Mercurial > repos > bgruening > diamond

comparison macros.xml @ 9:f921014aba5a draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 828c844036743151594e57cc19811f4c8d9179b3"
author iuc
date Sat, 27 Nov 2021 09:48:10 +0000
parents 54f751e413f4
children 1e3323a44643
comparison
equal deleted inserted replaced
8:54f751e413f4 9:f921014aba5a
1 <macros> 1 <macros>
2 <token name="@VERSION@">2.0.8</token> 2 <token name="@TOOL_VERSION@">2.0.8</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="@TOOL_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>
67 <option value="full_qqual">Query quality values</option> 67 <option value="full_qqual">Query quality values</option>
68 <option value="qstrand">Query strand</option> 68 <option value="qstrand">Query strand</option>
69 <option value="cigar">Cigar</option> 69 <option value="cigar">Cigar</option>
70 <yield/> 70 <yield/>
71 </param> 71 </param>
72 <param argument="--unal" type="boolean" label="Report unaligned queries" truevalue="1" falsevalue="0" checked="false"/>
72 </when> 73 </when>
73 <when value="100"> 74 <when value="100">
74 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/> 75 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
75 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/> 76 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
76 </when> 77 </when>
97 </when> 98 </when>
98 </conditional> 99 </conditional>
99 </xml> 100 </xml>
100 101
101 <xml name="block_size_low_sens"> 102 <xml name="block_size_low_sens">
102 <param name="block_size" argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" /> 103 <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" />
103 </xml> 104 </xml>
104 105
105 <xml name="block_size_hi_sens"> 106 <xml name="block_size_hi_sens">
106 <param name="block_size" argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" /> 107 <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" help="" />
107 </xml> 108 </xml>
108 109
109 <xml name="citations"> 110 <xml name="citations">
110 <citations> 111 <citations>
111 <citation type="doi">10.1038/nmeth.3176</citation> 112 <citation type="doi">10.1038/nmeth.3176</citation>
143 --outfmt '5' 144 --outfmt '5'
144 --out '$blast_xml' 145 --out '$blast_xml'
145 #else if $output.outfmt == "6" 146 #else if $output.outfmt == "6"
146 --outfmt '6' #echo ' '.join(str($output.fields).split(',')) 147 --outfmt '6' #echo ' '.join(str($output.fields).split(','))
147 --out '$blast_tabular' 148 --out '$blast_tabular'
149 --unal $output.unal
148 #else if $output.outfmt == "100" 150 #else if $output.outfmt == "100"
149 --outfmt '100' 151 --outfmt '100'
152 $output.salltitles
153 $output.sallseqid
150 --out output.daa 154 --out output.daa
151 #else if $output.outfmt == "101" 155 #else if $output.outfmt == "101"
152 --outfmt '101' 156 --outfmt '101'
157 $output.salltitles
158 $output.sallseqid
153 --out '$sam_output' 159 --out '$sam_output'
154 #else if $output.outfmt == "102" 160 #else if $output.outfmt == "102"
155 --outfmt '102' 161 --outfmt '102'
156 --out '$tax_output' 162 --out '$tax_output'
157 #end if 163 #end if