Mercurial > repos > iuc > umi_tools_dedup

comparison umi-tools_dedup.xml @ 18:362719583a9f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/umi_tools commit 11a7415c7f8a44a3f990080533c1de43a41d1e2e
author iuc
date Fri, 28 Feb 2025 20:39:27 +0000
parents b63f68b03f4a
children
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17:02bf280a89d0 18:362719583a9f
2 <description>Extract UMI from fastq files</description> 2 <description>Extract UMI from fastq files</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="bio_tools"/> 6 <expand macro="bio_tools"/>
7 <expand macro="requirements"> 7 <expand macro="requirements"/>
8 <requirement type="package" version="1.21">samtools</requirement>
9 </expand>
10 <command detect_errors="exit_code"><![CDATA[ 8 <command detect_errors="exit_code"><![CDATA[
11 @LINK_SAM_BAM_INPUT@ 9 @LINK_SAM_BAM_INPUT@
12 10
13 echo $input.ext && 11 echo $input.ext &&
14 umi_tools dedup 12 umi_tools dedup
109 <param name="method" value="unique" /> 107 <param name="method" value="unique" />
110 </section> 108 </section>
111 <output name="output" file="dedup_out4.bam" ftype="bam" lines_diff="2"/> 109 <output name="output" file="dedup_out4.bam" ftype="bam" lines_diff="2"/>
112 </test> 110 </test>
113 <test expect_num_outputs="1"> 111 <test expect_num_outputs="1">
114 <param name="input" value="group_in5.bam" ftype="bam" /> 112 <param name="input" value="group_in4.bam" ftype="bam" />
115 <section name="advanced"> 113 <section name="advanced">
116 <param name="random_seed" value="0" /> 114 <param name="random_seed" value="0" />
117 </section> 115 </section>
118 <conditional name="bc"> 116 <conditional name="bc">
119 <param name="extract_umi_method" value="read_id" /> 117 <param name="extract_umi_method" value="tag" />
120 <param name="umi_tag" value="BX" /> 118 <param name="umi_tag" value="BX" />
121 </conditional> 119 </conditional>
122 <section name="umi"> 120 <section name="umi">
123 <param name="method" value="cluster" /> 121 <param name="method" value="cluster" />
124 </section> 122 </section>
125 <output name="output" file="dedup_out5.bam" ftype="bam" lines_diff="2"/> 123 <output name="output" file="dedup_out5.bam" ftype="bam" lines_diff="2"/>
126 </test> 124 </test>
127 <test expect_num_outputs="1"> 125 <test expect_num_outputs="1">
128 <param name="input" value="group_in6.bam" ftype="bam" /> 126 <param name="input" value="group_in4.bam" ftype="bam" />
129 <section name="advanced"> 127 <section name="advanced">
130 <param name="random_seed" value="0" /> 128 <param name="random_seed" value="0" />
131 </section> 129 </section>
132 <conditional name="bc"> 130 <conditional name="bc">
133 <param name="extract_umi_method" value="read_id" /> 131 <param name="extract_umi_method" value="tag" />
134 <param name="umi_tag" value="BX" /> 132 <param name="umi_tag" value="BX" />
135 </conditional> 133 </conditional>
136 <section name="umi"> 134 <section name="umi">
137 <param name="method" value="directional" /> 135 <param name="method" value="directional" />
138 </section> 136 </section>
139 <output name="output" file="dedup_out6.bam" ftype="bam" lines_diff="2"/> 137 <output name="output" file="dedup_out6.bam" ftype="bam" lines_diff="2"/>
140 </test> 138 </test>
141 <test expect_num_outputs="5"> 139 <test expect_num_outputs="5">
142 <param name="input" value="group_in6.bam" ftype="bam" /> 140 <param name="input" value="group_in4.bam" ftype="bam" />
143 <section name="advanced"> 141 <section name="advanced">
144 <param name="random_seed" value="0" /> 142 <param name="random_seed" value="0" />
145 </section> 143 </section>
146 <conditional name="bc"> 144 <conditional name="bc">
147 <param name="extract_umi_method" value="read_id" /> 145 <param name="extract_umi_method" value="tag" />
148 <param name="umi_tag" value="BX" /> 146 <param name="umi_tag" value="BX" />
149 </conditional> 147 </conditional>
150 <section name="umi"> 148 <section name="umi">
151 <param name="method" value="directional" /> 149 <param name="method" value="directional" />
152 </section> 150 </section>