Mercurial > repos > miller-lab > genome_diversity
diff phylogenetic_tree.xml @ 24:248b06e86022
Added gd_genotype datatype. Modified tools to support new datatype.
author | Richard Burhans <burhans@bx.psu.edu> |
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date | Tue, 28 May 2013 16:24:19 -0400 |
parents | f04f40a36cc8 |
children | 8997f2ca8c7a |
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--- a/phylogenetic_tree.xml Wed May 22 15:58:18 2013 -0400 +++ b/phylogenetic_tree.xml Tue May 28 16:24:19 2013 -0400 @@ -1,26 +1,41 @@ -<tool id="gd_phylogenetic_tree" name="Phylogenetic Tree" version="1.0.0"> +<tool id="gd_phylogenetic_tree" name="Phylogenetic Tree" version="1.1.0"> <description>: Show genetic relationships among individuals</description> <command interpreter="python"> - phylogenetic_tree.py "$input" + phylogenetic_tree.py "$input" "$output" "$output.files_path" + + #if $input_type.choice == '0' + "gd_snp" + #if $input_type.data_source.choice == '0' + "sequence_coverage" + "$input_type.data_source.minimum_coverage" + "$input_type.data_source.minimum_quality" + #else if $input_type.data_source.choice == '1' + "estimated_genotype" + #end if + #else if $input_type.choice == '1' + "gd_genotype" + #end if + #if $individuals.choice == '0' "all_individuals" #else if $individuals.choice == '1' - "$p1_input" + "$individuals.p1_input" #end if - "$output" "$output.files_path" "$minimum_coverage" "$minimum_quality" + #if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0') "none" #else "$input.metadata.dbkey" #end if - "$data_source" + #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style]) #if $draw_tree_options == '' "" #else "-$draw_tree_options" #end if + #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns) #set $arg = '%s:%s' % ($individual_col, $individual_name) "$arg" @@ -28,7 +43,31 @@ </command> <inputs> - <param name="input" type="data" format="gd_snp" label="SNP dataset" /> + <conditional name="input_type"> + <param name="choice" type="select" format="integer" label="Input format"> + <option value="0" selected="true">gd_snp</option> + <option value="1">gd_genotype</option> + </param> + <when value="0"> + <param name="input" type="data" format="gd_snp" label="SNP dataset" /> + + <conditional name="data_source"> + <param name="choice" type="select" format="integer" label="Distance metric"> + <option value="0">sequence coverage</option> + <option value="1" selected="true">estimated genotype</option> + </param> + <when value="0"> + <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum SNP coverage" /> + <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum SNP quality" + help="Note: minimum coverage and minimum quality cannot both be 0" /> + </when> + <when value="1"/> + </conditional> + </when> + <when value="1"> + <param name="input" type="data" format="gd_genotype" label="Genotype dataset" /> + </when> + </conditional> <conditional name="individuals"> <param name="choice" type="select" label="Compute for"> @@ -41,21 +80,11 @@ </when> </conditional> - <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum SNP coverage" /> - - <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum SNP quality" - help="Note: minimum coverage and minimum quality cannot both be 0" /> - <param name="include_reference" type="select" format="integer" label="Include reference sequence"> <option value="1" selected="true">Yes</option> <option value="0">No</option> </param> - <param name="data_source" type="select" format="integer" label="Distance metric"> - <option value="0" selected="true">sequence coverage</option> - <option value="1">estimated genotype</option> - </param> - <param name="branch_style" type="select" display="radio"> <label>Branch type</label> <option value="" selected="true">square</option> @@ -110,12 +139,13 @@ **Dataset formats** -The input dataset is in gd_snp_ format. +The input dataset is in gd_snp_ or gd_genotype_ format. The output is a composite dataset, containing the tree in both text (Newick_) and PostScript formats, as well as supplemental text information. (`Dataset missing?`_) .. _gd_snp: ./static/formatHelp.html#gd_snp +.. _gd_genotype: ./static/formatHelp.html#gd_genotype .. _Newick: http://evolution.genetics.washington.edu/phylip/newicktree.html .. _Dataset missing?: ./static/formatHelp.html