Mercurial > repos > bgruening > diamond
comparison macros.xml @ 6:64be1ac21109 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author | bgruening |
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date | Thu, 27 Sep 2018 06:30:30 -0400 |
parents | df7738595640 |
children | 62c9df8382c2 |
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5:3c6b132b154a | 6:64be1ac21109 |
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1 <macros> | 1 <macros> |
2 <token name="@VERSION@">0.8.24</token> | 2 <token name="@VERSION@">0.9.21</token> |
3 | 3 |
4 <xml name="requirements"> | 4 <xml name="requirements"> |
5 <requirements> | 5 <requirements> |
6 <requirement type="package" version="@VERSION@">diamond</requirement> | 6 <requirement type="package" version="@VERSION@">diamond</requirement> |
7 </requirements> | 7 </requirements> |
8 </xml> | 8 </xml> |
9 | 9 |
10 <xml name="stdio"> | 10 <xml name="stdio"> |
11 <stdio> | 11 <stdio> |
12 <!-- disabled error detection by exit code to be able to detect oom errors by | |
13 regex, can be reenabled when https://github.com/galaxyproject/galaxy/pull/6338 is merged | |
14 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" /> | |
15 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />--> | |
16 <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" /> | |
17 <regex match=".+" source="stderr" level="fatal" description=""/> | |
12 </stdio> | 18 </stdio> |
13 </xml> | 19 </xml> |
14 | 20 |
15 <xml name="version_command"> | 21 <xml name="version_command"> |
16 <version_command>diamond version</version_command> | 22 <version_command>diamond version</version_command> |
17 </xml> | 23 </xml> |
18 | 24 |
25 <xml name="output_type_macro"> | |
26 <conditional name="output"> | |
27 <param argument="--outfmt" type="select" label="Format of output file " help=""> | |
28 <option value="0">BLAST pairwise</option> | |
29 <option value="5">BLAST XML</option> | |
30 <option value="6">BLAST tabular</option> | |
31 <option value="100">DAA</option> | |
32 <option value="101">SAM</option> | |
33 <option value="102">Taxonomic classification</option> | |
34 </param> | |
35 <when value="0"/> | |
36 <when value="5"/> | |
37 <when value="6"> | |
38 <param name="fields" type="select" label="Tabular fields" help="" multiple="true"> | |
39 <option value="qseqid" selected="true">Query Seq - id</option> | |
40 <option value="sseqid" selected="true">Subject Seq - id</option> | |
41 <option value="sallseqid">All subject Seq - id(s)</option> | |
42 <option value="qlen">Query sequence length</option> | |
43 <option value="slen">Subject sequence length</option> | |
44 <option value="pident" selected="true">Percentage of identical matches</option> | |
45 <option value="length" selected="true">Alignment length</option> | |
46 <option value="nident">Number of identical matches</option> | |
47 <option value="mismatch" selected="true">Number of mismatches</option> | |
48 <option value="positive">Number of positive - scoring matches</option> | |
49 <option value="gapopen" selected="true">Number of gap openings</option> | |
50 <option value="gaps">Total number of gaps</option> | |
51 <option value="ppos">Percentage of positive - scoring matches</option> | |
52 <option value="qstart" selected="true">Start of alignment in query</option> | |
53 <option value="qend" selected="true">End of alignment in query</option> | |
54 <option value="sstart" selected="true">Start of alignment in subject</option> | |
55 <option value="send" selected="true">End of alignment in subject</option> | |
56 <option value="qseq">Aligned part of query sequence</option> | |
57 <option value="sseq">Aligned part of subject sequence</option> | |
58 <option value="evalue" selected="true">Expect value</option> | |
59 <option value="bitscore" selected="true">Bit score</option> | |
60 <option value="score">Raw score</option> | |
61 <option value="qframe">Query frame</option> | |
62 <option value="btop">Blast traceback operations(BTOP)</option> | |
63 <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option> | |
64 <option value="stitle">Subject Title</option> | |
65 <option value="salltitles">All Subject Title(s)</option> | |
66 <option value="qcovhsp">Query Coverage Per HSP</option> | |
67 <option value="qtitle">Query title</option> | |
68 </param> | |
69 </when> | |
70 <when value="100"> | |
71 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> | |
72 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/> | |
73 </when> | |
74 <when value="101"> | |
75 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> | |
76 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/> | |
77 </when> | |
78 <when value="102"/> | |
79 </conditional> | |
80 </xml> | |
81 | |
82 <xml name="hit_filter_macro"> | |
83 <conditional name="hit_filter"> | |
84 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?"> | |
85 <option value="max">Maximum number of target sequences</option> | |
86 <option value="top">Percentage of top alignment score</option> | |
87 </param> | |
88 <when value="max"> | |
89 <param name="max_target_seqs" argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" help="Setting this to 0 will report all alignments that were found." /> | |
90 </when> | |
91 <when value="top"> | |
92 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" help="For example, setting this to 10 will report all align- | |
93 ments whose score is at most 10% lower than the best alignment score for a query." /> | |
94 </when> | |
95 </conditional> | |
96 </xml> | |
97 | |
19 <xml name="citations"> | 98 <xml name="citations"> |
20 <citations> | 99 <citations> |
21 <citation type="doi">10.1038/nmeth.3176</citation> | 100 <citation type="doi">10.1038/nmeth.3176</citation> |
22 </citations> | 101 </citations> |
23 </xml> | 102 </xml> |
103 | |
104 | |
105 <xml name="output_macro"> | |
106 <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}"> | |
107 <filter>output["outfmt"] == "0"</filter> | |
108 </data> | |
109 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> | |
110 <filter>output["outfmt"] == "5"</filter> | |
111 </data> | |
112 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}"> | |
113 <filter>output["outfmt"] == "6"</filter> | |
114 </data> | |
115 <!-- for daa diamond appends the .daa extension -> hence from_work_dir --> | |
116 <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa"> | |
117 <filter>output["outfmt"] == "100"</filter> | |
118 </data> | |
119 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}"> | |
120 <filter>output["outfmt"] == "101"</filter> | |
121 </data> | |
122 <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}"> | |
123 <filter>output["outfmt"] == "102"</filter> | |
124 </data> | |
125 </xml> | |
126 | |
127 <token name="@OUTPUT_ARGS@"> | |
128 #if $output.outfmt == "0" | |
129 --outfmt '0' | |
130 --out '$blast_pairw' | |
131 #else if $output.outfmt == "5" | |
132 --outfmt '5' | |
133 --out '$blast_xml' | |
134 #else if $output.outfmt == "6" | |
135 --outfmt '6' #echo ' '.join(str($output.fields).split(',')) | |
136 --out '$blast_tabular' | |
137 #else if $output.outfmt == "100" | |
138 --outfmt '100' | |
139 --out output.daa | |
140 #else if $output.outfmt == "101" | |
141 --outfmt '101' | |
142 --out '$sam_output' | |
143 #else if $output.outfmt == "102" | |
144 --outfmt '102' | |
145 --out '$tax_output' | |
146 #end if | |
147 </token> | |
148 | |
149 <token name="@HITFILTER_ARGS@"> | |
150 #if str($hit_filter.hit_filter_select) == 'max': | |
151 --max-target-seqs '$hit_filter.max_target_seqs' | |
152 #else: | |
153 --top '$hit_filter.top' | |
154 #end if | |
155 </token> | |
24 </macros> | 156 </macros> |