Mercurial > repos > bgruening > diamond

comparison macros.xml @ 7:62c9df8382c2 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/diamond commit b2d290a8b609ebbc7f4b93716370143c41062ad4"
author bgruening
date Tue, 03 Dec 2019 17:40:05 -0500
parents 64be1ac21109
children 54f751e413f4
comparison
equal deleted inserted replaced
6:64be1ac21109 7:62c9df8382c2
1 <macros> 1 <macros>
2 <token name="@VERSION@">0.9.21</token> 2 <token name="@VERSION@">0.9.29</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" /> 12 <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" />--> 13 <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" /> 14 <regex match="Failed to allocate sufficient memory." source="stderr" level="fatal_oom" />
17 <regex match=".+" source="stderr" level="fatal" description=""/>
18 </stdio> 15 </stdio>
19 </xml> 16 </xml>
20 17
21 <xml name="version_command"> 18 <xml name="version_command">
22 <version_command>diamond version</version_command> 19 <version_command>diamond version</version_command>
63 <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option> 60 <option value="staxids">unique Subject Taxonomy ID(s), separated by a ';' (in numerical order)</option>
64 <option value="stitle">Subject Title</option> 61 <option value="stitle">Subject Title</option>
65 <option value="salltitles">All Subject Title(s)</option> 62 <option value="salltitles">All Subject Title(s)</option>
66 <option value="qcovhsp">Query Coverage Per HSP</option> 63 <option value="qcovhsp">Query Coverage Per HSP</option>
67 <option value="qtitle">Query title</option> 64 <option value="qtitle">Query title</option>
65 <option value="full_qseq">Query sequence</option>
66 <option value="full_sseq">Subject sequence</option>
67 <option value="qqual">Query quality values for the aligned part of the query</option>
68 <option value="full_qqual">Query quality values</option>
69 <option value="qstrand">Query strand</option>
68 </param> 70 </param>
69 </when> 71 </when>
70 <when value="100"> 72 <when value="100">
71 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> 73 <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=""/> 74 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>