Mercurial > repos > iuc > semibin_generate_sequence_features

comparison generate_sequence_features.xml @ 2:f5aff7c9a65d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/semibin commit a9fc83e0029266f910b549d5d1eef6a9bc3e3f7b
author iuc
date Tue, 25 Mar 2025 15:49:59 +0000
parents cae8e4d4f726
children b55f0ce54d97
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1:cae8e4d4f726 2:f5aff7c9a65d
11 <command detect_errors="exit_code"><![CDATA[ 11 <command detect_errors="exit_code"><![CDATA[
12 #import re 12 #import re
13 @BAM_FILES@ 13 @BAM_FILES@
14 @FASTA_FILES@ 14 @FASTA_FILES@
15 15
16 SemiBin 16 SemiBin2
17 #if $mode.select == 'single' or $mode.select == 'co' 17 #if $mode.select == 'single' or $mode.select == 'co'
18 generate_sequence_features_single 18 generate_sequence_features_single
19 #else 19 #else
20 generate_sequence_features_multi 20 generate_sequence_features_multi
21 --separator '$separator' 21 --separator '$separator'
23 --input-fasta 'contigs.fasta' 23 --input-fasta 'contigs.fasta'
24 --input-bam *.bam 24 --input-bam *.bam
25 --output 'output' 25 --output 'output'
26 --threads \${GALAXY_SLOTS:-1} 26 --threads \${GALAXY_SLOTS:-1}
27 @MIN_LEN@ 27 @MIN_LEN@
28 #if str($ml_threshold) != '' 28 #if $ml_threshold:
29 --ml-threshold $ml_threshold 29 --ml-threshold $ml_threshold
30 #end if 30 #end if
31 ]]></command> 31 ]]></command>
32 <inputs> 32 <inputs>
33 <expand macro="mode_fasta_bam"/> 33 <expand macro="mode_fasta_bam"/>