Mercurial > repos > greg > gene_family_classifier

comparison gene_family_classifier.xml @ 8:d678d4c2e9e1 draft

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author greg
date Wed, 21 Dec 2016 10:13:04 -0500
parents 4415ee993192
children c7010d37df2c
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7:4415ee993192 8:d678d4c2e9e1
10 <regex match="Error:" /> 10 <regex match="Error:" />
11 <regex match="Exception:" /> 11 <regex match="Exception:" />
12 </stdio> 12 </stdio>
13 <command> 13 <command>
14 <![CDATA[ 14 <![CDATA[
15 #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes': 15 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
16 #set orthogroups_fasta_dir = $options_type.create_orthogroup_cond.coding_sequences.extra_files_path 16 #import os
17 mkdir -p $orthogroups_fasta_dir && 17 #set orthogroups_src_dir = $os.path.join('geneFamilyClassification_dir', 'orthogroups_fasta')
18 #set orthogroups_dest_dir = $options_type.create_orthogroup_cond.coding_sequences.extra_files_path
19 mkdir -p $orthogroups_dest_dir &&
18 #end if 20 #end if
19 GeneFamilyClassifier 21 GeneFamilyClassifier
20 --proteins "$input" 22 --proteins "$input"
21 --scaffold "$scaffold" 23 --scaffold "$scaffold"
22 --method $method 24 --method $method
32 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences" 34 --coding_sequences "$options_type.create_orthogroup_cond.coding_sequences"
33 #end if 35 #end if
34 #end if 36 #end if
35 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 37 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
36 --num_threads \${GALAXY_SLOTS:-4} 38 --num_threads \${GALAXY_SLOTS:-4}
37 #if str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes': 39 #if str($options_type.options_type_selector) == 'advanced' and str($options_type.create_orthogroup_cond.create_orthogroup) == 'yes':
38 && cp "./geneFamilyClassification_dir/orthogroups_fasta/*" $orthogroups_fasta_dir 40 && mv $orthogroups_src_dir/* $orthogroups_dest_dir
39 #end if 41 #end if
40 ]]> 42 ]]>
41 </command> 43 </command>
42 <inputs> 44 <inputs>
43 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/> 45 <param name="input" format="fasta" type="data" label="Amino acids (proteins) sequences fasta file"/>