Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 3:fd6773b7bb3f draft

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Uploaded
author greg
date Wed, 04 Jan 2017 09:40:42 -0500
parents 56ff8d706414
children 37b56c1befaa
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2:56ff8d706414 3:fd6773b7bb3f
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 #import os
16 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
17 #set dest_dir = $output.extra_files_path
18 mkdir -p $dest_dir &&
15 PhylogenomicsAnalysis 19 PhylogenomicsAnalysis
16 --orthogroup_faa "$orthogroup_fna.extra_files_path" 20 --orthogroup_faa "$orthogroup_fna.extra_files_path"
17 --scaffold "$scaffold" 21 --scaffold "$scaffold"
18 --method $method 22 --method $method
19 #if str($options_type.options_type_selector) == 'advanced': 23 #if str($options_type.options_type_selector) == 'advanced':
59 #end if 63 #end if
60 #end if 64 #end if
61 #end if 65 #end if
62 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds" 66 --scaffold_dir "${GALAXY_DATA_INDEX_DIR}/plant_tribes/scaffolds"
63 --num_threads \${GALAXY_SLOTS:-4} && 67 --num_threads \${GALAXY_SLOTS:-4} &&
64 echo "Sequence alignments and corresponding phylogenies: `ls -l phylogenomicsAnalysis_dir/orthogroups_fasta | wc -l` files" > $output && 68 echo "Sequence alignments and corresponding phylogenies: `ls $src_dir | wc -l` files" > $output &&
65 ls phylogenomicsAnalysis_dir/orthogroups_fasta >> $output && 69 ls $src_dir >> $output &&
66 mv phylogenomicsAnalysis_dir/orthogroups_fasta/* $output.extra_files_path 70 mv $src_dir/* $dest_dir
67 ]]> 71 ]]>
68 </command> 72 </command>
69 <inputs> 73 <inputs>
70 <param name="orthogroup_fna" format="fasta" type="data" label="Gene family classification coding sequences (CDS) fasta file for which orthogroup fasta files were created"/> 74 <param name="orthogroup_fna" format="fasta" type="data" label="Gene family classification coding sequences (CDS) fasta file for which orthogroup fasta files were created"/>
71 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold"> 75 <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">