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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 958bbd9e30ae4d320f872f1ab5e1bacfb28b1a00"
author | iuc |
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date | Sat, 17 Apr 2021 10:41:00 +0000 |
parents | ee356d7a5518 |
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<?xml version="1.0"?> <tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>converts PacBio basecall format (bax.h5) into BAM</description> <macros> <token name="@TOOL_VERSION@">0.0.11</token> <token name="@VERSION_SUFFIX@">0</token> </macros> <edam_topics> <edam_topic>topic_3168</edam_topic> <!-- Topic - Laboratory techniques - Sequencing --> </edam_topics> <edam_operations> <edam_operation>operation_3434</edam_operation> <!-- Operation - Conversion --> </edam_operations> <requirements> <requirement type="package" version="@TOOL_VERSION@">bax2bam</requirement> </requirements> <version_command><![CDATA[bax2bam --version]]></version_command> <command detect_errors="exit_code"><![CDATA[ ## skipped -h/--help, --xml, -f, --output-xml, --ccs (see https://github.com/PacificBiosciences/pbbioconda/issues/215) ## run bax2bam #for $file in $files '$file' #end for -o 'output' $readtype #if $pulsefeatures --pulsefeatures=$pulsefeatures #end if $losslessframes $internal ]]></command> <inputs> <param name="files" type="data" format="h5" multiple="true" label="Select files" help="Should be from the same movie."/> <param name="readtype" type="select" label="Select output read type"> <option value="--hqregion">Hqregion</option> <option value="--polymeraseread">Polymeraseread</option> <option value="--subread">Subread</option> </param> <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in output BAM"> <option value="DeletionQV" selected="true">dq - DeletionQV</option> <option value="DeletionTag" selected="true">dt - DeletionTag</option> <option value="InsertionQV" selected="true">iq - InsertionQV</option> <option value="IPD" selected="true">ip - IPD</option> <option value="MergeQV" selected="true">mq - MergeQV</option> <option value="PulseWidth" selected="true">pw - PulseWidth</option> <option value="SubstitutionQV" selected="true">sq - SubstitutionQV</option> <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option> </param> <param argument="--losslessframes" type="boolean" truevalue="--losslessframes" falsevalue="" label="Store full, 16-bit IPD/PulseWidth data?" help="Instead of downsampled, 8-bit encoding."/> <param argument="--internal" type="boolean" truevalue="--internal" falsevalue="" checked="false" label="Output BAMs in internal mode?" help="Currently this indicates that non-sequencing ZMWs should be included in the output scraps BAM file, if applicable."/> </inputs> <outputs> <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${tool.name} on ${on_string}: Scraps"> <filter>readtype == '--subread'</filter> </data> <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${tool.name} on ${on_string}: Subreads"> <filter>readtype == '--subread'</filter> </data> <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${tool.name} on ${on_string}: Hqregions"> <filter>readtype == '--hqregion'</filter> </data> <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${tool.name} on ${on_string}: Lqregions"> <filter>readtype == '--hqregion'</filter> </data> <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: Polymerase"> <filter>readtype == '--polymeraseread'</filter> </data> </outputs> <tests> <!-- test data source https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ --> <!-- #1 subread, default --> <test expect_num_outputs="2"> <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> <param name="readtype" value="--subread"/> <output name="output_scrap"> <assert_contents> <has_size value="113578" delta="100"/> </assert_contents> </output> <output name="output_subread"> <assert_contents> <has_size value="242552" delta="100"/> </assert_contents> </output> </test> <!-- #2 hqregion, default --> <test expect_num_outputs="2"> <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> <param name="readtype" value="--hqregion"/> <output name="output_hqregion"> <assert_contents> <has_size value="232342" delta="100"/> </assert_contents> </output> <output name="output_hqregion"> <assert_contents> <has_size value="232342" delta="100"/> </assert_contents> </output> </test> <!-- #3 polymeraseread, default --> <test expect_num_outputs="1"> <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> <param name="readtype" value="--polymeraseread"/> <output name="output_polymeraseread"> <assert_contents> <has_size value="333195" delta="100"/> </assert_contents> </output> </test> <!-- #4 subread, custom --> <test expect_num_outputs="2"> <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> <param name="readtype" value="--subread"/> <param name="pulsefeatures" value="SubstitutionTag"/> <param name="losslessframes" value="true"/> <param name="internal" value="true"/> <output name="output_scrap"> <assert_contents> <has_size value="23497" delta="100"/> </assert_contents> </output> <output name="output_subread"> <assert_contents> <has_size value="45147" delta="100"/> </assert_contents> </output> </test> </tests> <help><![CDATA[ .. class:: infomark **What it does** bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format. **Input** - Sample files that should be from the same movie (bax.h5) **Output** - Converted sample (BAM) .. class:: infomark **References** More information can be found on the GitHub repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_. ]]></help> <citations> <citation type="bibtex"> @misc{PacificBiosciences2018, author = {Pacific Biosciences}, year = {2018}, title = {bax2bam}, publisher = {GitHub}, journal = {GitHub repository}, url = {https://github.com/pacificbiosciences/bax2bam/}, } </citation> </citations> </tool>