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comparison macros.xml @ 10:1e3323a44643 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/diamond commit b9f434bf71431a3b9548eb17fcc2639b3b6f8b01"
author iuc
date Fri, 22 Apr 2022 13:51:34 +0000
parents f921014aba5a
children
comparison
equal deleted inserted replaced
9:f921014aba5a 10:1e3323a44643
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">2.0.8</token> 2 <token name="@TOOL_VERSION@">2.0.15</token>
3 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>
17 <version_command>diamond version | cut -d" " -f 3</version_command> 17 <version_command>diamond version | cut -d" " -f 3</version_command>
18 </xml> 18 </xml>
19 19
20 <xml name="output_type_macro"> 20 <xml name="output_type_macro">
21 <conditional name="output"> 21 <conditional name="output">
22 <param argument="--outfmt" type="select" label="Format of output file " help=""> 22 <param argument="--outfmt" type="select" label="Format of output file" help="">
23 <option value="0">BLAST pairwise</option> 23 <option value="0">BLAST pairwise</option>
24 <option value="5">BLAST XML</option> 24 <option value="5">BLAST XML</option>
25 <option value="6">BLAST tabular</option> 25 <option value="6">BLAST tabular</option>
26 <option value="100">DAA</option> 26 <option value="100">DAA</option>
27 <option value="101">SAM</option> 27 <option value="101">SAM</option>
88 <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?"> 88 <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> 89 <option value="max">Maximum number of target sequences</option>
90 <option value="top">Percentage of top alignment score</option> 90 <option value="top">Percentage of top alignment score</option>
91 </param> 91 </param>
92 <when value="max"> 92 <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" help="Setting this to 0 will report all alignments that were found." /> 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"
94 help="Setting this to 0 will report all alignments that were found." />
94 </when> 95 </when>
95 <when value="top"> 96 <when value="top">
96 <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- 97 <param argument="--top" type="integer" value="0" label="Keep alignments within the given percentage range of the top alignment score for a query"
97 ments 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." />
98 </when> 99 </when>
99 </conditional> 100 </conditional>
100 </xml> 101 </xml>
101 102
102 <xml name="block_size_low_sens"> 103 <xml name="block_size_low_sens">
103 <param argument="--block-size" type="float" value="2" label="Block size in billions of sequence letters to be processed at a time" help="" /> 104 <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
106 disk space, but also improve performance" />
104 </xml> 107 </xml>
105 108
106 <xml name="block_size_hi_sens"> 109 <xml name="block_size_hi_sens">
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="" /> 110 <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
112 disk space, but also improve performance" />
108 </xml> 113 </xml>
109 114
110 <xml name="citations"> 115 <xml name="citations">
111 <citations> 116 <citations>
112 <citation type="doi">10.1038/nmeth.3176</citation> 117 <citation type="doi">10.1038/nmeth.3176</citation>
114 </xml> 119 </xml>
115 120
116 121
117 <xml name="output_macro"> 122 <xml name="output_macro">
118 <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}"> 123 <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}">
119 <filter>output["outfmt"] == "0"</filter> 124 <filter>output_section["output"]["outfmt"] == "0"</filter>
120 </data> 125 </data>
121 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}"> 126 <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}">
122 <filter>output["outfmt"] == "5"</filter> 127 <filter>output_section["output"]["outfmt"] == "5"</filter>
123 </data> 128 </data>
124 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}"> 129 <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}">
125 <filter>output["outfmt"] == "6"</filter> 130 <filter>output_section["output"]["outfmt"] == "6"</filter>
126 </data> 131 </data>
127 <!-- for daa diamond appends the .daa extension -> hence from_work_dir --> 132 <!-- for daa diamond appends the .daa extension -> hence from_work_dir -->
128 <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa"> 133 <data format="daa" name="daa_output" label="${tool.name} on ${on_string}" from_work_dir="output.daa">
129 <filter>output["outfmt"] == "100"</filter> 134 <filter>output_section["output"]["outfmt"] == "100"</filter>
130 </data> 135 </data>
131 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}"> 136 <data format="sam" name="sam_output" label="${tool.name} on ${on_string}">
132 <filter>output["outfmt"] == "101"</filter> 137 <filter>output_section["output"]["outfmt"] == "101"</filter>
133 </data> 138 </data>
134 <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}"> 139 <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}">
135 <filter>output["outfmt"] == "102"</filter> 140 <filter>output_section["output"]["outfmt"] == "102"</filter>
136 </data> 141 </data>
137 </xml> 142 </xml>
138 143
139 <token name="@OUTPUT_ARGS@"> 144 <token name="@OUTPUT_ARGS@">
140 #if $output.outfmt == "0" 145 #if $output_section.output.outfmt == "0"
141 --outfmt '0' 146 --outfmt '0'
142 --out '$blast_pairw' 147 --out '$blast_pairw'
143 #else if $output.outfmt == "5" 148 #else if $output_section.output.outfmt == "5"
144 --outfmt '5' 149 --outfmt '5'
145 --out '$blast_xml' 150 --out '$blast_xml'
146 #else if $output.outfmt == "6" 151 #else if $output_section.output.outfmt == "6"
147 --outfmt '6' #echo ' '.join(str($output.fields).split(',')) 152 --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(','))
148 --out '$blast_tabular' 153 --out '$blast_tabular'
149 --unal $output.unal 154 --unal $output_section.output.unal
150 #else if $output.outfmt == "100" 155 #else if $output_section.output.outfmt == "100"
151 --outfmt '100' 156 --outfmt '100'
152 $output.salltitles 157 $output_section.output.salltitles
153 $output.sallseqid 158 $output_section.output.sallseqid
154 --out output.daa 159 --out output.daa
155 #else if $output.outfmt == "101" 160 #else if $output_section.output.outfmt == "101"
156 --outfmt '101' 161 --outfmt '101'
157 $output.salltitles 162 $output_section.output.salltitles
158 $output.sallseqid 163 $output_section.output.sallseqid
159 --out '$sam_output' 164 --out '$sam_output'
160 #else if $output.outfmt == "102" 165 #else if $output_section.output.outfmt == "102"
161 --outfmt '102' 166 --outfmt '102'
162 --out '$tax_output' 167 --out '$tax_output'
163 #end if 168 #end if
164 </token> 169 </token>
165 170