Mercurial > repos > iuc > bax2bam
changeset 2:0cd3f1c577de draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 958bbd9e30ae4d320f872f1ab5e1bacfb28b1a00"
| author | iuc |
|---|---|
| date | Sat, 17 Apr 2021 10:40:28 +0000 |
| parents | bbed92d5d4d9 |
| children | |
| files | bax2bam.xml macros.xml test-data/hqregions.bam test-data/lqregions.bam test-data/polymerase.bam test-data/scraps.bam test-data/scraps_custom.bam test-data/subreads.bam test-data/subreads_custom.bam |
| diffstat | 9 files changed, 90 insertions(+), 63 deletions(-) [+] |
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--- a/bax2bam.xml Thu Nov 28 20:34:13 2019 +0000 +++ b/bax2bam.xml Sat Apr 17 10:40:28 2021 +0000 @@ -1,94 +1,133 @@ <?xml version="1.0"?> -<tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> +<tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>converts PacBio basecall format (bax.h5) into BAM</description> <macros> - <import>macros.xml</import> + <token name="@TOOL_VERSION@">0.0.11</token> + <token name="@VERSION_SUFFIX@">0</token> </macros> - <expand macro="requirements"/> - <stdio></stdio> + <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[ - bax2bam - #for $file in $files - '$file' - #end for - -o output - $readtype - #if $pulsefeatures - --pulsefeatures=$pulsefeatures - #end if - $losslessframes - $internal +## 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="Files" help="Should be from the same movie."/> - <param name="readtype" type="select" label="Output read type" help=""> - <option value="--subread">subread</option> - <option value="--hqregion">hqregion</option> - <option value="--polymeraseread">polymeraseread</option> + <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 the output BAM." help=""> + <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="MergeQV" selected="true">mq - MergeQV</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="" checked="false" label="Store full, 16-bit IPD/PulseWidth data" help="Instead of (default) 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."/> + <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 ${on_string}: scraps"> + <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${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 ${on_string}: subreads"> + <data name="output_subread" from_work_dir="output.subreads.bam" format="bam" label="${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 ${on_string}: hqregions"> + <data name="output_hqregion" from_work_dir="output.hqregions.bam" format="bam" label="${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 ${on_string}: lqregions"> + <data name="output_lqregion" from_work_dir="output.lqregions.bam" format="bam" label="${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 ${on_string}: polymerase"> + <data name="output_polymeraseread" from_work_dir="output.polymerase.bam" format="bam" label="${tool.name} on ${on_string}: Polymerase"> <filter>readtype == '--polymeraseread'</filter> </data> </outputs> - <tests> - <!-- source of test data: https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ --> - <!-- #1: read type: subread --> - <test> + <!-- 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" file="scraps.bam" compare="sim_size" delta="100"/> - <output name="output_subread" file="subreads.bam" compare="sim_size" delta="100"/> + <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: read type: hqregion --> - <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" file="hqregions.bam" compare="sim_size" delta="100"/> - <output name="output_hqregion" file="lqregions.bam" compare="sim_size" delta="100"/> + <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: read type: polymeraseread --> - <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" file="polymerase.bam" compare="sim_size" delta="100"/> + <output name="output_polymeraseread"> + <assert_contents> + <has_size value="333195" delta="100"/> + </assert_contents> + </output> </test> - <!-- #4: read type: subread, custom parameters --> - <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" file="scraps_custom.bam" compare="sim_size" delta="100"/> - <output name="output_subread" file="subreads_custom.bam" compare="sim_size" delta="100"/> + <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[ @@ -101,17 +140,17 @@ **Input** -bax.h5 files that should be from the same movie. +- Sample files that should be from the same movie (bax.h5) **Output** -A single BAM file. +- 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>`_. + 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"> @@ -125,4 +164,4 @@ } </citation> </citations> -</tool> +</tool> \ No newline at end of file
--- a/macros.xml Thu Nov 28 20:34:13 2019 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -<macros> - <token name="@TOOL_VERSION@">0.0.9</token> - - <token name="@WRAPPER_VERSION@">galaxy0</token> - - <xml name="requirements"> - <requirements> - <requirement type="package" version="@TOOL_VERSION@">bax2bam</requirement> - <yield/> - </requirements> - </xml> -</macros> \ No newline at end of file