Mercurial > repos > iuc > coverm_contig
comparison macros.xml @ 5:b9c38856e540 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 339c91447e45305efa0eed6952ef391db8e5d207
author | iuc |
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date | Sun, 12 Nov 2023 14:30:50 +0000 |
parents | 1dcea261abbe |
children | 28d740f2c0b0 |
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4:1dcea261abbe | 5:b9c38856e540 |
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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"> |