Mercurial > repos > bgruening > deeptools_alignmentsieve

comparison alignmentSieve.xml @ 9:5e3816edfd1b draft default tip

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planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 810c1359b884661d3f5c7372be0f0f88c859a3b9
author bgruening
date Thu, 01 Jun 2023 10:13:21 +0000
parents 28b2aa3ac6a6
children
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8:df2ed8fd1f50 9:5e3816edfd1b
1 <tool id="deeptools_alignmentsieve" name="alignmentsieve" version="@WRAPPER_VERSION@.0"> 1 <tool id="deeptools_alignmentsieve" name="alignmentsieve" version="@TOOL_VERSION@+galaxy0" profile="@GALAXY_VERSION@">
2 <description>Filter BAM/CRAM files according to specified parameters</description> 2 <description>Filter BAM/CRAM files according to specified parameters</description>
3 <macros> 3 <macros>
4 <token name="@BINARY@">alignmentSieve</token> 4 <token name="@BINARY@">alignmentSieve</token>
5 <import>deepTools_macros.xml</import> 5 <import>deepTools_macros.xml</import>
6 </macros> 6 </macros>
134 <tests> 134 <tests>
135 <test> 135 <test>
136 <param name="bamfile" value="paired_chr2L.bam" ftype="bam" /> 136 <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />
137 <param name="minMappingQuality" value="10" /> 137 <param name="minMappingQuality" value="10" />
138 <param name="filterMetrics" value="True" /> 138 <param name="filterMetrics" value="True" />
139 <output name="outFile" file="alignmentSieve.bam" ftype="bam" /> 139 <output name="outFile" file="alignmentSieve.bam" ftype="bam" lines_diff="1" />
140 <output name="filterMetricsFile" file="alignmentSieve.txt" ftype="tabular" /> 140 <output name="filterMetricsFile" file="alignmentSieve.txt" ftype="tabular" />
141 </test> 141 </test>
142 <test> 142 <test>
143 <param name="bamfile" value="paired_chr2L.bam" ftype="bam" /> 143 <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />
144 <param name="minMappingQuality" value="10" /> 144 <param name="minMappingQuality" value="10" />
148 </test> 148 </test>
149 <test> 149 <test>
150 <param name="bamfile" value="paired_chr2L.bam" ftype="bam" /> 150 <param name="bamfile" value="paired_chr2L.bam" ftype="bam" />
151 <param name="minMappingQuality" value="10" /> 151 <param name="minMappingQuality" value="10" />
152 <param name="shift" value="1 -2 3 -4" /> 152 <param name="shift" value="1 -2 3 -4" />
153 <output name="outFile" file="alignmentSieve2.bam" ftype="bam" /> 153 <output name="outFile" file="alignmentSieve2.bam" ftype="bam" lines_diff="2" />
154 </test> 154 </test>
155 <test> 155 <test>
156 <param name="bamfile" value="paired_chr2L.cram" ftype="cram" /> 156 <param name="bamfile" value="paired_chr2L.cram" ftype="cram" />
157 <param name="minMappingQuality" value="10" /> 157 <param name="minMappingQuality" value="10" />
158 <param name="shift" value="1 -2 3 -4" /> 158 <param name="shift" value="1 -2 3 -4" />
159 <output name="outFile" file="alignmentSieve3.bam" ftype="bam" /> 159 <output name="outFile" file="alignmentSieve3.bam" ftype="bam" lines_diff="2" />
160 </test> 160 </test>
161 </tests> 161 </tests>
162 162
163 <help> 163 <help>
164 <![CDATA[ 164 <![CDATA[