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comparison gene_family_aligner.xml @ 56:f782812220e1 draft

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author greg
date Thu, 05 Oct 2017 14:14:56 -0400
parents 259901da9ed5
children 9c9c2ea494ba
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55:259901da9ed5 56:f782812220e1
1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0"> 1 <tool id="plant_tribes_gene_family_aligner" name="GeneFamilyAligner" version="@WRAPPER_VERSION@.3.0">
2 <description>aligns integrated orthologous gene family clusters</description> 2 <description>aligns integrated orthologous gene family clusters</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements_gene_family_aligner" /> 6 <requirements>
7 <requirement type="package" version="1.0.3">plant_tribes_gene_family_aligner</requirement>
8 </requirements>
7 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
8 #set alignment_method = $alignment_method_cond.alignment_method 10 #set alignment_method = $alignment_method_cond.alignment_method
9 #set input_dir = 'input_dir' 11 #set input_dir = 'input_dir'
10 mkdir $input_dir && 12 mkdir $input_dir &&
11 #for $i in $input: 13 #for $i in $input:
46 #end if 48 #end if
47 #end if 49 #end if
48 ]]></command> 50 ]]></command>
49 <inputs> 51 <inputs>
50 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup fasta files" /> 52 <param name="input" format="fasta" type="data_collection" collection_type="list" label="Proteins orthogroup fasta files" />
51 <expand macro="cond_alignment_method" /> 53 <conditional name="alignment_method_cond">
52 <expand macro="param_codon_alignments" /> 54 <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">
53 <expand macro="cond_remove_gappy_sequences" /> 55 <option value="mafft" selected="true">MAFFT</option>
56 <option value="pasta">PASTA</option>
57 </param>
58 <when value="mafft" />
59 <when value="pasta">
60 <param name="pasta_iter_limit" type="integer" value="3" min="1" label="PASTA iteration limit" />
61 </when>
62 </conditional>
63 <param name="codon_alignments" type="select" label="Codon alignments">
64 <option value="yes" selected="true">Yes</option>
65 <option value="no">No</option>
66 </param>
67 <conditional name="remove_gappy_sequences_cond">
68 <param name="remove_gappy_sequences" type="select" label="Alignment post-processing configuration">
69 <option value="no" selected="true">No</option>
70 <option value="yes">Yes</option>
71 </param>
72 <when value="no" />
73 <when value="yes">
74 <conditional name="trim_type_cond">
75 <param name="trim_type" type="select" label="Trimming method">
76 <option value="gap_trimming" selected="true">Gap score based trimming</option>
77 <option value="automated_trimming">Automated heuristic trimming</option>
78 </param>
79 <when value="gap_trimming">
80 <param name="gap_trimming" type="float" optional="true" min="0" max="1.0" label="Gap score" />
81 </when>
82 <when value="automated_trimming" />
83 </conditional>
84 <conditional name="remove_sequences_with_gaps_cond">
85 <param name="remove_sequences_with_gaps" type="select" label="Remove sequences">
86 <option value="no" selected="true">No</option>
87 <option value="yes">Yes</option>
88 </param>
89 <when value="no" />
90 <when value="yes">
91 <param name="remove_sequences_with_gaps_of" type="float" optional="true" min="0" max="1" label="Coverage score" />
92 <param name="iterative_realignment" type="integer" optional="true" min="0" label="Realignment iteration limit" />
93 </when>
94 </conditional>
95 <param name="output_pristine_alignments" type="select" display="radio" label="Output non-filtered, non-trimmed alignemnts?" help="In addition to trimmed/filtered alignments">
96 <option value="no" selected="true">No</option>
97 <option value="yes">Yes</option>
98 </param>
99 </when>
100 </conditional>
54 </inputs> 101 </inputs>
55 <outputs> 102 <outputs>
56 <collection name="primary_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}"> 103 <collection name="primary_faa" type="list" label="${tool.name} (primary orthogroup protein alignments) on ${on_string}">
57 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_faa" format="fasta" /> 104 <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_aln_faa" format="fasta" />
58 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter> 105 <filter>remove_gappy_sequences_cond['remove_gappy_sequences'] == 'no'</filter>