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comparison comebin.xml @ 3:ddfb9c10740a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit f33c09bd4b736c401cdc037e328c7be4a24d8cf5
author iuc
date Thu, 21 Aug 2025 08:48:35 +0000
parents 15f6ef1d7c96
children
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2:5910c5106cdc 3:ddfb9c10740a
9 9
10 #import re 10 #import re
11 11
12 mkdir 'outputs' 'bam_files' && 12 mkdir 'outputs' 'bam_files' &&
13 13
14 #set $safename = re.sub('[^\w\-_\.]', '_', $assembly_file.element_identifier) 14 #set $safename_fasta = re.sub('[^\w\-_\.]', '_', $assembly_file.element_identifier)
15 ln -s '$assembly_file' '${safename}.fasta' && 15 ln -s '$assembly_file' '${safename_fasta}.fasta' &&
16 16
17 #for $file in $bam_files: 17 #for $file in $bam_files:
18 #set $safename = re.sub('[^\w\-_\.]', '_', $file.element_identifier) 18 #set $safename = re.sub('[^\w\-_\.]', '_', $file.element_identifier)
19 ln -s '$file' './bam_files/${safename}.bam' && 19 ln -s '$file' './bam_files/${safename}.bam' &&
20 #end for 20 #end for
21 21
22 run_comebin.sh 22 run_comebin.sh
23 -a 'assembly_file.fasta' 23 -a '${safename_fasta}.fasta'
24 -o 'outputs' 24 -o 'outputs'
25 -p 'bam_files' 25 -p 'bam_files'
26 -t \${GALAXY_SLOTS:-12} 26 -t \${GALAXY_SLOTS:-12}
27 -l ${loss} 27 -l ${loss}
28 -n ${learning} 28 -n ${learning}
45 <collection name="bins" type="list" format="fasta" label="${tool.name}: BINS"> 45 <collection name="bins" type="list" format="fasta" label="${tool.name}: BINS">
46 <discover_datasets pattern="__name__" directory="outputs/comebin_res/comebin_res_bins/"/> 46 <discover_datasets pattern="__name__" directory="outputs/comebin_res/comebin_res_bins/"/>
47 </collection> 47 </collection>
48 </outputs> 48 </outputs>
49 <tests> 49 <tests>
50 <test expect_exit_code="1" expect_failure="true"> 50 <test expect_num_outputs="1">
51 <param name="assembly_file" ftype="fasta" value="input_single.fasta"/> 51 <param name="assembly_file" ftype="fasta" value="input_single.fasta"/>
52 <param name="bam_files" ftype="bam" value="input_single.bam"/> 52 <param name="bam_files" ftype="bam" value="input_single.bam"/>
53 <param name="learning" value="6"/> 53 <param name="learning" value="6"/>
54 <param name="loss" value="0.15"/> 54 <param name="loss" value="0.15"/>
55 <param name="emb_comebin" value="2048"/> 55 <param name="emb_comebin" value="2048"/>