Mercurial > repos > bgruening > diamond

comparison macros.xml @ 6:64be1ac21109 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit 2f6d48e1d2161d03411d9fbb4fc3d16f0fa3d2e1
author bgruening
date Thu, 27 Sep 2018 06:30:30 -0400
parents df7738595640
children 62c9df8382c2
comparison
equal deleted inserted replaced
5:3c6b132b154a 6:64be1ac21109
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>