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comparison macros.xml @ 12:60f307965815 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit 62db819c1db857d3fba94dc4e290ee0f50f7928d
author iuc
date Mon, 03 Feb 2025 16:01:01 +0000
parents 1e3323a44643
children 20d92dc4c6cb
comparison
equal deleted inserted replaced
11:e8ac2b53f262 12:60f307965815
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.0.15</token> 2 <token name="@TOOL_VERSION@">2.1.11</token>
3 <token name="@VERSION_SUFFIX@">0</token> 3 <token name="@VERSION_SUFFIX@">0</token>
4 <xml name="requirements"> 4 <xml name="requirements">
5 <requirements> 5 <requirements>
6 <requirement type="package" version="@TOOL_VERSION@">diamond</requirement> 6 <requirement type="package" version="@TOOL_VERSION@">diamond</requirement>
7 </requirements> 7 </requirements>
8 </xml> 8 </xml>
9
10 <xml name="stdio"> 9 <xml name="stdio">
11 <stdio> 10 <stdio>
12 <regex match="Failed to allocate" source="stderr" level="fatal_oom" /> 11 <regex match="Failed to allocate" source="stderr" level="fatal_oom"/>
13 </stdio> 12 </stdio>
14 </xml> 13 </xml>
15
16 <xml name="version_command"> 14 <xml name="version_command">
17 <version_command>diamond version | cut -d" " -f 3</version_command> 15 <version_command>diamond version | cut -d" " -f 3</version_command>
18 </xml> 16 </xml>
19
20 <xml name="output_type_macro"> 17 <xml name="output_type_macro">
21 <conditional name="output"> 18 <conditional name="output">
22 <param argument="--outfmt" type="select" label="Format of output file" help=""> 19 <param argument="--outfmt" type="select" label="Format of output file" help="">
23 <option value="0">BLAST pairwise</option> 20 <option value="0">BLAST pairwise</option>
24 <option value="5">BLAST XML</option> 21 <option value="5">BLAST XML</option>
25 <option value="6">BLAST tabular</option> 22 <option value="6">BLAST tabular</option>
26 <option value="100">DAA</option> 23 <option value="100">DAA</option>
27 <option value="101">SAM</option> 24 <option value="101">SAM</option>
28 <option value="102">Taxonomic classification</option> 25 <option value="102">Taxonomic classification</option>
26 <option value="104">JSON (flat)</option>
29 </param> 27 </param>
30 <when value="0"/> 28 <when value="0"/>
31 <when value="5"/> 29 <when value="5"/>
32 <when value="6"> 30 <when value="6">
33 <param name="fields" type="select" label="Tabular fields" help="" multiple="true"> 31 <param name="fields" type="select" label="Tabular fields" help="" multiple="true">
67 <option value="full_qqual">Query quality values</option> 65 <option value="full_qqual">Query quality values</option>
68 <option value="qstrand">Query strand</option> 66 <option value="qstrand">Query strand</option>
69 <option value="cigar">Cigar</option> 67 <option value="cigar">Cigar</option>
70 <yield/> 68 <yield/>
71 </param> 69 </param>
72 <param argument="--unal" type="boolean" label="Report unaligned queries" truevalue="1" falsevalue="0" checked="false"/>
73 </when> 70 </when>
74 <when value="100"> 71 <when value="100">
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> 72 </when>
78 <when value="101"> 73 <when value="101">
79 <param argument="--salltitles" type="boolean" truevalue="--salltitles" falsevalue="" checked="true" label="Include full subject titles in DAA file?" help=""/>
80 <param argument="--sallseqid" type="boolean" truevalue="--sallseqid" falsevalue="" checked="true" label="Include all subject ids in DAA file?" help=""/>
81 </when> 74 </when>
82 <when value="102"/> 75 <when value="102">
76 <param argument="--include-lineage" type="boolean" truevalue="--include-lineage" falsevalue="" checked="false" label="Include lineage in the taxonomic classification format"/>
77 </when>
78 <when value="104"/>
83 </conditional> 79 </conditional>
84 </xml> 80 </xml>
85
86 <xml name="hit_filter_macro"> 81 <xml name="hit_filter_macro">
87 <conditional name="hit_filter"> 82 <conditional name="hit_filter">
88 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?"> 83 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?">
89 <option value="max">Maximum number of target sequences</option> 84 <option value="max">Maximum number of target sequences</option>
90 <option value="top">Percentage of top alignment score</option> 85 <option value="top">Percentage of top alignment score</option>
91 </param> 86 </param>
92 <when value="max"> 87 <when value="max">
93 <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" 88 <param 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."/>
94 help="Setting this to 0 will report all alignments that were found." />
95 </when> 89 </when>
96 <when value="top"> 90 <when value="top">
97 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query" 91 <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 alignments whose score is at most 10% lower than the best alignment score for a query."/>
98 help="For example, setting this to 10 will report all alignments whose score is at most 10% lower than the best alignment score for a query." />
99 </when> 92 </when>
100 </conditional> 93 </conditional>
101 </xml> 94 </xml>
102
103 <xml name="block_size_low_sens"> 95 <xml name="block_size_low_sens">
104 <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" 96 <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time"
105 help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary 97 help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary disk space, but also improve performance"/>
106 disk space, but also improve performance" />
107 </xml> 98 </xml>
108
109 <xml name="block_size_hi_sens"> 99 <xml name="block_size_hi_sens">
110 <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time" 100 <param argument="--block-size" type="float" value="0.4" label="Block size in billions of sequence letters to be processed at a time"
111 help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary 101 help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary disk space, but also improve performance"/>
112 disk space, but also improve performance" />
113 </xml> 102 </xml>
114
115 <xml name="citations"> 103 <xml name="citations">
116 <citations> 104 <citations>
117 <citation type="doi">10.1038/nmeth.3176</citation> 105 <citation type="doi">10.1038/s41592-021-01101-x</citation>
118 </citations> 106 </citations>
119 </xml> 107 </xml>
120
121
122 <xml name="output_macro"> 108 <xml name="output_macro">
123 <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}"> 109 <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}: Blast pairwise">
124 <filter>output_section["output"]["outfmt"] == "0"</filter> 110 <filter>output_section["output"]["outfmt"] == "0"</filter>
125 </data> 111 </data>
126 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> 112 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}: Blast XML">
127 <filter>output_section["output"]["outfmt"] == "5"</filter> 113 <filter>output_section["output"]["outfmt"] == "5"</filter>
128 </data> 114 </data>
129 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}"> 115 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}: Blast Tabular">
130 <filter>output_section["output"]["outfmt"] == "6"</filter> 116 <filter>output_section["output"]["outfmt"] == "6"</filter>
131 </data> 117 </data>
132 <!-- for daa diamond appends the .daa extension -> hence from_work_dir --> 118 <!-- for daa diamond appends the .daa extension -> hence from_work_dir -->
133 <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa"> 119 <data format="daa" name="daa_output" label="${tool.name} on ${on_string}: DAA" from_work_dir="output.daa">
134 <filter>output_section["output"]["outfmt"] == "100"</filter> 120 <filter>output_section["output"]["outfmt"] == "100"</filter>
135 </data> 121 </data>
136 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}"> 122 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}: SAM">
137 <filter>output_section["output"]["outfmt"] == "101"</filter> 123 <filter>output_section["output"]["outfmt"] == "101"</filter>
138 </data> 124 </data>
139 <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}"> 125 <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}: Taxonomic classification">
140 <filter>output_section["output"]["outfmt"] == "102"</filter> 126 <filter>output_section["output"]["outfmt"] == "102"</filter>
141 </data> 127 </data>
128 <data format="json" name="json_output" label="${tool.name} on ${on_string}: Json flat">
129 <filter>output_section["output"]["outfmt"] == "104"</filter>
130 </data>
142 </xml> 131 </xml>
143
144 <token name="@OUTPUT_ARGS@"> 132 <token name="@OUTPUT_ARGS@">
145 #if $output_section.output.outfmt == "0" 133 #if $output_section.output.outfmt == "0"
146 --outfmt '0' 134 --outfmt '0'
147 --out '$blast_pairw' 135 --out '$blast_pairw'
148 #else if $output_section.output.outfmt == "5" 136 #else if $output_section.output.outfmt == "5"
149 --outfmt '5' 137 --outfmt '5'
150 --out '$blast_xml' 138 --out '$blast_xml'
151 #else if $output_section.output.outfmt == "6" 139 #else if $output_section.output.outfmt == "6"
152 --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(',')) 140 --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(','))
153 --out '$blast_tabular' 141 --out '$blast_tabular'
154 --unal $output_section.output.unal
155 #else if $output_section.output.outfmt == "100" 142 #else if $output_section.output.outfmt == "100"
156 --outfmt '100' 143 --outfmt '100'
157 $output_section.output.salltitles
158 $output_section.output.sallseqid
159 --out output.daa 144 --out output.daa
160 #else if $output_section.output.outfmt == "101" 145 #else if $output_section.output.outfmt == "101"
161 --outfmt '101' 146 --outfmt '101'
162 $output_section.output.salltitles
163 $output_section.output.sallseqid
164 --out '$sam_output' 147 --out '$sam_output'
165 #else if $output_section.output.outfmt == "102" 148 #else if $output_section.output.outfmt == "102"
166 --outfmt '102' 149 --outfmt '102'
167 --out '$tax_output' 150 --out '$tax_output'
151 $output_section.output.include_lineage
168 #end if 152 #end if
169 </token> 153 </token>
170
171 <token name="@HITFILTER_ARGS@"> 154 <token name="@HITFILTER_ARGS@">
172 #if str($hit_filter.hit_filter_select) == 'max': 155 #if str($hit_filter.hit_filter_select) == 'max':
173 --max-target-seqs '$hit_filter.max_target_seqs' 156 --max-target-seqs '$hit_filter.max_target_seqs'
174 #else: 157 #else:
175 --top '$hit_filter.top' 158 --top '$hit_filter.top'