</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	557 <option value="continuity">continuity: Rate of non-gaps (non-indels) in the alignment block</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	558 <option value="confrac">confrac: Rate of non-gaps (non-indels) in the alignment block (as fraction)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	559 <option value="con%">con%: Rate of non-gaps (non-indels) in the alignment block (as %)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	560 <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>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	561 <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>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	562 <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>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	563 <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>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	564 <option value="shingle">shingle: A measurement of the shingle overlap between the target and the query</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	565 <option value="number">number: The alignment number, counted as alignments are written to output (1-base)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	566 <option value="znumber">znumber: The alignment number, counted as alignments are written to output (0-base)</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	567 <sanitizer invalid_char="">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	568 <valid initial="string.letters,string.digits"><add value="%" /> </valid>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	569 </sanitizer>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	570 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	571 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	572 <when value="maf">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	573 <param name="maf_type" type="select" display="radio" argument="--format=maf" label="Seleat MAF flavor" help="MAF is a multiple alignment format developed at UCSC">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	574 <option value="maf">MAF</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	575 <option value="maf+">MAF with additional stats</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	576 <option value="maf-">MAF without header and comments</option>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	577 </param>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	578 </when>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	579 <when value="blastn">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	580 <!-- Do nothing -->
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	581 </when>
9 15b1af922236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 8 diff changeset	582 <when value="paf">
15b1af922236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 8 diff changeset	583 <!-- Do nothing -->
15b1af922236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 8 diff changeset	584 </when>
5 ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	585 <when value="differences">
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	586 <!-- Do nothing -->
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	587 </when>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	588 </conditional>
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	589 <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"/>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	590 </section>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	591 </inputs>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	592 <outputs>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	593 <data format="tabular" name="output" label="${tool.name} on ${on_string}: mapped reads">
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	594 <change_format>
9 15b1af922236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz commit 2f47e1d9794907e95166dbd039f54139d5ca5595 iuc parents: 8 diff changeset	595 <when input="output_format.out.format" value="paf" format="paf" />
5 ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	596 <when input="output_format.out.format" value="bam" format="bam" />
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	597 <when input="output_format.out.format" value="maf" format="maf" />
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	598 <when input="output_format.out.format" value="differences" format="interval" />
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	599 </change_format>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	600 </data>
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	601 <data format="png" name="out_plot" label="${tool.name} on ${on_string}: dot plot">
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	602 <filter>output_format['rplot']</filter>
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	603 </data>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	604 </outputs>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	605 <tests>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	606 <test expect_num_outputs="1">
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	607 <param name="ref_source" value="cached" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	608 <param name="target_2bit" value="phiX174" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	609 <param name="query" value="phiX_split.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	610 <param name="strand" value="--strand=both" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	611 <param name="format" value="general_def" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	612 <output name="output" value="test1.out" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	613 </test>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	614 <test expect_num_outputs="1">
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	615 <param name="ref_source" value="history" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	616 <param name="target" value="phiX_split.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	617 <param name="query" value="phiX.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	618 <param name="strand" value="--strand=both" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	619 <param name="format" value="general_def" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	620 <output name="output" value="test2.out" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	621 </test>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	622 <test expect_num_outputs="1">
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	623 <param name="ref_source" value="history" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	624 <param name="target" value="phiX_split.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	625 <param name="query" value="phiX.fasta" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	626 <param name="strand" value="--strand=both" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	627 <param name="score_file" value="score_file.txt" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	628 <param name="format" value="general_def" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	629 <output name="output" value="test3.out" />
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	630 </test>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	631 <test expect_num_outputs="1">
3 c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	632 <param name="ref_source" value="history" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	633 <param name="target" value="chrM_mouse.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	634 <param name="query" value="chrM_human.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	635 <param name="strand" value="--strand=both" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	636 <param name="format" value="blastn" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	637 <output name="output" value="test4.out" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	638 </test>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	639 <test expect_num_outputs="1">
3 c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	640 <param name="ref_source" value="history" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	641 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	642 <param name="query" ftype="fastq.bz2" value="chrM_mouse.fq.bz2" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	643 <param name="strand" value="--strand=both" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	644 <param name="format" value="blastn" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	645 <output name="output" value="test5.out" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	646 </test>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	647 <test expect_num_outputs="1">
3 c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	648 <param name="ref_source" value="history" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	649 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	650 <param name="query" ftype="fastq.gz" value="chrM_mouse.fq.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	651 <param name="strand" value="--strand=both" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	652 <param name="format" value="blastn" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	653 <output name="output" value="test5.out" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	654 </test>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	655 <test expect_num_outputs="1">
3 c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	656 <param name="ref_source" value="history" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	657 <param name="target" ftype="fasta.gz" value="chrM_human.fa.gz" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	658 <param name="query" ftype="fastq" value="chrM_mouse.fq" />
7 86f2c3695694 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 8c6730485b00a47419ebe86278e4bd669377e3e2" iuc parents: 6 diff changeset	659 <param name="lastz_32" value="true" />
3 c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	660 <param name="strand" value="--strand=both" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	661 <param name="format" value="blastn" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	662 <output name="output" value="test5.out" />
c3767eaae954 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413 iuc parents: 2 diff changeset	663 </test>
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	664 <test expect_num_outputs="1">
5 ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	665 <param name="ref_source" value="cached" />
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	666 <param name="target_2bit" value="phiX174" />
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	667 <param name="query" value="phiX_split.fasta" />
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	668 <param name="strand" value="--strand=both" />
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	669 <param name="format" value="differences" />
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	670 <output name="output" value="test6.out" />
ec4affe27298 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 25c49a61a5358cc7ab016fb5847328af7e67a24c" iuc parents: 4 diff changeset	671 </test>
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	672 </tests>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	673
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	674 <help><![CDATA[
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	675
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	676 What is does
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	677
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	678 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.
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	679
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	680 .. class:: infomark
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	681
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	682 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.
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	683
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	684 .. class:: warningmark
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	685
8 da6f44d06921 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 1075d38f2a8eaffb824771a5c4fe70c36aa15f2c iuc parents: 7 diff changeset	686 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.
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	687
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	688 About LASTZ parameters
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	689
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	690 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>`_.
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	691
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	692 Defaults
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	693
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	694 here are defaults for some of the most important parameters::
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	695
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	696 --seed=<pattern> set seed pattern (12of19, 14of22, or general pattern)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	697 (default is 1110100110010101111)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	698 SEE "Seeding" SECTION -> "Select seed type"
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	699
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	700 --[no]transition allow (or don't) one transition in a seed hit
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	701 (by default a transition is allowed)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	702 SEE "Seeding" SECTION -> "Allow transitions"
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	703
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	704 --[no]chain perform chaining
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	705 (by default no chaining is performed)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	706 SEE "Chaining" SECTION
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	707
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	708 --[no]gapped perform gapped alignment (instead of gap-free)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	709 (by default gapped alignment is performed)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	710 SEE "Gapped extension" SECTION
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	711
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	712 --strand=both search both strands
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	713 --strand=plus search + strand only (matching strand of query spec)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	714 (by default both strands are searched)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	715 SEE "Where to look" SECTION
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	716
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	717 --scores=<file> read substitution and gap scores from a file
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	718 SEE "Scoring" SECTION
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	719
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	720 --xdrop=<score> set x-drop threshold (default is 10sub[A][A])
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	721 SEE "HSPs" SECTION
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	722
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	723 --ydrop=<score> set y-drop threshold (default is open+300extend)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	724 SEE "Gapped extension" SECTION
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	725
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	726 --hspthresh=<score> set threshold for high scoring pairs (default is 3000)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	727 ungapped extensions scoring lower are discarded
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	728 <score> can also be a percentage or base count
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	729 SEE "HSPs" SECTION
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	730
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	731 --gappedthresh=<score> set threshold for gapped alignments
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	732 gapped extensions scoring lower are discarded
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	733 <score> can also be a percentage or base count
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	734 (default is to use same value as --hspthresh)
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	735 SEE "Gapped extension" SECTION
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	736
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	737
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	738 Substitution matrix
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	739
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	740 By default the HOXD70 substitution scores are used (from `Chiaromonte et al. 2002 <https://www.ncbi.nlm.nih.gov/pubmed/11928468>`_)::
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	741
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	742 bad_score = X:-1000 # used for sub['X'][] and sub[]['X']
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	743 fill_score = -100 # used when sub[][] is not defined
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	744 gap_open_penalty = 400
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	745 gap_extend_penalty = 30
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	746
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	747 A C G T
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	748 A 91 -114 -31 -123
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	749 C -114 100 -125 -31
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	750 G -31 -125 100 -114
0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	751 T -123 -31 -114 91
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	752
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	753 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).
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	754
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	755 Output
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	756
4 0acd9701676b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit a7e9d5b3906b7ebb35b1c29c3a8e8203b2cefccd iuc parents: 3 diff changeset	757 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>`_.
2 8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	758
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	759 ]]>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	760 </help>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	761 <expand macro="citations"/>
8e9252994649 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit c5379af63b23648020a4709f8ed9d9eac26582aa iuc parents: diff changeset	762 </tool>

Mercurial > repos > devteam > lastz

annotate lastz.xml @ 9:15b1af922236 draft default tip