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comparison coverm_contig.xml @ 1:688a777e1b19 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112
author iuc
date Tue, 24 Jan 2023 12:33:11 +0000
parents 6941d0d453ba
children f8cb3f0a19fa
comparison
equal deleted inserted replaced
0:6941d0d453ba 1:688a777e1b19
1 <tool id="coverm_contig" name="CoverM-CONTIG" version="@TOOL_VERSION@" python_template_version="3.5"> 1 <tool id="coverm_contig" name="CoverM contig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>Calculate coverage of individual contigs</description>
2 <macros> 3 <macros>
3 <import>macros.xml</import> 4 <import>macros.xml</import>
4 <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
5 <token name="@TOOL_VERSION@">0.2.1</token>
6 </macros> 5 </macros>
7 <expand macro="requirements"/> 6 <expand macro="requirements"/>
8 <command><![CDATA[ 7 <command><![CDATA[
9 #if $reads.read_type == "single" or $reads.read_type == "interleaved" 8 #if $reads.read_type == "single" or $reads.read_type == "interleaved"
10 mkdir -p reads1 && 9 mkdir -p reads1 &&
222 --min-covered-fraction $cov.min_covered_fraction 221 --min-covered-fraction $cov.min_covered_fraction
223 #end if 222 #end if
224 #if $cov.contig_end_exclusion: 223 #if $cov.contig_end_exclusion:
225 --contig-end-exclusion $cov.contig_end_exclusion 224 --contig-end-exclusion $cov.contig_end_exclusion
226 #end if 225 #end if
227 #if $cov.cond_methods.trimmed_mean 226 #if $cov.cond_methods.trimmed_mean == "trimmed_mean"
228 #if $cov.cond_methods.trim_min: 227 #if $cov.cond_methods.trim_min:
229 --trim-min $cov.cond_methods.trim_min 228 --trim-min $cov.cond_methods.trim_min
230 #end if 229 #end if
231 #if $cov.cond_methods.trim_max: 230 #if $cov.cond_methods.trim_max:
232 --trim_max $cov.cond_methods.trim_max 231 --trim_max $cov.cond_methods.trim_max
236 #if $out.output_format: 235 #if $out.output_format:
237 --output-format $out.output_format 236 --output-format $out.output_format
238 #end if 237 #end if
239 --output-file output.tsv 238 --output-file output.tsv
240 --threads \${GALAXY_SLOTS:-1} 239 --threads \${GALAXY_SLOTS:-1}
241 2> stdout.txt
242 ]]></command> 240 ]]></command>
243 <inputs> 241 <inputs>
244 <expand macro="reads_for_contig" /> 242 <expand macro="reads_for_contig" />
245 <expand macro="add_reads" /> 243 <expand macro="add_reads" />
246 <section name="shar" title="Sharding" expanded="false"> 244 <section name="shar" title="Sharding" expanded="false">