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comparison bamtools.xml @ 7:ddb22028b552 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools commit 862f05b5053f55def8007194a702019418697cb5
author iuc
date Fri, 13 Jan 2023 12:17:31 +0000
parents e4490b16f0d7
children 970e6333f07e
comparison
equal deleted inserted replaced
6:e4490b16f0d7 7:ddb22028b552
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool id="bamtools" name="Convert, Merge, Randomize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> 2 <tool id="bamtools" name="Operate on and transform BAM" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
3 <description>BAM datasets and perform other transformations</description> 3 <description>datasets in various ways</description>
4 <macros> 4 <macros>
5 <import>macros.xml</import> 5 <import>macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"> 7 <expand macro="requirements">
8 <requirement type="package" version="1.16.1">samtools</requirement> 8 <requirement type="package" version="1.16.1">samtools</requirement>
144 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" /> 144 <when input="analysis_type.format_type.format_type_selector" value="bed" format="bed" />
145 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" /> 145 <when input="analysis_type.format_type.format_type_selector" value="fasta" format="fasta" />
146 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" /> 146 <when input="analysis_type.format_type.format_type_selector" value="fastq" format="fastq" />
147 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" /> 147 <when input="analysis_type.format_type.format_type_selector" value="sam" format="sam" />
148 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" /> 148 <when input="analysis_type.format_type.format_type_selector" value="pileup" format="pileup" />
149 <when input="analysis_type.format_type.format_type_selector" value="json" format="json" />
149 <when input="analysis_type.analysis_type_selector" value="count" format="tabular" /> 150 <when input="analysis_type.analysis_type_selector" value="count" format="tabular" />
150 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" /> 151 <when input="analysis_type.analysis_type_selector" value="coverage" format="tabular" />
151 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" /> 152 <when input="analysis_type.analysis_type_selector" value="merge" format="bam" />
152 <when input="analysis_type.analysis_type_selector" value="random" format="bam" /> 153 <when input="analysis_type.analysis_type_selector" value="random" format="bam" />
153 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" /> 154 <when input="analysis_type.analysis_type_selector" value="revert" format="bam" />
190 191
191 ----- 192 -----
192 193
193 **Convert** 194 **Convert**
194 195
195 Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either 196 Converts BAM dataset(s) into BED, FASTA, FASTQ, JSON, Pileup, SAM, or YAML formats. Note that the conversion to the pileup format requires providing a reference sequence either cached on this Galaxy instance, or provided by you as a FASTA dataset from History.
196 cashed at this Galaxy instance, or provided by you as a FASTA dataset from History.
197 197
198 ----- 198 -----
199 199
200 **Count** 200 **Count**
201 201
202 Counts a number of alignments in a BAM dataset(s). 202 Counts the number of alignments in a BAM dataset(s).
203 203
204 ----- 204 -----
205 205
206 **Coverage** 206 **Coverage**
207 207
209 209
210 ----- 210 -----
211 211
212 **Header** 212 **Header**
213 213
214 Prints header from a BAM dataset(s). 214 Prints the header of a BAM dataset.
215 215
216 ------ 216 ------
217 217
218 **Merge** 218 **Merge**
219 219
220 Merges multiple BAM datasets into a single one. Obviously, you need to select multiple BAMs as input, which is done by pressing the "**Add new BAM dataset(s) to filter**" button. 220 Merges multiple BAM datasets into a single one.
221 221
222 ------ 222 ------
223 223
224 **Random** 224 **Random**
225 225