Mercurial > repos > dfornika > tetyper

comparison tetyper.xml @ 25:98d8bd5e9058 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 876fbf06fbe477a12faf070b89e9a56137cd01d7-dirty"
author dfornika
date Mon, 13 Jan 2020 21:11:00 +0000
parents ea14ef930fc5
children
comparison
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24:ea14ef930fc5 25:98d8bd5e9058
53 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/> 53 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
54 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/> 54 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
55 </when> 55 </when>
56 </conditional> 56 </conditional>
57 <conditional name="snp_profiles_source"> 57 <conditional name="snp_profiles_source">
58 <param name="snp_profiles_source_selector" type="select" label="Select a SNP profile from your history or use one from a tool data table?"> 58 <param name="snp_profiles_source_selector" type="select" optional="true"
59 label="Select a SNP profile from your history or use one from a tool data table?">
59 <option value="tool_data_table">From tool data table</option> 60 <option value="tool_data_table">From tool data table</option>
60 <option value="history" selected="true">From history</option> 61 <option value="history" selected="true">From history</option>
61 </param> 62 </param>
62 <when value="tool_data_table"> 63 <when value="tool_data_table">
63 <param name="snp_profiles" type="select" format="tabular" optional="true"> 64 <param name="snp_profiles" type="select" format="tabular" label="SNP Profile">
64 <options from_data_table="tetyper_snp_profiles"> 65 <options from_data_table="tetyper_snp_profiles">
65 <validator type="no_options" message="No TETyper SNP profiles are available" /> 66 <validator type="no_options" message="No TETyper SNP profiles are available" />
66 </options> 67 </options>
67 </param> 68 </param>
68 </when> 69 </when>
69 <when value="history"> 70 <when value="history">
70 <param name="snp_profiles" type="data" format="tabular" label="SNP Profile" help="A three-column tabular file with SNP profile definitions" optional="true"/> 71 <param name="snp_profiles" type="data" format="tabular" label="SNP Profile"
72 help="A three-column tabular file with SNP profile definitions"/>
71 </when> 73 </when>
72 </conditional> 74 </conditional>
73 <conditional name="struct_profiles_source"> 75 <conditional name="struct_profiles_source">
74 <param name="struct_profiles_source_selector" type="select" label="Select a structural variant profile from your history or use one from a tool data table?"> 76 <param name="struct_profiles_source_selector" type="select" optional="true"
77 label="Select a structural variant profile from your history or use one from a tool data table?">
75 <option value="tool_data_table">From tool data table</option> 78 <option value="tool_data_table">From tool data table</option>
76 <option value="history" selected="true">From history</option> 79 <option value="history" selected="true">From history</option>
77 </param> 80 </param>
78 <when value="tool_data_table"> 81 <when value="tool_data_table">
79 <param name="struct_profiles" type="select" format="tabular" optional="true"> 82 <param name="struct_profiles" type="select" format="tabular"
83 label="Structural Variant Profile">
80 <options from_data_table="tetyper_struct_profiles"> 84 <options from_data_table="tetyper_struct_profiles">
81 <validator type="no_options" message="No TETyper structural variant profiles are available" /> 85 <validator type="no_options" message="No TETyper structural variant profiles are available" />
82 </options> 86 </options>
83 </param> 87 </param>
84 </when> 88 </when>
85 <when value="history"> 89 <when value="history">
86 <param name="struct_profiles" type="data" format="tabular" label="Structural Variant Profile" help="A two-column tabular file with structural variant profile definitions" optional="true"/> 90 <param name="struct_profiles" type="data" format="tabular"
91 label="Structural Variant Profile"
92 help="A two-column tabular file with structural variant profile definitions"/>
87 </when> 93 </when>
88 </conditional> 94 </conditional>
89 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/> 95 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
90 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/> 96 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
91 <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/> 97 <param name="min_reads" type="integer" min="1" value="10" max="100" label="Minimum Reads" help="Minimum read number for including a specific flanking sequence."/>