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comparison tetyper.xml @ 1:36093854bfc7 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 4030df6d601b303f2ac8ee977a469bf3ee0e4992"
author iuc
date Sat, 18 Jan 2020 15:04:39 -0500
parents 8bc80c2a15b3
children edcf603bedfd
comparison
equal deleted inserted replaced
0:8bc80c2a15b3 1:36093854bfc7
1 <tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy1">
2 <description>Transposable Element Typer</description> 2 <description>Transposable Element Typer</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.1</token> 4 <token name="@TOOL_VERSION@">1.1</token>
5 </macros> 5 </macros>
6 <requirements> 6 <requirements>
19 --flank_len '${flank_length}' 19 --flank_len '${flank_length}'
20 --min_reads '${min_reads}' 20 --min_reads '${min_reads}'
21 --min_each_strand '${min_each_strand}' 21 --min_each_strand '${min_each_strand}'
22 --min_mapped_len '${min_mapped_len}' 22 --min_mapped_len '${min_mapped_len}'
23 --min_qual '${min_qual}' 23 --min_qual '${min_qual}'
24 #if $snp_profiles 24 #if str( $snp_profiles_source.snp_profiles_source_selector ) == "tool_data_table":
25 --snp_profiles '${snp_profiles}' 25 --snp_profiles '$snp_profiles_source.snp_profiles.fields.path'
26 #elif str( $snp_profiles_source.snp_profiles_source_selector ) == 'history':
27 --snp_profiles '$snp_profiles_source.snp_profiles'
26 #end if 28 #end if
27 #if $struct_profiles 29 #if str( $struct_profiles_source.struct_profiles_source_selector ) == "tool_data_table":
28 --struct_profiles '${struct_profiles}' 30 --struct_profiles '$struct_profiles_source.struct_profiles.fields.path'
31 #elif str( $struct_profiles_source.struct_profiles_source_selector ) == 'history':
32 --struct_profiles '$struct_profiles_source.struct_profiles'
29 #end if 33 #end if
30 --outprefix output 34 --outprefix output
31 ]]> 35 ]]>
32 </command> 36 </command>
33 <inputs> 37 <inputs>
42 <when value="paired"> 46 <when value="paired">
43 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/> 47 <param format="fastq,fastq.gz" name="forward_input" type="data" label="Forward strand" help="FASTQ dataset"/>
44 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/> 48 <param format="fastq,fastq.gz" name="reverse_input" type="data" label="Reverse strand" help="FASTQ dataset"/>
45 </when> 49 </when>
46 </conditional> 50 </conditional>
51 <conditional name="snp_profiles_source">
52 <param name="snp_profiles_source_selector" type="select"
53 label="Select a SNP profile from your history or use one from a tool data table?">
54 <option value="No" selected="true">No SNP profile</option>
55 <option value="tool_data_table">SNP profile from tool data table</option>
56 <option value="history">SNP profile from history</option>
57 </param>
58 <when value="No"/>
59 <when value="tool_data_table">
60 <param name="snp_profiles" type="select" format="tabular" label="SNP Profile">
61 <options from_data_table="tetyper_snp_profiles">
62 <validator type="no_options" message="No TETyper SNP profiles are available" />
63 </options>
64 </param>
65 </when>
66 <when value="history">
67 <param name="snp_profiles" type="data" format="tabular" label="SNP Profile"
68 help="A three-column tabular file with SNP profile definitions"/>
69 </when>
70 </conditional>
71 <conditional name="struct_profiles_source">
72 <param name="struct_profiles_source_selector" type="select"
73 label="Select a structural variant profile from your history or use one from a tool data table?">
74 <option value="No" selected="true">No structural variant profile</option>
75 <option value="tool_data_table">Structural variant profile from tool data table</option>
76 <option value="history" selected="true">Structural variant profile from history</option>
77 </param>
78 <when value="No"/>
79 <when value="tool_data_table">
80 <param name="struct_profiles" type="select" format="tabular"
81 label="Structural Variant Profile">
82 <options from_data_table="tetyper_struct_profiles">
83 <validator type="no_options" message="No TETyper structural variant profiles are available" />
84 </options>
85 </param>
86 </when>
87 <when value="history">
88 <param name="struct_profiles" type="data" format="tabular"
89 label="Structural Variant Profile"
90 help="A two-column tabular file with structural variant profile definitions"/>
91 </when>
92 </conditional>
47 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/> 93 <param name="reference" type="data" format="fasta" label="Transposable Element Reference"/>
48 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/> 94 <param name="flank_length" type="integer" min="4" value="5" max="16" label="Flank Length" help="Length of flanking region to extract."/>
49 <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."/> 95 <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."/>
50 <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/> 96 <param name="min_each_strand" type="integer" min="1" value="1" max="100" label="Minimum Reads (each strand)" help="Minimum read number for each strand for including a specific flanking sequence."/>
51 <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/> 97 <param name="min_mapped_len" type="integer" min="8" value="30" max="100" label="Minimum Mapped Length" help="Minimum length of mapping for a read to be used in determining flanking sequences. Higher values are more robust to spurious mapping. Lower values will recover more reads."/>
52 <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." /> 98 <param name="min_qual" type="integer" min="0" value="10" max="100" label="Minimum quality" help="Minimum quality value across extracted flanking sequence." />
53 <param name="snp_profiles" type="data" format="text" label="SNP Profiles" optional="true" />
54 <param name="struct_profiles" type="data" format="text" label="Structural Variant Profiles" optional="true" />
55 <param name="include_log" type="boolean" label="Include log in output"/> 99 <param name="include_log" type="boolean" label="Include log in output"/>
56 </inputs> 100 </inputs>
57 <outputs> 101 <outputs>
58 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/> 102 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
59 <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/> 103 <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>
78 <conditional name="collection_paired"> 122 <conditional name="collection_paired">
79 <param name="selector" value="paired" /> 123 <param name="selector" value="paired" />
80 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" /> 124 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
81 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" /> 125 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
82 </conditional> 126 </conditional>
83 <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" /> 127 <conditional name="snp_profiles_source">
84 <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" /> 128 <param name="snp_profiles_source_selector" value="history" />
129 <param name="snp_profiles" value="Tn4401b_snp_profiles.txt" />
130 </conditional>
131 <conditional name="struct_profiles_source">
132 <param name="struct_profiles_source_selector" value="history" />
133 <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
134 </conditional>
135 <output name="summary" file="output_summary_2.txt" />
136 </test>
137 <test>
138 <param name="reference" value="Tn4401b-1.fasta" />
139 <conditional name="collection_paired">
140 <param name="selector" value="paired" />
141 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
142 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
143 </conditional>
144 <conditional name="snp_profiles_source">
145 <param name="snp_profiles_source_selector" value="tool_data_table" />
146 <param name="snp_profiles" value="Tn4401b_snp_profiles" />
147 </conditional>
148 <conditional name="struct_profiles_source">
149 <param name="struct_profiles_source_selector" value="tool_data_table" />
150 <param name="struct_profiles" value="Tn4401b_struct_profiles" />
151 </conditional>
85 <output name="summary" file="output_summary_2.txt" /> 152 <output name="summary" file="output_summary_2.txt" />
86 </test> 153 </test>
87 </tests> 154 </tests>
88 <help> 155 <help>
89 <![CDATA[ 156 <![CDATA[