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comparison tetyper.xml @ 3:2ccf19849796 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tetyper commit 56cee5183887f0b50dadaae1a5cc5bc80c290bdd
author iuc
date Sun, 15 Dec 2024 09:07:56 +0000
parents 287335d65198
children
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2:287335d65198 3:2ccf19849796
1 <tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy1"> 1 <tool id="tetyper" name="TETyper" version="@TOOL_VERSION@+galaxy2" profile="23.1">
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>
103 <outputs> 103 <outputs>
104 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/> 104 <data name="summary" format="tabular" from_work_dir="output_summary.txt" label="${tool.name} on ${on_string}: summary"/>
105 <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/> 105 <data name="snps" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: SNPs"/>
106 <data name="blast" format="tabular" from_work_dir="output_blast.txt" label="${tool.name} on ${on_string}: BLAST alignment"/> 106 <data name="blast" format="tabular" from_work_dir="output_blast.txt" label="${tool.name} on ${on_string}: BLAST alignment"/>
107 <data name="alignment" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: BWA alignment"/> 107 <data name="alignment" format="bam" from_work_dir="output.bam" label="${tool.name} on ${on_string}: BWA alignment"/>
108 <data name="log" format="text" from_work_dir="output.log" label="${tool.name} on ${on_string}: log"> 108 <data name="log" format="txt" from_work_dir="output.log" label="${tool.name} on ${on_string}: log">
109 <filter>include_log</filter> 109 <filter>include_log</filter>
110 </data> 110 </data>
111 </outputs> 111 </outputs>
112 <tests> 112 <tests>
113 <test> 113 <test expect_num_outputs="4">
114 <param name="reference" value="Tn4401b-1.fasta" /> 114 <param name="reference" value="Tn4401b-1.fasta" />
115 <conditional name="collection_paired"> 115 <conditional name="collection_paired">
116 <param name="selector" value="paired" /> 116 <param name="selector" value="paired" />
117 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" /> 117 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
118 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" /> 118 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
119 </conditional> 119 </conditional>
120 <output name="summary" file="output_summary_1.txt" /> 120 <output name="summary" file="output_summary_1.txt" />
121 </test> 121 </test>
122 <test> 122 <test expect_num_outputs="4">
123 <param name="reference" value="Tn4401b-1.fasta" /> 123 <param name="reference" value="Tn4401b-1.fasta" />
124 <conditional name="collection_paired"> 124 <conditional name="collection_paired">
125 <param name="selector" value="paired" /> 125 <param name="selector" value="paired" />
126 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" /> 126 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
127 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" /> 127 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
134 <param name="struct_profiles_source_selector" value="history" /> 134 <param name="struct_profiles_source_selector" value="history" />
135 <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" /> 135 <param name="struct_profiles" value="Tn4401b_struct_profiles.txt" />
136 </conditional> 136 </conditional>
137 <output name="summary" file="output_summary_2.txt" /> 137 <output name="summary" file="output_summary_2.txt" />
138 </test> 138 </test>
139 <test> 139 <test expect_num_outputs="5">
140 <param name="reference" value="Tn4401b-1.fasta" /> 140 <param name="reference" value="Tn4401b-1.fasta" />
141 <conditional name="collection_paired"> 141 <conditional name="collection_paired">
142 <param name="selector" value="paired" /> 142 <param name="selector" value="paired" />
143 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" /> 143 <param name="forward_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_1.fastq" />
144 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" /> 144 <param name="reverse_input" value="ERR1911133_Tn4401b-1_mapped_subsampled_2.fastq" />
149 </conditional> 149 </conditional>
150 <conditional name="struct_profiles_source"> 150 <conditional name="struct_profiles_source">
151 <param name="struct_profiles_source_selector" value="tool_data_table" /> 151 <param name="struct_profiles_source_selector" value="tool_data_table" />
152 <param name="struct_profiles" value="Tn4401b_struct_profiles" /> 152 <param name="struct_profiles" value="Tn4401b_struct_profiles" />
153 </conditional> 153 </conditional>
154 <param name="include_log" value="true"/>
154 <output name="summary" file="output_summary_2.txt" /> 155 <output name="summary" file="output_summary_2.txt" />
156 <output name="snps">
157 <assert_contents>
158 <has_size min="1"/>
159 </assert_contents>
160 </output>
161 <output name="blast">
162 <assert_contents>
163 <has_n_lines n="2"/>
164 <has_n_columns n="12"/>
165 </assert_contents>
166 </output>
167 <output name="alignment">
168 <assert_contents>
169 <has_size min="1"/>
170 </assert_contents>
171 </output>
172 <output name="log">
173 <assert_contents>
174 <has_text text="Final output written to: output_summary.txt"/>
175 </assert_contents>
176 </output>
155 </test> 177 </test>
156 </tests> 178 </tests>
157 <help> 179 <help>
158 <![CDATA[ 180 <![CDATA[
159 **What it does** 181 **What it does**