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comparison samtools_view.xml @ 11:df20f1fd453f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_view commit 1d2666cfe206ef538fd811dbccaec2e8f3c6f7f0"
author iuc
date Wed, 13 Oct 2021 13:11:51 +0000
parents 350bbc5c2ffd
children c370440f901e
comparison
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10:350bbc5c2ffd 11:df20f1fd453f
1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="samtools_view" name="Samtools view" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description> 2 <description>- reformat, filter, or subsample SAM, BAM or CRAM</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 <token name="@REF_DATA@"> 5 <token name="@REF_DATA@">
6 ## additional reference data 6 ## additional reference data
311 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set"> 311 <param name="exclusive_filter_all" argument="-G" type="select" multiple="True" label="Exclude reads with all of the following flags set">
312 <expand macro="flag_options" /> 312 <expand macro="flag_options" />
313 </param> 313 </param>
314 <param argument="--tag" type="text" optional="true" label="Filter by tag" help="Only include reads with tag STR1 and associated value STR2. Write in the format STR1:STR2 (see help for more details)." /> 314 <param argument="--tag" type="text" optional="true" label="Filter by tag" help="Only include reads with tag STR1 and associated value STR2. Write in the format STR1:STR2 (see help for more details)." />
315 <!-- TODO implement -D --> 315 <!-- TODO implement -D -->
316 <param argument="--qname-file" format="text" optional="true" type="data" label="Filter by readnames" help="Only output alignments with readnames that are listed in this file." /> 316 <param argument="--qname-file" format="txt" optional="true" type="data" label="Filter by readnames" help="Only output alignments with readnames that are listed in this file." />
317 </section> 317 </section>
318 <section name="subsample_config" title="Configure subsampling" expanded="false"> 318 <section name="subsample_config" title="Configure subsampling" expanded="false">
319 <conditional name="subsampling_mode"> 319 <conditional name="subsampling_mode">
320 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment"> 320 <param name="select_subsample" type="select" argument="-s" label="Subsample alignment">
321 <option value="fraction">Specify a downsampling factor</option> 321 <option value="fraction">Specify a downsampling factor</option>