Mercurial > repos > miller-lab > genome_diversity
diff make_phylip.xml @ 35:ea52b23f1141
Bug fixes for Draw variants, Phylip, and gd_d_tools
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Wed, 20 Nov 2013 13:46:10 -0500 |
parents | a631c2f6d913 |
children | 51cd0307fb70 |
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--- a/make_phylip.xml Mon Sep 23 13:37:19 2013 -0400 +++ b/make_phylip.xml Wed Nov 20 13:46:10 2013 -0500 @@ -1,19 +1,19 @@ -<tool id="gd_make_phylip" name="Phylip" version="1.0.0" force_history_refresh="True"> +<tool id="gd_make_phylip" name="Phylip" version="1.1.0" force_history_refresh="True"> <description>: prepare data for phylogenetic analysis</description> <command interpreter="python"> #set $zero_based = 1 - #set $gen_chrClmn = int($input.metadata.scaffold) - $zero_based - #set $gen_posClmn = int($input.metadata.pos) - $zero_based + #set $gen_chrClmn = int($input.metadata.ref) - $zero_based + #set $gen_posClmn = int($input.metadata.rPos) - $zero_based #set $gen_refClmn = int($input.metadata.pos) - $zero_based + 1 #set $gen_altrClmn = int($input.metadata.pos) - $zero_based + 2 - make_phylip.py '--altrClmn=$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' + 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' #if $input_type.choice == '0' - #set $cov_chrClmn = int($input_type.coverage_input.metadata.scaffold) - $zero_based - #set $cov_posClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + #set $cov_chrClmn = int($input_type.coverage_input.metadata.ref) - $zero_based + #set $cov_posClmn = int($input_type.coverage_input.metadata.rPos) - $zero_based #set $cov_refClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 1 #set $cov_altrClmn = int($input_type.coverage_input.metadata.pos) - $zero_based + 2 - '--altrClmnCvrg=$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=$cov_refClmn' + '--altrClmnCvrg=$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' #else if $input_type.choice == '1' #set $fchrClmn = int($input_type.annotation_input.metadata.chromCol) - $zero_based #set $strandClmn = int($input_type.annotation_input.metadata.strandCol) - $zero_based @@ -28,6 +28,8 @@ #end if </command> + <code file="make_phylip_hooks.py" /> + <inputs> <param name="input" type="data" format="gd_genotype,gd_snp" label="Genotype/SNP dataset"> <validator type="metadata" check="scaffold" message="scaffold missing" />