annotate spaln.xml @ 2:dd0cd2319ae5 draft

"planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"
author iuc
date Fri, 19 Nov 2021 10:09:15 +0000
parents 37b5e1f0b544
children 32c11a4b5dbf
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
1 <tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0">
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
2 <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
3 <macros>
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
4 <import>macros.xml</import>
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
5 </macros>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
6 <edam_topics>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
7 <edam_topic>topic_3512</edam_topic>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
8 </edam_topics>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
9 <requirements>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
10 <requirement type="package" version="@TOOL_VERSION@">spaln</requirement>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
11 </requirements>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
12 <command detect_errors="aggressive"><![CDATA[
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
13 spaln -t\${GALAXY_SLOTS:-1} -O$format
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
14 #if str($species_params).strip() != ''
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
15 -T'${species_params}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
16 #end if
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
17 #if $adv.use == "yes"
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
18 -S'${adv.query_orientation}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
19 -V'${adv.hirschberg_threshold}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
20 -pa'${adv.polya_trim}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
21 ${adv.all_results}
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
22 -yu'${adv.gap_extension_penalty}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
23 -yv'${adv.gap_open_penalty}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
24 -yw'${adv.dp_matrix_scan_width}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
25 -ya'${adv.splice_stringency}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
26 -yj'${adv.gap_penalty_incline}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
27 -yk'${adv.gap_penalty_flex}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
28 '${adv.double_affine_gap}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
29 -ym'${adv.match_score}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
30 -yn'${adv.mismatch_score}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
31 -yo'${adv.stop_codon_penalty}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
32 -yx'${adv.frameshift_penalty}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
33 -yy'${adv.splice_site_weight}
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
34 -yz'${adv.coding_potential_weight}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
35 -yB'${adv.branch_point_weight}
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
36 -yL'${adv.min_intron_len}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
37 -yZ'${adv.intron_potential_weight}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
38 #if str($adv.max_gene_length).strip() != ''
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
39 -XG'${adv.max_gene_length}'
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
40 #end if
2
dd0cd2319ae5 "planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"
iuc
parents: 1
diff changeset
41 $adv.format_remote_queries
dd0cd2319ae5 "planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"
iuc
parents: 1
diff changeset
42 $adv.salvage_mode
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
43 #end if
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
44 '$genome' '$query' >'$output1'
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
45 ]]></command>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
46 <inputs>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
47 <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
48 <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
49 <param argument="-O" type="select" name="format" label="Output format">
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
50 <option value="0">GFF3 format genes</option>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
51 <option value="2">GFF3 format matches</option>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
52 <option value="3">BED format</option>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
53 <option value="4">Tabular format exon information</option>
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
54 </param>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
55 <param argument="-T" name="species_params" type="text" optional="true" label="Species to use for parameter setting" help="Choose a species table (e.g. cynosemi) from which to read parameters to optimise spaln" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
56 <conditional name="adv">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
57 <param type="select" name="use" label="Advanced settings">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
58 <option selected="true" value="no">No</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
59 <option value="yes">Yes</option>
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
60 </param>
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
61 <when value="no">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
62 </when>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
63 <when value="yes">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
64 <param argument="-S" name="query_orientation" type="select" label="DNA query orientation" help="Determines how to treat orientation of query sequence when searching">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
65 <option value="0">Infer orientation from sequence header (no poly-A/poly-T trimming)</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
66 <option value="1">Forward orientation only. Poly-A tail might be trimmed off</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
67 <option value="2">Reverse orientation only. Leading poly-T might be trimmed off</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
68 <option selected="true" value="3">Examine both orientations. Poly-A / Poly-T might be trimmed off</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
69 </param>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
70 <param argument="-V" name="hirschberg_threshold" type="integer" value="16777216" label="Minimum space to induce Hirschberg's algorithm" help="Default is 16M (16x1024x1024 bytes)" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
71 <param argument="-pa" name="polya_trim" type="integer" value="12" label="Limit 3' poly-As to this number of bases" help="poly-A/poly-T trimming is only done if -S (orientation) option is 0 or 3" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
72 <param argument="-pw" name="all_results" type="boolean" checked="false" truevalue="-pw" falsevalue="" label="Report results even if the score is below the threshold" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
73 <param argument="-yu" name="gap_extension_penalty" type="integer" value="3" label="Gap-extension penalty" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
74 <param argument="-yv" name="gap_open_penalty" type="integer" value="8" label="Gap-open penalty" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
75 <param argument="-yw" name="dp_matrix_scan_width" type="integer" value="100" label="Band width for DP matrix scan" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
76 <param argument="-ya" name="splice_stringency" type="select" label="Stringency of splice site selection" help="Which dinucleotide pairs to accept at the ends of an intron">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
77 <option value="0" selected="true">accept only the canonical pairs (GT..AG,GC..AG,AT..AC)</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
78 <option value="1">accept also AT..AN</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
79 <option value="2">allow up to one mismatch from GT..AG</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
80 <option value="3">accept any pairs</option>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
81 </param>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
82 <param argument="-yj" name="gap_penalty_incline" type="float" value="0.6" label="Incline of long gap penalty" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
83 <param argument="-yk" name="gap_penalty_flex" type="integer" value="7" label="Flex point where the incline of gap penalty changes" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
84 <param argument="-yl3" name="double_affine_gap" type="boolean" checked="false" truevalue="-yl3" falsevalue="" label="Use double affine gap penalty" help="Use the double affine gap rathr than single affine gap penalty calculation" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
85 <param argument="-ym" name="match_score" type="integer" value="2" label="Nucleotide match score" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
86 <param argument="-yn" name="mismatch_score" type="integer" value="-6" label="Nucleotide mismatch score" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
87 <param argument="-yo" name="stop_codon_penalty" type="integer" value="100" label="Penalty for a premature termination codon" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
88 <param argument="-yx" name="frameshift_penalty" type="integer" value="100" label="Penalty for a frame shift error" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
89 <param argument="-yy" name="splice_site_weight" type="integer" value="8" label="Weight for splice site signal" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
90 <param argument="-yz" name="coding_potential_weight" type="integer" value="2" label="Weight for coding potential" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
91 <param argument="-yB" name="branch_point_weight" type="integer" value="0" label="Weight for branch point signal" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
92 <param argument="-yL" name="min_intron_len" type="integer" value="30" label="Minimum expected length of intron" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
93 <param argument="-yZ" name="intron_potential_weight" type="integer" value="0" label="Weight for intron potential" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
94 <param argument="-XG" name="max_gene_length" type="text" label="Reset maximum expected gene size, suffix k or M is effective" />
2
dd0cd2319ae5 "planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"
iuc
parents: 1
diff changeset
95 <param argument="-yX" name="format_remote_queries" type="boolean" checked="false" truevalue="-yX" falsevalue="" label="Format for remote queries" help="More sensitive but less economic than the default" />
dd0cd2319ae5 "planemo upload for repository https://github.com/ogotoh/spaln commit c06dea51e720899c3245d203c3a0abc9f179583f"
iuc
parents: 1
diff changeset
96 <param argument="-XS" name="salvage_mode" type="boolean" checked="false" truevalue="-XS" falsevalue="" label="Activate salvage mode" help="Examine all positively scored blocks. Considerably slow." />
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
97 </when>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
98 </conditional>
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
99 </inputs>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
100 <outputs>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
101 <data name="output1" format="tabular">
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
102 <change_format>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
103 <!-- these values correspond with the format options of the spaln command, not all of which are current supported -->
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
104 <when input="format" value="0" format="gff3" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
105 <when input="format" value="2" format="gff3" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
106 <when input="format" value="3" format="bed12" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
107 <when input="format" value="4" format="tabular" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
108 </change_format>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
109 <!-- <actions> .. <conditional> .. <when> .. <action> current does not work in Galaxy,
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
110 something that https://github.com/galaxyproject/galaxy/pull/7197 is addressing, so this is
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
111 commented out till that is merged
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
112 <actions>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
113 <conditional name="format">
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
114 <when value="4">
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
115 <action type="metadata" name="column_names" default="rID,gID,%id,ExonL,MisMch,Unpair,ref_l,ref_r,tgt_l,tgt_r,eScore,IntrnL,iScore,Sig3/I,Sig5/T # - X P DiNuc" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
116 </when>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
117 </conditional>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
118 </actions>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
119 -->
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
120 </data>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
121 </outputs>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
122 <tests>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
123 <test>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
124 <param name="genome" ftype="fasta" value="genome.fasta" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
125 <param name="query" ftype="fasta" value="query.fasta" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
126 <param name="format" value="0"/>
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
127 <conditional name="adv">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
128 <param name="use" value="no" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
129 </conditional>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
130 <output name="output1" ftype="gff3" value="output1_gff_genes.gff3" />
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
131 </test>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
132 <test>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
133 <param name="genome" ftype="fasta" value="genome.fasta" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
134 <param name="query" ftype="fasta" value="query.fasta" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
135 <param name="format" value="2"/>
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
136 <conditional name="adv">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
137 <param name="use" value="no" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
138 </conditional>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
139 <output name="output1" ftype="gff3" value="output1_gff_matches.gff3" />
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
140 </test>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
141 <test>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
142 <param name="genome" ftype="fasta" value="genome.fasta" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
143 <param name="query" ftype="fasta" value="query.fasta" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
144 <param name="format" value="3"/>
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
145 <conditional name="adv">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
146 <param name="use" value="no" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
147 </conditional>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
148 <output name="output1" ftype="bed12" value="output1.bed12" />
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
149 </test>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
150 <test>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
151 <param name="genome" ftype="fasta" value="genome.fasta" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
152 <param name="query" ftype="fasta" value="query.fasta" />
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
153 <param name="format" value="4"/>
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
154 <conditional name="adv">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
155 <param name="use" value="no" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
156 </conditional>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
157 <output name="output1" ftype="tabular" value="output1.tabular" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
158 </test>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
159 <test>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
160 <param name="genome" ftype="fasta" value="genome.fasta" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
161 <param name="query" ftype="fasta" value="query.fasta" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
162 <param name="format" value="4"/>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
163 <param name="species_params" value="cynosemi" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
164 <conditional name="adv">
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
165 <param name="use" value="no" />
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
166 </conditional>
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
167 <output name="output1" ftype="tabular" value="output2.tabular" />
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
168 </test>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
169 </tests>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
170 <help><![CDATA[
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
171 Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
172 protein sequences onto a whole genomic sequence in a single job.
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
173
1
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
174 This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln. This algorithm
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
175 takes FASTA format query and genome sequence and finds an alignment of the query (either cDNA or protein)
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
176 against the genome.
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
177
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
178 Spaln optionally takes a species name to use for parameter setting (the "-T" parameter). The
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
179 "List spaln parameter tables" (list_spaln_tables) can be used to find a parameter file that is
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
180 close (in terms of taxonomic distance) to your species of interest. Use of this setting is recommended.
37b5e1f0b544 "planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
iuc
parents: 0
diff changeset
181
0
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
182
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
183 .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
184 ]]></help>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
185 <citations>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
186 <citation type="doi">0.1093/nar/gkn105</citation>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
187 </citations>
95ea8d97abb4 planemo upload for repository https://github.com/ogotoh/spaln commit af52c6b4c904f6291953881111d415d5b86ee4d6
iuc
parents:
diff changeset
188 </tool>