Mercurial > repos > greg > phylogenomics_analysis

comparison phylogenomics_analysis.xml @ 10:b3712c598290 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author greg
date Thu, 05 Jan 2017 14:56:53 -0500
parents 0ca4bba49038
children cac8a85418c2
comparison
equal deleted inserted replaced
9:0ca4bba49038 10:b3712c598290
12 </stdio> 12 </stdio>
13 <command> 13 <command>
14 <![CDATA[ 14 <![CDATA[
15 #import os 15 #import os
16 #import sys 16 #import sys
17 #if not os.exists($orthogroup_faa.extra_files_path): 17 #set invalid_input = "The selected input is not a valid list of sequences classified into gene family clusters, select another input."
18 print > sys.stderr("The select input is not a valid list of sequences classified into gene family clusters, select another input.") 18 #if not $os.path.exists($orthogroup_faa.extra_files_path):
19 print > $sys.stderr($invalid_input)
20 $sys.exit(1)
19 #end if 21 #end if
20 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta') 22 #set src_dir = $os.path.join('phylogenomicsAnalysis_dir', 'orthogroups_fasta')
23 #set num_orthogroup_faa = `ls $src_dir/*.faa | wc -l`
24 #if $num_orthogroup_faa == 0:
25 print > $sys.stderr($invalid_input)
26 $sys.exit(1)
27 #end if
28 #set num_orthogroup_fna = `ls $src_dir/*.fna | wc -l`
21 #set dest_dir = $output.extra_files_path 29 #set dest_dir = $output.extra_files_path
22 mkdir -p $dest_dir && 30 mkdir -p $dest_dir &&
23 PhylogenomicsAnalysis 31 PhylogenomicsAnalysis
24 --orthogroup_faa "$orthogroup_faa.extra_files_path" 32 --orthogroup_faa "$orthogroup_faa.extra_files_path"
25 --scaffold "$scaffold" 33 --scaffold "$scaffold"
41 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit 49 --pasta_iter_limit $multiple_sequence_alignments_option_cond.pasta_iter_limit
42 #end if 50 #end if
43 #if str($multiple_codon_alignments) == 'yes': 51 #if str($multiple_codon_alignments) == 'yes':
44 --codon_alignments 52 --codon_alignments
45 #if str($use_corresponding_coding_sequences) == 'yes': 53 #if str($use_corresponding_coding_sequences) == 'yes':
54 #if $num_orthogroup_fna == 0:
55 print > $sys.stderr("No corresponding coding sequences were generated for the selected input. You must not have selected 'Yes' for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected input.")
56 $sys.exit(1)
57 #end if
46 --orthogroup_fna 58 --orthogroup_fna
47 #end if 59 #end if
48 --sequence_type $multiple_codon_alignments_cond.sequence_type 60 --sequence_type $multiple_codon_alignments_cond.sequence_type
49 #end if 61 #end if
50 #end if 62 #end if
126 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference - (dna)"> 138 <param name="sequence_type" type="select" label="Sequence type used in the phylogenetic inference - (dna)">
127 <option value="protein" selected="true">Amino acid based</option> 139 <option value="protein" selected="true">Amino acid based</option>
128 <option value="dna">Nucleotide based</option> 140 <option value="dna">Nucleotide based</option>
129 </param> 141 </param>
130 <conditional name="use_corresponding_coding_sequences_cond"> 142 <conditional name="use_corresponding_coding_sequences_cond">
131 <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Ignored if 'No' was selected for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected 'sequences classified into gene family clusters' input above"> 143 <param name="use_corresponding_coding_sequences" type="select" label="Use corresponding coding sequences if available?" help="Must have selected 'Yes' for the 'Create corresponding coding sequences?' option in the GeneFamilyClassifier tool for the selected input above">
132 <option value="no" selected="true">No</option> 144 <option value="no" selected="true">No</option>
133 <option value="yes">Yes</option> 145 <option value="yes">Yes</option>
134 </param> 146 </param>
135 <when value="no" /> 147 <when value="no" />
136 <when value="yes" /> 148 <when value="yes" />