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comparison macros.xml @ 2:dbf5571a8140 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit 13abac83068b126399ec415141007a48c2efaa84
author iuc
date Fri, 10 Nov 2023 20:49:03 +0000
parents 4d561bdc2c31
children
comparison
equal deleted inserted replaced
1:4d561bdc2c31 2:dbf5571a8140
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <macros> 2 <macros>
3 <token name="@TOOL_VERSION@">1.5.1</token> 3 <token name="@TOOL_VERSION@">2.0.2</token>
4 <token name="@VERSION_SUFFIX@">0</token> 4 <token name="@VERSION_SUFFIX@">0</token>
5 <token name="@PROFILE@">21.01</token> 5 <token name="@PROFILE@">21.01</token>
6 <xml name="biotools"> 6 <xml name="biotools">
7 <xrefs> 7 <xrefs>
8 <xref type="bio.tools">semibin</xref> 8 <xref type="bio.tools">semibin</xref>
13 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement> 13 <requirement type="package" version="@TOOL_VERSION@">semibin</requirement>
14 <yield/> 14 <yield/>
15 </requirements> 15 </requirements>
16 </xml> 16 </xml>
17 <xml name="version"> 17 <xml name="version">
18 <version_command>SemiBin -v</version_command> 18 <version_command>SemiBin2 -v</version_command>
19 </xml> 19 </xml>
20 <xml name="mode_fasta_bam"> 20 <xml name="mode_fasta_bam">
21 <conditional name="mode"> 21 <conditional name="mode">
22 <expand macro="mode_select"/> 22 <expand macro="mode_select"/>
23 <when value="single"> 23 <when value="single">
107 #else 107 #else
108 ln -s '$e' '${identifier}.fasta' && 108 ln -s '$e' '${identifier}.fasta' &&
109 #end if 109 #end if
110 #end for 110 #end for
111 #set $separator = ':' 111 #set $separator = ':'
112 SemiBin concatenate_fasta 112 SemiBin2 concatenate_fasta
113 --input-fasta *.fasta 113 --input-fasta *.fasta
114 --output 'output' 114 --output 'output'
115 --separator '$separator' 115 --separator '$separator'
116 --compression none
116 -m $mode.multi_fasta.min_len 117 -m $mode.multi_fasta.min_len
117 && 118 &&
118 ln -s 'output/concatenated.fa' 'contigs.fasta' && 119 ln -s 'output/concatenated.fa' 'contigs.fasta' &&
119 #end if 120 #end if
120 #end if 121 #end if
220 <xml name="batch-size"> 221 <xml name="batch-size">
221 <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/> 222 <param argument="--batch-size" type="integer" min="0" value="2048" label="Batch size used in the training process"/>
222 </xml> 223 </xml>
223 <xml name="orf-finder"> 224 <xml name="orf-finder">
224 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins"> 225 <param argument="--orf-finder" type="select" label="ORF finder used to estimate the number of bins">
225 <option value="prodigal" selected="true">Prodigal</option> 226 <option value="fast-naive" selected="true">Fast-Naive</option>
227 <option value="prodigal">Prodigal</option>
226 <option value="fraggenescan">Fraggenescan</option> 228 <option value="fraggenescan">Fraggenescan</option>
227 </param> 229 </param>
228 </xml> 230 </xml>
229 <xml name="max-node"> 231 <xml name="max-node">
230 <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/> 232 <param argument="--max-node" type="float" min="0" max="1" value="1" label="Fraction of contigs that considered to be binned"/>
249 </param> 251 </param>
250 </xml> 252 </xml>
251 <xml name="minfasta-kbs"> 253 <xml name="minfasta-kbs">
252 <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/> 254 <param argument="--minfasta-kbs" type="integer" min="0" value="200" label="Miminimum bin size in Kbps"/>
253 </xml> 255 </xml>
254 <xml name="no-recluster"> 256 <xml name="write_pre_reclustering_bins">
255 <param argument="--no-recluster" type="boolean" truevalue="--no-recluster" falsevalue="" checked="false" label="Do not recluster bins?"/> 257 <param argument="--write-pre-reclustering-bins" type="boolean" truevalue="--write-pre-reclustering-bins" falsevalue="" checked="false" label="Return also the pre reclustered bins?"/>
256 </xml> 258 </xml>
257 <xml name="data"> 259 <xml name="data">
258 <param argument="--data" type="data" format="csv" label="Train data"/> 260 <param argument="--data" type="data" format="csv" label="Train data"/>
259 </xml> 261 </xml>
260 <xml name="data_output_single"> 262 <xml name="data_output_single">
308 </collection> 310 </collection>
309 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs"> 311 <collection name="multi_contigs" type="list" label="${tool.name} on ${on_string}: Contigs">
310 <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter> 312 <filter>mode["select"]=="multi" and extra_output and "contigs" in extra_output</filter>
311 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" /> 313 <discover_datasets pattern="(?P&lt;designation&gt;.*).fa" format="fasta" directory="output/samples/" />
312 </collection> 314 </collection>
315
313 </xml> 316 </xml>
314 <xml name="train_output"> 317 <xml name="train_output">
315 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" /> 318 <data name="model" format="h5" from_work_dir="output/model.h5" label="${tool.name} on ${on_string}: Semi-supervised deep learning model" />
316 </xml> 319 </xml>
317 <xml name="cannot_link_output"> 320 <xml name="cannot_link_output">