Mercurial > repos > iuc > samtools_coverage

comparison samtools_coverage.xml @ 5:ddbd49b892e5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/sam_to_bam commit c508c3af0f4121dcc38e0be63db00a604e997b8a
author iuc
date Thu, 19 Jun 2025 12:58:44 +0000
parents f4f7f632815d
children
comparison
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4:f4f7f632815d 5:ddbd49b892e5
98 <data name="output" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}" /> 98 <data name="output" format="tabular" from_work_dir="outfile" label="${tool.name} on ${on_string}" />
99 </outputs> 99 </outputs>
100 100
101 <tests> 101 <tests>
102 <test> 102 <test>
103 <param name="input" value="test_1.bam" ftype="bam" /> 103 <conditional name="condition_input">
104 <param name="input" value="test_1.bam" ftype="bam" />
105 </conditional>
104 <output name="output" file="results_1.tabular" ftype="tabular" /> 106 <output name="output" file="results_1.tabular" ftype="tabular" />
105 </test> 107 </test>
106 <test> 108 <test>
107 <param name="input" value="test_1.bam" ftype="bam" /> 109 <conditional name="condition_input">
108 <param name="histogram_select" value="yes" /> 110 <param name="input" value="test_1.bam" ftype="bam" />
109 <param name="n_bins" value="50" /> 111 </conditional>
112 <conditional name="condition_histogram">
113 <param name="histogram_select" value="yes" />
114 <param name="n_bins" value="50" />
115 </conditional>
110 <output name="output" file="results_2.txt" ftype="tabular" /> 116 <output name="output" file="results_2.txt" ftype="tabular" />
111 </test> 117 </test>
112 <test> 118 <test>
113 <param name="input_pooling" value="Yes" /> 119 <conditional name="condition_input">
114 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> 120 <param name="input_pooling" value="Yes" />
115 <param name="histogram_select" value="yes" /> 121 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
116 <param name="n_bins" value="100" /> 122 </conditional>
123 <conditional name="condition_histogram">
124 <param name="histogram_select" value="yes" />
125 <param name="n_bins" value="100" />
126 </conditional>
117 <output name="output" file="results_3.txt" ftype="tabular" /> 127 <output name="output" file="results_3.txt" ftype="tabular" />
118 </test> 128 </test>
119 <test><!-- test with a region (requires index) --> 129 <test><!-- test with a region (requires index) -->
120 <param name="input" value="test_1.bam" ftype="bam" /> 130 <conditional name="condition_input">
121 <param name="region" value="ref1" /> 131 <param name="input" value="test_1.bam" ftype="bam" />
132 </conditional>
133 <section name="additional_options">
134 <param name="region" value="ref1" />
135 </section>
122 <output name="output" file="results_4.tabular" ftype="tabular" /> 136 <output name="output" file="results_4.tabular" ftype="tabular" />
123 </test> 137 </test>
124 <test><!-- test with pooled BAMs and a region --> 138 <test><!-- test with pooled BAMs and a region -->
125 <param name="input_pooling" value="Yes" /> 139 <conditional name="condition_input">
126 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" /> 140 <param name="input_pooling" value="Yes" />
127 <param name="region" value="ref2" /> 141 <param name="input_bams" value="test_1.bam,test_2.bam" ftype="bam" />
142 </conditional>
143 <section name="additional_options">
144 <param name="region" value="ref2" />
145 </section>
128 <output name="output" file="results_5.tabular" ftype="tabular" /> 146 <output name="output" file="results_5.tabular" ftype="tabular" />
129 </test> 147 </test>
130 </tests> 148 </tests>
131 <help><![CDATA[ 149 <help><![CDATA[
132 **What it does** 150 **What it does**