Mercurial > repos > bgruening > diamond
comparison diamond.xml @ 3:830516f9521b draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 0a893f1ee7f73d24004a43ec1ba6a4cc03fbfab0
author | bgruening |
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date | Wed, 26 Jul 2017 10:30:52 -0400 |
parents | df7738595640 |
children | 64be1ac21109 |
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2:fd14bf35c9fd | 3:830516f9521b |
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1 <tool id="bg_diamond" name="Diamond" version="@VERSION@"> | 1 <tool id="bg_diamond" name="Diamond" version="@VERSION@.1"> |
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 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
16 #end if | 16 #end if |
17 | 17 |
18 && | 18 && |
19 | 19 |
20 diamond | 20 diamond |
21 $method_select | 21 $method_select.method_select |
22 --threads "\${GALAXY_SLOTS:-12}" | 22 --threads "\${GALAXY_SLOTS:-12}" |
23 --db ./database | 23 --db ./database |
24 --query '$query' | 24 --query '$query' |
25 --query-gencode '$query_gencode' | 25 #if $method_select.method_select == "blastx" |
26 --query-gencode '$query_gencode' | |
27 #end if | |
26 | 28 |
27 #if $output.outfmt == "5" | 29 #if $output.outfmt == "5" |
28 --outfmt '5' | 30 --outfmt '5' |
29 --out '$blast_xml' | 31 --out '$blast_xml' |
30 $output.salltitles | 32 $output.salltitles |
36 --out '$sam_output' | 38 --out '$sam_output' |
37 $output.salltitles | 39 $output.salltitles |
38 #end if | 40 #end if |
39 | 41 |
40 --compress '0' | 42 --compress '0' |
41 $sensitive | 43 #if $sensitivity == "1" |
42 $more_sensitive | 44 --sensitive |
45 #else if $sensitivity == "2" | |
46 --more-sensitive | |
47 #end if | |
48 | |
43 --gapopen '$gapopen' | 49 --gapopen '$gapopen' |
44 --gapextend '$gapextend' | 50 --gapextend '$gapextend' |
45 --matrix '$matrix' | 51 --matrix '$matrix' |
46 --seg '$seg' | 52 --seg '$seg' |
47 | 53 |
62 --block-size '$block_size' | 68 --block-size '$block_size' |
63 ]]> | 69 ]]> |
64 </command> | 70 </command> |
65 | 71 |
66 <inputs> | 72 <inputs> |
67 <param name="method_select" type="select" label="What do you want to align?" help="(--blastp/--blastx)"> | 73 <conditional name="method_select"> |
68 <option value="blastp">Align amino acid query sequences (blastp)</option> | 74 <param name="method_select" type="select" label="What do you want to align?" help="(--blastp/--blastx)"> |
69 <option value="blastx">Align DNA query sequences (blastx)</option> | 75 <option value="blastp">Align amino acid query sequences (blastp)</option> |
70 </param> | 76 <option value="blastx">Align DNA query sequences (blastx)</option> |
77 </param> | |
78 <when value="blastx"> | |
79 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help=""> | |
80 <option value="1">The Standard Code</option> | |
81 <option value="2">The Vertebrate Mitochondrial Code</option> | |
82 <option value="3">The Yeast Mitochondrial Code</option> | |
83 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
84 <option value="5">The Invertebrate Mitochondrial Code</option> | |
85 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
86 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option> | |
87 <option value="10">The Euplotid Nuclear Code</option> | |
88 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option> | |
89 <option value="12">The Alternative Yeast Nuclear Code</option> | |
90 <option value="13">The Ascidian Mitochondrial Code</option> | |
91 <option value="14">The Alternative Flatworm Mitochondrial Code</option> | |
92 <option value="16">Chlorophycean Mitochondrial Code</option> | |
93 <option value="21">Trematode Mitochondrial Code</option> | |
94 <option value="22">Scenedesmus obliquus Mitochondrial Code</option> | |
95 <option value="23">Thraustochytrium Mitochondrial Code</option> | |
96 <option value="24">Pterobranchia Mitochondrial Code</option> | |
97 <option value="5">Candidate Division SR1 and Gracilibacteria Code</option> | |
98 <option value="26">Pachysolen tannophilus Nuclear Code</option> | |
99 </param> | |
100 </when> | |
101 <when value="blastp"> | |
102 </when> | |
103 </conditional> | |
71 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" /> | 104 <param argument="--query" type="data" format="fasta,fastq" label="Input query file in FASTA or FASTQ format" /> |
72 <conditional name="ref_db_source"> | 105 <conditional name="ref_db_source"> |
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"> | 106 <param name="db_source" type="select" label="Will you select a reference database from your history or use a built-in index?" help="Built-ins were indexed using default options"> |
74 <option value="indexed">Use a built-in index</option> | 107 <option value="indexed">Use a built-in index</option> |
75 <option value="history">Use one from the history</option> | 108 <option value="history">Use one from the history</option> |
76 </param> | 109 </param> |
77 <when value="indexed"> | 110 <when value="indexed"> |
78 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin"> | 111 <param name="index" type="select" label="Select a reference database" help="If your database of interest is not listed, contact your Galaxy admin"> |
79 <options from_data_table="diamond_database"> | 112 <options from_data_table="diamond_database"> |
80 <filter type="sort_by" column="2"/> | 113 <filter type="sort_by" column="2"/> |
81 <validator type="no_options" message="No indexes are available for the selected input dataset"/> | 114 <validator type="no_options" message="No indexes are available for the selected input dataset"/> |
82 </options> | 115 </options> |
83 </param> | 116 </param> |
84 </when> | 117 </when> |
85 <when value="history"> | 118 <when value="history"> |
86 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" /> | 119 <param name="reference_database" type="data" format="dmnd" label="Select the reference database" /> |
87 </when> | 120 </when> |
88 </conditional> | 121 </conditional> |
89 <param name="query_gencode" argument="--query-gencode" type="select" label="Genetic code used for translation of query in BLASTX mode" help=""> | |
90 <option value="1">The Standard Code</option> | |
91 <option value="2">The Vertebrate Mitochondrial Code</option> | |
92 <option value="3">The Yeast Mitochondrial Code</option> | |
93 <option value="4">The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code</option> | |
94 <option value="5">The Invertebrate Mitochondrial Code</option> | |
95 <option value="6">The Ciliate, Dasycladacean and Hexamita Nuclear Code</option> | |
96 <option value="9">The Echinoderm and Flatworm Mitochondrial Code</option> | |
97 <option value="10">The Euplotid Nuclear Code</option> | |
98 <option value="11">The Bacterial, Archaeal and Plant Plastid Code</option> | |
99 <option value="12">The Alternative Yeast Nuclear Code</option> | |
100 <option value="13">The Ascidian Mitochondrial Code</option> | |
101 <option value="14">The Alternative Flatworm Mitochondrial Code</option> | |
102 <option value="16">Chlorophycean Mitochondrial Code</option> | |
103 <option value="21">Trematode Mitochondrial Code</option> | |
104 <option value="22">Scenedesmus obliquus Mitochondrial Code</option> | |
105 <option value="23">Thraustochytrium Mitochondrial Code</option> | |
106 <option value="24">Pterobranchia Mitochondrial Code</option> | |
107 <option value="5">Candidate Division SR1 and Gracilibacteria Code</option> | |
108 <option value="26">Pachysolen tannophilus Nuclear Code</option> | |
109 </param> | |
110 <conditional name="output"> | 122 <conditional name="output"> |
111 <param argument="--outfmt" type="select" label="Format of output file " help=""> | 123 <param argument="--outfmt" type="select" label="Format of output file " help=""> |
112 <option value="5">BLAST XML</option> | 124 <option value="5">BLAST XML</option> |
113 <option value="6">BLAST tabular</option> | 125 <option value="6">BLAST tabular</option> |
114 <option value="101">SAM</option> | 126 <option value="101">SAM</option> |
148 </when> | 160 </when> |
149 <when value="101"> | 161 <when value="101"> |
150 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/> | 162 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full length subject titles in output?" help=""/> |
151 </when> | 163 </when> |
152 </conditional> | 164 </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=""/> | 165 <param name='sensitivity' type="select" label="Sensitivity Mode" help="Choose one of the sensitivity modes. More sensitivity may increase computation time"> |
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."/> | 166 <option value="0" selected="True">Default</option> |
167 <option value="1">Sensitive</option> | |
168 <option value="2">More Sensitive</option> | |
169 </param> | |
155 <param argument="--gapopen" type="integer" value="11" label="Gap open penalty" help="" /> | 170 <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="" /> | 171 <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)"> | 172 <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> | 173 <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> | 174 <option value="BLOSUM50">BLOSUM50 ((9-13)/3; (12-16)/2; (15-19)/1)</option> |
210 <test> | 225 <test> |
211 <param name="method_select" value="blastp" /> | 226 <param name="method_select" value="blastp" /> |
212 <param name="query" value="protein.fasta" ftype="fasta"/> | 227 <param name="query" value="protein.fasta" ftype="fasta"/> |
213 <param name="db_source" value="history"/> | 228 <param name="db_source" value="history"/> |
214 <param name="reference_database" value="db.dmnd"/> | 229 <param name="reference_database" value="db.dmnd"/> |
215 <param name="query_gencode" value="1"/> | |
216 <param name="outfmt" value="6"/> | 230 <param name="outfmt" value="6"/> |
217 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> | 231 <param name="fields" value="qseqid,sseqid,pident,length,mismatch,gapopen,qstart,qend,sstart,send,evalue,bitscore"/> |
218 <param name="sensitive" value=""/> | 232 <param name="sensitivity" value="0"/> |
219 <param name="more_sensitive" value=""/> | |
220 <param name="gapopen" value="11"/> | 233 <param name="gapopen" value="11"/> |
221 <param name="gapextend" value="1"/> | 234 <param name="gapextend" value="1"/> |
222 <param name="matrix" value="BLOSUM62"/> | 235 <param name="matrix" value="BLOSUM62"/> |
223 <param name="seg" value="yes"/> | 236 <param name="seg" value="yes"/> |
224 <param name="hit_filter_select" value="max"/> | 237 <param name="hit_filter_select" value="max"/> |
240 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. | 253 DIAMOND_ is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. |
241 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting | 254 On Illumina reads of length 100-150bp, in fast mode, DIAMOND is about 20,000 times faster than BLASTX, while reporting |
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 | 255 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 |
243 times faster than BLASTX, finding more than 94% of all matches. | 256 times faster than BLASTX, finding more than 94% of all matches. |
244 | 257 |
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. | 258 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 recommended for small datasets. |
246 | 259 |
247 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ | 260 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/ |
248 | 261 |
249 **Input** | 262 **Input** |
250 | 263 |