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comparison spaln.xml @ 1:37b5e1f0b544 draft

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"planemo upload for repository https://github.com/ogotoh/spaln commit 4cfc21ef8456ca8b8da0a8a8c045b8a472858608"
author iuc
date Thu, 16 Jul 2020 07:57:10 -0400
parents 95ea8d97abb4
children dd0cd2319ae5
comparison
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0:95ea8d97abb4 1:37b5e1f0b544
1 <tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="spaln" name="Spaln: align cDNA or Protein to genome" version="@TOOL_VERSION@+galaxy0">
2 <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description> 2 <description>Maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence.</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">2.3.2</token> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <edam_topics> 6 <edam_topics>
7 <edam_topic>topic_3512</edam_topic> 7 <edam_topic>topic_3512</edam_topic>
8 </edam_topics> 8 </edam_topics>
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">spaln</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">spaln</requirement>
11 </requirements> 11 </requirements>
12 <command detect_errors="aggressive"><![CDATA[ 12 <command detect_errors="aggressive"><![CDATA[
13 spaln -t\${GALAXY_SLOTS:-1} -O$format -o '$output1' '$genome' '$query' 13 spaln -t\${GALAXY_SLOTS:-1} -O$format
14 #if str($species_params).strip() != ''
15 -T'${species_params}'
16 #end if
17 #if $adv.use == "yes"
18 -S'${adv.query_orientation}'
19 -V'${adv.hirschberg_threshold}'
20 -pa'${adv.polya_trim}'
21 ${adv.all_results}
22 -yu'${adv.gap_extension_penalty}'
23 -yv'${adv.gap_open_penalty}'
24 -yw'${adv.dp_matrix_scan_width}'
25 -ya'${adv.splice_stringency}'
26 -yj'${adv.gap_penalty_incline}'
27 -yk'${adv.gap_penalty_flex}'
28 '${adv.double_affine_gap}'
29 -ym'${adv.match_score}'
30 -yn'${adv.mismatch_score}'
31 -yo'${adv.stop_codon_penalty}'
32 -yx'${adv.frameshift_penalty}'
33 -yy'${adv.splice_site_weight}
34 -yz'${adv.coding_potential_weight}'
35 -yB'${adv.branch_point_weight}
36 -yL'${adv.min_intron_len}'
37 -yZ'${adv.intron_potential_weight}'
38 #if str($adv.max_gene_length).strip() != ''
39 -XG'${adv.max_gene_length}'
40 #end if
41 #end if
42 '$genome' '$query' >'$output1'
14 ]]></command> 43 ]]></command>
15 <inputs> 44 <inputs>
16 <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" /> 45 <param type="data" name="genome" format="fasta" label="Genome sequence to search (FASTA format)" />
17 <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" /> 46 <param type="data" name="query" format="fasta" label="Query sequence(s) (protein or cDNA)" />
18 <param argument="-O" type="select" name="format" label="Output format"> 47 <param argument="-O" type="select" name="format" label="Output format">
19 <option value="0">GFF3 format genes</option> 48 <option value="0">GFF3 format genes</option>
20 <option value="2">GFF3 format matches</option> 49 <option value="2">GFF3 format matches</option>
21 <option value="3">BED format</option> 50 <option value="3">BED format</option>
22 <option value="4">Tabular format exon information</option> 51 <option value="4">Tabular format exon information</option>
52 </param>
53 <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" />
54 <conditional name="adv">
55 <param type="select" name="use" label="Advanced settings">
56 <option selected="true" value="no">No</option>
57 <option value="yes">Yes</option>
23 </param> 58 </param>
59 <when value="no">
60 </when>
61 <when value="yes">
62 <param argument="-S" name="query_orientation" type="select" label="DNA query orientation" help="Determines how to treat orientation of query sequence when searching">
63 <option value="0">Infer orientation from sequence header (no poly-A/poly-T trimming)</option>
64 <option value="1">Forward orientation only. Poly-A tail might be trimmed off</option>
65 <option value="2">Reverse orientation only. Leading poly-T might be trimmed off</option>
66 <option selected="true" value="3">Examine both orientations. Poly-A / Poly-T might be trimmed off</option>
67 </param>
68 <param argument="-V" name="hirschberg_threshold" type="integer" value="16777216" label="Minimum space to induce Hirschberg's algorithm" help="Default is 16M (16x1024x1024 bytes)" />
69 <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" />
70 <param argument="-pw" name="all_results" type="boolean" checked="false" truevalue="-pw" falsevalue="" label="Report results even if the score is below the threshold" />
71 <param argument="-yu" name="gap_extension_penalty" type="integer" value="3" label="Gap-extension penalty" />
72 <param argument="-yv" name="gap_open_penalty" type="integer" value="8" label="Gap-open penalty" />
73 <param argument="-yw" name="dp_matrix_scan_width" type="integer" value="100" label="Band width for DP matrix scan" />
74 <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">
75 <option value="0" selected="true">accept only the canonical pairs (GT..AG,GC..AG,AT..AC)</option>
76 <option value="1">accept also AT..AN</option>
77 <option value="2">allow up to one mismatch from GT..AG</option>
78 <option value="3">accept any pairs</option>
79 </param>
80 <param argument="-yj" name="gap_penalty_incline" type="float" value="0.6" label="Incline of long gap penalty" />
81 <param argument="-yk" name="gap_penalty_flex" type="integer" value="7" label="Flex point where the incline of gap penalty changes" />
82 <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" />
83 <param argument="-ym" name="match_score" type="integer" value="2" label="Nucleotide match score" />
84 <param argument="-yn" name="mismatch_score" type="integer" value="-6" label="Nucleotide mismatch score" />
85 <param argument="-yo" name="stop_codon_penalty" type="integer" value="100" label="Penalty for a premature termination codon" />
86 <param argument="-yx" name="frameshift_penalty" type="integer" value="100" label="Penalty for a frame shift error" />
87 <param argument="-yy" name="splice_site_weight" type="integer" value="8" label="Weight for splice site signal" />
88 <param argument="-yz" name="coding_potential_weight" type="integer" value="2" label="Weight for coding potential" />
89 <param argument="-yB" name="branch_point_weight" type="integer" value="0" label="Weight for branch point signal" />
90 <param argument="-yL" name="min_intron_len" type="integer" value="30" label="Minimum expected length of intron" />
91 <param argument="-yZ" name="intron_potential_weight" type="integer" value="0" label="Weight for intron potential" />
92 <param argument="-XG" name="max_gene_length" type="text" label="Reset maximum expected gene size, suffix k or M is effective" />
93 </when>
94 </conditional>
24 </inputs> 95 </inputs>
25 <outputs> 96 <outputs>
26 <data name="output1" format="tabular"> 97 <data name="output1" format="tabular">
27 <change_format> 98 <change_format>
28 <!-- these values correspond with the format options of the spaln command, not all of which are current supported --> 99 <!-- these values correspond with the format options of the spaln command, not all of which are current supported -->
47 <tests> 118 <tests>
48 <test> 119 <test>
49 <param name="genome" ftype="fasta" value="genome.fasta" /> 120 <param name="genome" ftype="fasta" value="genome.fasta" />
50 <param name="query" ftype="fasta" value="query.fasta" /> 121 <param name="query" ftype="fasta" value="query.fasta" />
51 <param name="format" value="0"/> 122 <param name="format" value="0"/>
52 <output name="output1" value="output1_gff_genes.gff3" /> 123 <conditional name="adv">
124 <param name="use" value="no" />
125 </conditional>
126 <output name="output1" ftype="gff3" value="output1_gff_genes.gff3" />
53 </test> 127 </test>
54 <test> 128 <test>
55 <param name="genome" ftype="fasta" value="genome.fasta" /> 129 <param name="genome" ftype="fasta" value="genome.fasta" />
56 <param name="query" ftype="fasta" value="query.fasta" /> 130 <param name="query" ftype="fasta" value="query.fasta" />
57 <param name="format" value="2"/> 131 <param name="format" value="2"/>
58 <output name="output1" value="output1_gff_matches.gff3" /> 132 <conditional name="adv">
133 <param name="use" value="no" />
134 </conditional>
135 <output name="output1" ftype="gff3" value="output1_gff_matches.gff3" />
59 </test> 136 </test>
60 <test> 137 <test>
61 <param name="genome" ftype="fasta" value="genome.fasta" /> 138 <param name="genome" ftype="fasta" value="genome.fasta" />
62 <param name="query" ftype="fasta" value="query.fasta" /> 139 <param name="query" ftype="fasta" value="query.fasta" />
63 <param name="format" value="3"/> 140 <param name="format" value="3"/>
64 <output name="output1" value="output1.bed12" /> 141 <conditional name="adv">
142 <param name="use" value="no" />
143 </conditional>
144 <output name="output1" ftype="bed12" value="output1.bed12" />
65 </test> 145 </test>
66 <test> 146 <test>
67 <param name="genome" ftype="fasta" value="genome.fasta" /> 147 <param name="genome" ftype="fasta" value="genome.fasta" />
68 <param name="query" ftype="fasta" value="query.fasta" /> 148 <param name="query" ftype="fasta" value="query.fasta" />
69 <param name="format" value="4"/> 149 <param name="format" value="4"/>
70 <output name="output1" value="output1.tabular" /> 150 <conditional name="adv">
151 <param name="use" value="no" />
152 </conditional>
153 <output name="output1" ftype="tabular" value="output1.tabular" />
154 </test>
155 <test>
156 <param name="genome" ftype="fasta" value="genome.fasta" />
157 <param name="query" ftype="fasta" value="query.fasta" />
158 <param name="format" value="4"/>
159 <param name="species_params" value="cynosemi" />
160 <conditional name="adv">
161 <param name="use" value="no" />
162 </conditional>
163 <output name="output1" ftype="tabular" value="output2.tabular" />
71 </test> 164 </test>
72 </tests> 165 </tests>
73 <help><![CDATA[ 166 <help><![CDATA[
74 Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or 167 Spaln_ (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or
75 protein sequences onto a whole genomic sequence in a single job. 168 protein sequences onto a whole genomic sequence in a single job.
76 169
77 This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln with default parameters. 170 This Galaxy wrapper currently only supports the default (i.e. *-O3*) algorithm for Spaln. This algorithm
171 takes FASTA format query and genome sequence and finds an alignment of the query (either cDNA or protein)
172 against the genome.
173
174 Spaln optionally takes a species name to use for parameter setting (the "-T" parameter). The
175 "List spaln parameter tables" (list_spaln_tables) can be used to find a parameter file that is
176 close (in terms of taxonomic distance) to your species of interest. Use of this setting is recommended.
177
78 178
79 .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/ 179 .. _Spaln: http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/
80 ]]></help> 180 ]]></help>
81 <citations> 181 <citations>
82 <citation type="doi">0.1093/nar/gkn105</citation> 182 <citation type="doi">0.1093/nar/gkn105</citation>