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comparison macros.xml @ 5:b9c38856e540 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 339c91447e45305efa0eed6952ef391db8e5d207
author iuc
date Sun, 12 Nov 2023 14:30:50 +0000
parents 1dcea261abbe
children 28d740f2c0b0
comparison
equal deleted inserted replaced
4:1dcea261abbe 5:b9c38856e540
1 <macros> 1 <macros>
2 <token name="@TOOL_VERSION@">0.6.1</token> 2 <token name="@TOOL_VERSION@">0.6.1</token>
3 <token name="@VERSION_SUFFIX@">2</token> 3 <token name="@VERSION_SUFFIX@">3</token>
4 <token name="@PROFILE@">22.01</token> 4 <token name="@PROFILE@">22.01</token>
5 <xml name="requirements"> 5 <xml name="requirements">
6 <requirements> 6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement> 7 <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>
8 </requirements> 8 </requirements>
72 <when value="history"> 72 <when value="history">
73 <param argument="--genome-fasta-files" type="data" format="fasta" multiple="true" label="FASTA files of each genome"/> 73 <param argument="--genome-fasta-files" type="data" format="fasta" multiple="true" label="FASTA files of each genome"/>
74 </when> 74 </when>
75 <when value="builtin"> 75 <when value="builtin">
76 <param argument="--genome-fasta-files" type="select" multiple="true" label="Reference genome(s)"> 76 <param argument="--genome-fasta-files" type="select" multiple="true" label="Reference genome(s)">
77 <options from_data_table="all_fasta" /> 77 <options from_data_table="all_fasta">
78 <column name="name" index="2"/>
79 <column name="value" index="3"/>
80 </options>
78 </param> 81 </param>
79 </when> 82 </when>
80 </conditional> 83 </conditional>
81 </xml> 84 </xml>
82 <xml name="cond_single_genome"> 85 <xml name="cond_single_genome">
176 #set $fn = "ref/" + re.sub('[^\s\w\-\\.]', '_', str($ref.element_identifier)) 179 #set $fn = "ref/" + re.sub('[^\s\w\-\\.]', '_', str($ref.element_identifier))
177 #silent $ref_fp.append( $fn ) 180 #silent $ref_fp.append( $fn )
178 ln -s '$ref' '${fn}' && 181 ln -s '$ref' '${fn}' &&
179 ]]></token> 182 ]]></token>
180 <token name="@GENOME_FOR_READS@"><![CDATA[ 183 <token name="@GENOME_FOR_READS@"><![CDATA[
184 echo "GENOME_FOR_READS mapped.mode.genome.genomic.source=$mapped.mode.genome.genomic.source" &&
185 echo "GENOME_FOR_READS mapped.mode.genome.genomic.genome_fasta_files=$mapped.mode.genome.genomic.genome_fasta_files" &&
181 #if $mapped.mode.genome.genomic.source == 'history' 186 #if $mapped.mode.genome.genomic.source == 'history'
182 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files) 187 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files)
183 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.element_identifier)) 188 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.element_identifier))
184 #silent $genome_fp.append( $fn ) 189 #silent $genome_fp.append( $fn )
185 ln -s '$genome' '$fn' && 190 ln -s '$genome' '$fn' &&
186 #end for 191 #end for
187 #else 192 #else
188 #for $i, $genome in enumerate($mapped.mode.genome.genomic.genome_fasta_files) 193 #for $genome in $mapped.mode.genome.genomic.genome_fasta_files
189 #set $fn = re.sub('[^\s\w\-\\.]', '_', str($genome.fields.path.element_identifier)) 194 #silent $genome_fp.append($genome)
190 #silent $genome_fp.append( $fn )
191 ln -s '$genome' '$fn' &&
192 #end for 195 #end for
193 #end if 196 #end if
194 ]]></token> 197 ]]></token>
195 <xml name="co_assembly_reads"> 198 <xml name="co_assembly_reads">
196 <conditional name="read_type"> 199 <conditional name="read_type">