Mercurial > repos > bgruening > diamond
comparison diamond.xml @ 1:df7738595640 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit cc80b878817d052398db16574917900ebe15292e
author | bgruening |
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date | Mon, 06 Feb 2017 07:08:25 -0500 |
parents | 98037ef3d2a9 |
children | 830516f9521b |
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0:98037ef3d2a9 | 1:df7738595640 |
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1 <tool id="bg_diamond" name="Diamond" version="0.1.6.0"> | 1 <tool id="bg_diamond" name="Diamond" version="@VERSION@"> |
2 <description>alignment tool for short sequences against a protein database</description> | 2 <description>alignment tool for short sequences against a protein database</description> |
3 <requirements> | 3 <macros> |
4 <requirement type="package" version="0.6.13">diamond</requirement> | 4 <import>macros.xml</import> |
5 </requirements> | 5 </macros> |
6 <expand macro="requirements" /> | |
7 <expand macro="stdio" /> | |
8 <expand macro="version_command" /> | |
6 <command> | 9 <command> |
7 <![CDATA[ | 10 <![CDATA[ |
8 | 11 |
9 #if $ref_db_source.db_source == "history": | 12 #if $ref_db_source.db_source == "history": |
10 ln -s $ref_db_source.reference_database ./database.dmnd | 13 ln -s $ref_db_source.reference_database ./database.dmnd |
13 #end if | 16 #end if |
14 | 17 |
15 && | 18 && |
16 | 19 |
17 diamond | 20 diamond |
18 $method.method_select | 21 $method_select |
19 --threads "\${GALAXY_SLOTS:-12}" | 22 --threads "\${GALAXY_SLOTS:-12}" |
20 --db ./database | 23 --db ./database |
21 --query $query | 24 --query '$query' |
22 --out $blast_output | 25 --query-gencode '$query_gencode' |
23 ##--sam $sam_output | 26 |
24 --compress 0 | 27 #if $output.outfmt == "5" |
25 --tmpdir ./ | 28 --outfmt '5' |
29 --out '$blast_xml' | |
30 $output.salltitles | |
31 #else if $output.outfmt == "6" | |
32 --outfmt '6' #echo ' '.join(str($output.fields).split(',')) | |
33 --out '$blast_tabular' | |
34 #else if $output.outfmt == "101" | |
35 --outfmt '101' | |
36 --out '$sam_output' | |
37 $output.salltitles | |
38 #end if | |
39 | |
40 --compress '0' | |
41 $sensitive | |
42 $more_sensitive | |
43 --gapopen '$gapopen' | |
44 --gapextend '$gapextend' | |
45 --matrix '$matrix' | |
46 --seg '$seg' | |
26 | 47 |
27 #if str($hit_filter.hit_filter_select) == 'max': | 48 #if str($hit_filter.hit_filter_select) == 'max': |
28 --max-target-seqs $hit_filter.max | 49 --max-target-seqs '$hit_filter.max_target_seqs' |
29 #else: | 50 #else: |
30 --top $hit_filter.percentage | 51 --top '$hit_filter.top' |
31 #end if | 52 #end if |
32 | 53 |
33 #if str($filter_score.filter_score_select) == 'evalue': | 54 #if str($filter_score.filter_score_select) == 'evalue': |
34 --evalue $filter_score.evalue | 55 --evalue '$filter_score.evalue' |
35 #else: | 56 #else: |
36 --evalue $filter_score.bitscore | 57 --min-score '$filter_score.min_score' |
37 #end if | 58 #end if |
38 | 59 |
39 --id $identity | 60 --id '$id' |
40 $sensitive | 61 --query-cover '$query_cover' |
41 --gapopen $method.gapopen | 62 --block-size '$block_size' |
42 --gapextend $method.gapextend | |
43 --matrix $matrix | |
44 $seg | |
45 $salltitles | |
46 | |
47 ]]> | 63 ]]> |
48 </command> | 64 </command> |
65 | |
49 <inputs> | 66 <inputs> |
50 | 67 <param name="method_select" type="select" label="What do you want to align?" help="(--blastp/--blastx)"> |
51 <param name="query" type="data" format="fasta" label="Input query file in FASTA format" /> | 68 <option value="blastp">Align amino acid query sequences (blastp)</option> |
52 | 69 <option value="blastx">Align DNA query sequences (blastx)</option> |
70 </param> | |
71 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" /> | |
53 <conditional name="ref_db_source"> | 72 <conditional name="ref_db_source"> |
54 <param name="db_source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> | 73 <param name="db_source" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
55 <option value="indexed">Use a built-in index</option> | 74 <option value="indexed">Use a built-in index</option> |
56 <option value="history">Use one from the history</option> | 75 <option value="history">Use one from the history</option> |
57 </param> | 76 </param> |
60 <options from_data_table="diamond_database"> | 79 <options from_data_table="diamond_database"> |
61 <filter type="sort_by" column="2"/> | 80 <filter type="sort_by" column="2"/> |
62 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | 81 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
63 </options> | 82 </options> |
64 </param> | 83 </param> |
65 </when> <!-- build-in --> | 84 </when> |
66 <when value="history"> | 85 <when value="history"> |
67 <param name="reference_database" type="data" format="diamond_database" label="Select the reference database" /> | 86 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" /> |
68 </when> <!-- history --> | 87 </when> |
69 </conditional> | 88 </conditional> |
70 | 89 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help=""> |
71 <conditional name="method"> | 90 <option value="1">The Standard Code</option> |
72 <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)"> | 91 <option value="2">The Vertebrate Mitochondrial Code</option> |
73 <option value="blastp">Align amino acid query sequences (blastp)</option> | 92 <option value="3">The Yeast Mitochondrial Code</option> |
74 <option value="blastx">Align DNA query sequences (blastx)</option> | 93 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> |
75 </param> | 94 <option value="5">The Invertebrate Mitochondrial Code</option> |
76 <when value="blastp"> | 95 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> |
77 <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" /> | 96 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option> |
78 <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" /> | 97 <option value="10">The Euplotid Nuclear Code</option> |
79 </when> | 98 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option> |
80 <when value="blastx"> | 99 <option value="12">The Alternative Yeast Nuclear Code</option> |
81 <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" /> | 100 <option value="13">The Ascidian Mitochondrial Code</option> |
82 <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" /> | 101 <option value="14">The Alternative Flatworm Mitochondrial Code</option> |
83 </when> | 102 <option value="16">Chlorophycean Mitochondrial Code</option> |
84 </conditional> | 103 <option value="21">Trematode Mitochondrial Code</option> |
85 | 104 <option value="22">Scenedesmus obliquus Mitochondrial Code</option> |
86 <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)"> | 105 <option value="23">Thraustochytrium Mitochondrial Code</option> |
87 <option value="BLOSUM45">BLOSUM45</option> | 106 <option value="24">Pterobranchia Mitochondrial Code</option> |
88 <option value="BLOSUM50">BLOSUM50</option> | 107 <option value="5">Candidate Division SR1 and Gracilibacteria Code</option> |
89 <option value="BLOSUM62" selected="True">BLOSUM62</option> | 108 <option value="26">Pachysolen tannophilus Nuclear Code</option> |
90 <option value="BLOSUM80">BLOSUM80</option> | |
91 <option value="BLOSUM90">BLOSUM90</option> | |
92 <option value="PAM250">PAM250</option> | |
93 <option value="PAM70">PAM70</option> | |
94 <option value="PAM30">PAM30</option> | |
95 </param> | 109 </param> |
96 | 110 <conditional name="output"> |
111 <param argument="--outfmt" type="select" label="Format of output file " help=""> | |
112 <option value="5">BLAST XML</option> | |
113 <option value="6">BLAST tabular</option> | |
114 <option value="101">SAM</option> | |
115 </param> | |
116 <when value="5"> | |
117 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/> | |
118 </when> | |
119 <when value="6"> | |
120 <param name="fields" type="select" label="Tabular fields" help="" multiple="true"> | |
121 <option value="qseqid" selected="true">Query Seq - id</option> | |
122 <option value="sseqid" selected="true">Subject Seq - id</option> | |
123 <option value="sallseqid">All subject Seq - id(s)</option> | |
124 <option value="qlen">Query sequence length</option> | |
125 <option value="slen">Subject sequence length</option> | |
126 <option value="pident" selected="true">Percentage of identical matches</option> | |
127 <option value="length" selected="true">Alignment length</option> | |
128 <option value="nident">Number of identical matches</option> | |
129 <option value="mismatch" selected="true">Number of mismatches</option> | |
130 <option value="positive">Number of positive - scoring matches</option> | |
131 <option value="gapopen" selected="true">Number of gap openings</option> | |
132 <option value="gaps">Total number of gaps</option> | |
133 <option value="ppos">Percentage of positive - scoring matches</option> | |
134 <option value="qstart" selected="true">Start of alignment in query</option> | |
135 <option value="qend" selected="true">End of alignment in query</option> | |
136 <option value="sstart" selected="true">Start of alignment in subject</option> | |
137 <option value="send" selected="true">End of alignment in subject</option> | |
138 <option value="qseq">Aligned part of query sequence</option> | |
139 <option value="sseq">Aligned part of subject sequence</option> | |
140 <option value="evalue" selected="true">Expect value</option> | |
141 <option value="bitscore" selected="true">Bit score</option> | |
142 <option value="score">Raw score</option> | |
143 <option value="qframe">Query frame</option> | |
144 <option value="stitle">Subject Title</option> | |
145 <option value="salltitles">All Subject Title(s)</option> | |
146 <option value="qcovhsp">Query Coverage Per HSP</option> | |
147 </param> | |
148 </when> | |
149 <when value="101"> | |
150 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/> | |
151 </when> | |
152 </conditional> | |
153 <param argument="--sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" label="Trigger the sensitive alignment mode with a 16x9 seed shape configuration?" help=""/> | |
154 <param name="more_sensitive" argument="--more-sensitive" type="boolean" truevalue="--more-sensitive" falsevalue="" checked="false" label="Trigger the more sensitive mode?" help="This mode provides some additional sensitivity compared to the sensitive mode."/> | |
155 <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" /> | |
156 <param argument="--gapextend" type="integer" value="1" label="Gap extension penalty" help="" /> | |
157 <param argument="--matrix" type="select" label="Scoring matrix" help="In brackets are the supported values for (gap open)/(gap extend)"> | |
158 <option value="BLOSUM45">BLOSUM45 ((10-13)/3; (12-16)/2; (16-19)/1)</option> | |
159 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option> | |
160 <option value="BLOSUM62" selected="True">BLOSUM62 ((6-11)/2; (9-13)/1)</option> | |
161 <option value="BLOSUM80">BLOSUM80 ((6-9)/2; 13/2; 25/2; (9-11)/1)</option> | |
162 <option value="BLOSUM90">BLOSUM90 ((6-9)/2; (9-11)/1)</option> | |
163 <option value="PAM250">PAM250 ((11-15)/3; (13-17)/2; (17-21)/1)</option> | |
164 <option value="PAM70">PAM70 ((6-8)/2; (9-11)/1)</option> | |
165 <option value="PAM30">PAM30 ((5-7)/2; (8-10)/1)</option> | |
166 </param> | |
167 <param argument="--seg" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Enable SEG masking of low complexity segments in the query?" help=""/> | |
168 <conditional name="hit_filter"> | |
169 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?"> | |
170 <option value="max">Maximum number of target sequences</option> | |
171 <option value="top">Percentage of top alignment score</option> | |
172 </param> | |
173 <when value="max"> | |
174 <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to keep alignments for" help="" /> | |
175 </when> | |
176 <when value="top"> | |
177 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a quer" help="" /> | |
178 </when> | |
179 </conditional> | |
97 <conditional name="filter_score"> | 180 <conditional name="filter_score"> |
98 <param name="filter_score_select" type="select" label="Filter by score" help="(--evalue/--min-score)"> | 181 <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)"> |
99 <option value="evalue">Maximum e-value to report alignments</option> | 182 <option value="evalue">Maximum e-value to report alignments</option> |
100 <option value="bit">Minimum bit score to report alignments</option> | 183 <option value="min-score">Minimum bit score to report alignments</option> |
101 </param> | 184 </param> |
102 <when value="evalue"> | 185 <when value="evalue"> |
103 <param name="evalue" type="float" value="0.001" label="Filter by evalue" help="(--evalue)" /> | 186 <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment" /> |
104 </when> | 187 </when> |
105 <when value="bit"> | 188 <when value="min-score"> |
106 <param name="bitscore" type="integer" value="0" label="Filter by bit score" help="(--min-score)" /> | 189 <param name="min_score" argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)" /> |
107 </when> | 190 </when> |
108 </conditional> | 191 </conditional> |
109 | 192 <param argument="--id" type="integer" value="0" label="Minimum identity percentage to report an alignment" help="" /> |
110 <conditional name="hit_filter"> | 193 <param name="query_cover" argument="--query-cover" type="integer" value="0" label="Minimum query cover percentage to report an alignment" help="" /> |
111 <param name="hit_filter_select" type="select" label="Restrict number of hits by" help="(--max-target-seqs/--top)"> | 194 <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" /> |
112 <option value="max">Maximum number of target sequences</option> | |
113 <option value="percentage">Percentage of top alignment score</option> | |
114 </param> | |
115 <when value="max"> | |
116 <param name="max" type="integer" value="25" label="How many hits?" help="(--max-target-seqs)" /> | |
117 </when> | |
118 <when value="percentage"> | |
119 <param name="percentage" type="integer" value="0" label="How many percentage" help="(--top)" /> | |
120 </when> | |
121 </conditional> | |
122 | |
123 <param name="identity" type="integer" value="0" label="minimum identity to report an alignment" help="in percentage (--id)" /> | |
124 <param name="salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="false" | |
125 label="Print subject titles into the blast tabular format" help="(--salltitles)"/> | |
126 <param name="seg" type="boolean" truevalue="--seg yes" falsevalue="--seg no" checked="true" | |
127 label="Enable SEG masking of queries" help="(--seg)"/> | |
128 <param name="sensitive" type="boolean" truevalue="--sensitive" falsevalue="" checked="false" | |
129 label="Enable sensitive mode" help="(--sensitive)"/> | |
130 </inputs> | 195 </inputs> |
196 | |
131 <outputs> | 197 <outputs> |
132 <!--data format="sam" name="sam_output"/--> | 198 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> |
133 <data format="tabular" name="blast_output"/> | 199 <filter>output["outfmt"] == "5"</filter> |
200 </data> | |
201 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}"> | |
202 <filter>output["outfmt"] == "6"</filter> | |
203 </data> | |
204 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}"> | |
205 <filter>output["outfmt"] == "101"</filter> | |
206 </data> | |
134 </outputs> | 207 </outputs> |
208 | |
135 <tests> | 209 <tests> |
136 <test> | 210 <test> |
137 <param name="method" value="blastp"/> | 211 <param name="method_select" value="blastp" /> |
138 <param name="query" value="protein.fasta" ftype="fasta"/> | 212 <param name="query" value="protein.fasta" ftype="fasta"/> |
139 <param name="reference_database" value="diamond_makedb_result1.dmnd" ftype="diamond_database"/> | |
140 <param name="db_source" value="history"/> | 213 <param name="db_source" value="history"/> |
141 <output name="blast_output" file="diamond_result1.tabular" ftpye="tabular"/> | 214 <param name="reference_database" value="db.dmnd"/> |
215 <param name="query_gencode" value="1"/> | |
216 <param name="outfmt" value="6"/> | |
217 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> | |
218 <param name="sensitive" value=""/> | |
219 <param name="more_sensitive" value=""/> | |
220 <param name="gapopen" value="11"/> | |
221 <param name="gapextend" value="1"/> | |
222 <param name="matrix" value="BLOSUM62"/> | |
223 <param name="seg" value="yes"/> | |
224 <param name="hit_filter_select" value="max"/> | |
225 <param name="max_target_seqs" value="25" /> | |
226 <param name="filter_score_select" value="evalue"/> | |
227 <param name="evalue" value="0.001" /> | |
228 <param name="id" value="0"/> | |
229 <param name="query_cover" value="0"/> | |
230 <param name="block_size" value="2"/> | |
231 <output name="blast_tabular" file="diamond_results.tabular"/> | |
142 </test> | 232 </test> |
143 </tests> | 233 </tests> |
234 | |
144 <help> | 235 <help> |
145 <![CDATA[ | 236 <![CDATA[ |
146 | |
147 .. class:: infomark | |
148 | 237 |
149 **What it does** | 238 **What it does** |
150 | 239 |
151 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. | 240 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. |
152 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting | 241 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting |
153 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 | 242 about 80-90% of all matches that BLASTX finds, with an e-value of at most 1e-5. In sensitive mode, DIAMOND ist about 2,500 |
154 times faster than BLASTX, finding more than 94% of all matches. | 243 times faster than BLASTX, finding more than 94% of all matches. |
155 | 244 |
245 The DIAMOND algorithm is designed for the alignment of large datasets. The algorithm is not efficient for a small number of query sequences or only a single one of them, and speed will be low. BLAST is recommend for small datasets. | |
246 | |
156 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ | 247 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ |
248 | |
249 **Input** | |
250 | |
251 Input data is a large protein or nucleotide sequence file. | |
252 | |
253 | |
254 **Output** | |
255 | |
256 Diamond gives you a tabular output file with 12 columns: | |
257 | |
258 Column Description | |
259 1 Query Seq-id (ID of your sequence) | |
260 2 Subject Seq-id (ID of the database hit) | |
261 3 Percentage of identical matches | |
262 4 Alignment length | |
263 5 Number of mismatches | |
264 6 Number of gap openings | |
265 7 Start of alignment in query | |
266 8 End of alignment in query | |
267 9 Start of alignment in subject (database hit) | |
268 10 End of alignment in subject (database hit) | |
269 11 Expectation value (E-value) | |
270 12 Bit score | |
157 | 271 |
158 | 272 |
159 Supported values for gap open and gap extend parameters depending on the selected scoring matrix. | 273 Supported values for gap open and gap extend parameters depending on the selected scoring matrix. |
160 | 274 |
161 ======== ============================================ | 275 ======== ============================================ |
172 ======== ============================================ | 286 ======== ============================================ |
173 | 287 |
174 | 288 |
175 ]]> | 289 ]]> |
176 </help> | 290 </help> |
177 <citations> | 291 <expand macro="citations" /> |
178 <citation type="doi">10.1038/nmeth.3176</citation> | |
179 </citations> | |
180 </tool> | 292 </tool> |