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comparison make_phylip.xml @ 35:ea52b23f1141

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Bug fixes for Draw variants, Phylip, and gd_d_tools
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 13:46:10 -0500
parents a631c2f6d913
children 51cd0307fb70
comparison
equal deleted inserted replaced
34:f739a296a339 35:ea52b23f1141
1 <tool id="gd_make_phylip" name="Phylip" version="1.0.0" force_history_refresh="True"> 1 <tool id="gd_make_phylip" name="Phylip" version="1.1.0" force_history_refresh="True">
2 <description>: prepare data for phylogenetic analysis</description> 2 <description>: prepare data for phylogenetic analysis</description>
3 3
4 <command interpreter="python"> 4 <command interpreter="python">
5 #set $zero_based = 1 5 #set $zero_based = 1
6 #set $gen_chrClmn = int($input.metadata.scaffold) - $zero_based 6 #set $gen_chrClmn = int($input.metadata.ref) - $zero_based
7 #set $gen_posClmn = int($input.metadata.pos) - $zero_based 7 #set $gen_posClmn = int($input.metadata.rPos) - $zero_based
8 #set $gen_refClmn = int($input.metadata.pos) - $zero_based + 1 8 #set $gen_refClmn = int($input.metadata.pos) - $zero_based + 1
9 #set $gen_altrClmn = int($input.metadata.pos) - $zero_based + 2 9 #set $gen_altrClmn = int($input.metadata.pos) - $zero_based + 2
10 make_phylip.py '--altrClmn=$gen_altrClmn' '--chrClmn=$gen_chrClmn' '--gd_indivs=$indivs_input' '--input=$input' '--output=$output1' '--output_id=$output1.id' '--output_dir=$__new_file_path__' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn' 10 make_phylip.py '--altrClmn=$gen_altrClmn' '--chrClmn=$gen_chrClmn' '--gd_indivs=$indivs_input' '--input=$input' '--input_type=$input.ext' '--output=$output1' '--output_id=$output1.id' '--output_dir=$__new_file_path__' '--posClmn=$gen_posClmn' '--refClmn=$gen_refClmn'
11 #if $input_type.choice == '0' 11 #if $input_type.choice == '0'
12 #set $cov_chrClmn = int($input_type.coverage_input.metadata.scaffold) - $zero_based 12 #set $cov_chrClmn = int($input_type.coverage_input.metadata.ref) - $zero_based
13 #set $cov_posClmn = int($input_type.coverage_input.metadata.pos) - $zero_based 13 #set $cov_posClmn = int($input_type.coverage_input.metadata.rPos) - $zero_based
14 #set $cov_refClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 1 14 #set $cov_refClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 1
15 #set $cov_altrClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 2 15 #set $cov_altrClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 2
16 '--altrClmnCvrg=$cov_altrClmn' '--chrClmnCvrg=$cov_chrClmn' '--cvrgTreshold=$input_type.coverage_threshold' '--gd_indivs_cover=$indivs_input' '--indvlsPrctTrshld=$input_type.indivs_threshold' '--inputCover=$input_type.coverage_input' '--posClmnCvrg=$cov_posClmn' '--refClmnCvrg=$cov_refClmn' 16 '--altrClmnCvrg=$cov_altrClmn' '--chrClmnCvrg=$cov_chrClmn' '--cvrgTreshold=$input_type.coverage_threshold' '--gd_indivs_cover=$indivs_input' '--indvlsPrctTrshld=$input_type.indivs_threshold' '--inputCover=$input_type.coverage_input' '--inputCover_type=$input_type.coverage_input.ext' '--posClmnCvrg=$cov_posClmn' '--refClmnCvrg=$cov_refClmn'
17 #else if $input_type.choice == '1' 17 #else if $input_type.choice == '1'
18 #set $fchrClmn = int($input_type.annotation_input.metadata.chromCol) - $zero_based 18 #set $fchrClmn = int($input_type.annotation_input.metadata.chromCol) - $zero_based
19 #set $strandClmn = int($input_type.annotation_input.metadata.strandCol) - $zero_based 19 #set $strandClmn = int($input_type.annotation_input.metadata.strandCol) - $zero_based
20 #set $geneNameClmn = int($input_type.annotation_input.metadata.nameCol) - $zero_based 20 #set $geneNameClmn = int($input_type.annotation_input.metadata.nameCol) - $zero_based
21 #set $txStartClmn = int(str($input_type.tx_start_col)) - $zero_based 21 #set $txStartClmn = int(str($input_type.tx_start_col)) - $zero_based
25 #set $startExsClmn = int(str($input_type.exs_start_col)) - $zero_based 25 #set $startExsClmn = int(str($input_type.exs_start_col)) - $zero_based
26 #set $endExsClmn = int(str($input_type.exs_end_col)) - $zero_based 26 #set $endExsClmn = int(str($input_type.exs_end_col)) - $zero_based
27 '--cdsEndClmn=$cdsEndClmn' '--cdsStartClmn=$cdsStartClmn' '--endExsClmn=$endExsClmn' '--fchrClmn=$fchrClmn' '--geneNameClmn=$geneNameClmn' '--gene_info=$input_type.annotation_input' '--sequence=$input_type.fasta_input' '--startExsClmn=$startExsClmn' '--strandClmn=$strandClmn' '--txEndClmn=$txEndClmn' '--txStartClmn=$txStartClmn' 27 '--cdsEndClmn=$cdsEndClmn' '--cdsStartClmn=$cdsStartClmn' '--endExsClmn=$endExsClmn' '--fchrClmn=$fchrClmn' '--geneNameClmn=$geneNameClmn' '--gene_info=$input_type.annotation_input' '--sequence=$input_type.fasta_input' '--startExsClmn=$startExsClmn' '--strandClmn=$strandClmn' '--txEndClmn=$txEndClmn' '--txStartClmn=$txStartClmn'
28 #end if 28 #end if
29 </command> 29 </command>
30
31 <code file="make_phylip_hooks.py" />
30 32
31 <inputs> 33 <inputs>
32 <param name="input" type="data" format="gd_genotype,gd_snp" label="Genotype/SNP dataset"> 34 <param name="input" type="data" format="gd_genotype,gd_snp" label="Genotype/SNP dataset">
33 <validator type="metadata" check="scaffold" message="scaffold missing" /> 35 <validator type="metadata" check="scaffold" message="scaffold missing" />
34 <validator type="metadata" check="pos" message="pos missing" /> 36 <validator type="metadata" check="pos" message="pos missing" />