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comparison diamond.xml @ 0:98037ef3d2a9 draft

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author bgruening
date Sun, 08 Feb 2015 10:05:26 -0500
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children df7738595640
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-1:000000000000 0:98037ef3d2a9
1 <tool id="bg_diamond" name="Diamond" version="0.1.6.0">
2 <description>alignment tool for short sequences against a protein database</description>
3 <requirements>
4 <requirement type="package" version="0.6.13">diamond</requirement>
5 </requirements>
6 <command>
7 <![CDATA[
8
9 #if $ref_db_source.db_source == "history":
10 ln -s $ref_db_source.reference_database ./database.dmnd
11 #else:
12 ln -s ${ref_db_source.index.fields.db_path} ./database.dmnd
13 #end if
14
15 &&
16
17 diamond
18 $method.method_select
19 --threads "\${GALAXY_SLOTS:-12}"
20 --db ./database
21 --query $query
22 --out $blast_output
23 ##--sam $sam_output
24 --compress 0
25 --tmpdir ./
26
27 #if str($hit_filter.hit_filter_select) == 'max':
28 --max-target-seqs $hit_filter.max
29 #else:
30 --top $hit_filter.percentage
31 #end if
32
33 #if str($filter_score.filter_score_select) == 'evalue':
34 --evalue $filter_score.evalue
35 #else:
36 --evalue $filter_score.bitscore
37 #end if
38
39 --id $identity
40 $sensitive
41 --gapopen $method.gapopen
42 --gapextend $method.gapextend
43 --matrix $matrix
44 $seg
45 $salltitles
46
47 ]]>
48 </command>
49 <inputs>
50
51 <param name="query" type="data" format="fasta" label="Input query file in FASTA format" />
52
53 <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">
55 <option value="indexed">Use a built-in index</option>
56 <option value="history">Use one from the history</option>
57 </param>
58 <when value="indexed">
59 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact your Galaxy admin">
60 <options from_data_table="diamond_database">
61 <filter type="sort_by" column="2"/>
62 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
63 </options>
64 </param>
65 </when> <!-- build-in -->
66 <when value="history">
67 <param name="reference_database" type="data" format="diamond_database" label="Select the reference database" />
68 </when> <!-- history -->
69 </conditional>
70
71 <conditional name="method">
72 <param name="method_select" type="select" label="What do you want to align" help="(--blastp/--blastx)">
73 <option value="blastp">Align amino acid query sequences (blastp)</option>
74 <option value="blastx">Align DNA query sequences (blastx)</option>
75 </param>
76 <when value="blastp">
77 <param name="gapopen" type="integer" value="11" label="Gap open panalty" help="(--gapopen)" />
78 <param name="gapextend" type="integer" value="1" label="Gap extend panalty" help="(--gapextend)" />
79 </when>
80 <when value="blastx">
81 <param name="gapopen" type="integer" value="-1" label="Gap open panalty" help="(--gapopen)" />
82 <param name="gapextend" type="integer" value="-1" label="Gap extend panalty" help="(--gapextend)" />
83 </when>
84 </conditional>
85
86 <param name="matrix" type="select" label="Select scoring matrix" help="(--matrix)">
87 <option value="BLOSUM45">BLOSUM45</option>
88 <option value="BLOSUM50">BLOSUM50</option>
89 <option value="BLOSUM62" selected="True">BLOSUM62</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>
96
97 <conditional name="filter_score">
98 <param name="filter_score_select" type="select" label="Filter by score" help="(--evalue/--min-score)">
99 <option value="evalue">Maximum e-value to report alignments</option>
100 <option value="bit">Minimum bit score to report alignments</option>
101 </param>
102 <when value="evalue">
103 <param name="evalue" type="float" value="0.001" label="Filter by evalue" help="(--evalue)" />
104 </when>
105 <when value="bit">
106 <param name="bitscore" type="integer" value="0" label="Filter by bit score" help="(--min-score)" />
107 </when>
108 </conditional>
109
110 <conditional name="hit_filter">
111 <param name="hit_filter_select" type="select" label="Restrict number of hits by" help="(--max-target-seqs/--top)">
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>
131 <outputs>
132 <!--data format="sam" name="sam_output"/-->
133 <data format="tabular" name="blast_output"/>
134 </outputs>
135 <tests>
136 <test>
137 <param name="method" value="blastp"/>
138 <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"/>
141 <output name="blast_output" file="diamond_result1.tabular" ftpye="tabular"/>
142 </test>
143 </tests>
144 <help>
145 <![CDATA[
146
147 .. class:: infomark
148
149 **What it does**
150
151 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
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
154 times faster than BLASTX, finding more than 94% of all matches.
155
156 .. _DIAMOND: http://ab.inf.uni-tuebingen.de/software/diamond/
157
158
159 Supported values for gap open and gap extend parameters depending on the selected scoring matrix.
160
161 ======== ============================================
162 Matrix Supported values for (gap open)/(gap extend)
163 ======== ============================================
164 BLOSUM45 (10-13)/3; (12-16)/2; (16-19)/1
165 BLOSUM50 (9-13)/3; (12-16)/2; (15-19)/1
166 BLOSUM62 (6-11)/2; (9-13)/1
167 BLOSUM80 (6-9)/2; 13/2; 25/2; (9-11)/1
168 BLOSUM90 (6-9)/2; (9-11)/1
169 PAM250 (11-15)/3; (13-17)/2; (17-21)/1
170 PAM70 (6-8)/2; (9-11)/1
171 PAM30 (5-7)/2; (8-10)/1
172 ======== ============================================
173
174
175 ]]>
176 </help>
177 <citations>
178 <citation type="doi">10.1038/nmeth.3176</citation>
179 </citations>
180 </tool>