Mercurial > repos > iuc > bax2bam
changeset 0:413d28ca0b6f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 07edb81ab753f8ea6001875e84a68f820febfc88"
| author | iuc |
|---|---|
| date | Sat, 12 Oct 2019 06:50:34 -0400 |
| parents | |
| children | bbed92d5d4d9 |
| 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/set.1.bax.h5 test-data/set.2.bax.h5 test-data/set.3.bax.h5 test-data/subreads.bam test-data/subreads_custom.bam |
| diffstat | 12 files changed, 140 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bax2bam.xml Sat Oct 12 06:50:34 2019 -0400 @@ -0,0 +1,128 @@ +<?xml version="1.0"?> +<tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+@WRAPPER_VERSION@"> + <description>converts PacBio basecall format (bax.h5) into BAM</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <stdio></stdio> + <command detect_errors="exit_code"><![CDATA[ + bax2bam + #for $file in $files + '$file' + #end for + -o output + $readtype + #if $pulsefeatures + --pulsefeatures=$pulsefeatures + #end if + $losslessframes + $internal + ]]></command> + <inputs> + <param name="files" type="data" format="h5" multiple="true" label="Files" help="Should be from the same movie."/> + <param name="readtype" type="select" label="Output read type" help=""> + <option value="--subread">subread</option> + <option value="--hqregion">hqregion</option> + <option value="--polymeraseread">polymeraseread</option> + </param> + <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in the output BAM." help=""> + <option value="DeletionQV" selected="true">dq - DeletionQV</option> + <option value="DeletionTag" selected="true">dt - DeletionTag</option> + <option value="InsertionQV" selected="true">iq - InsertionQV</option> + <option value="IPD" selected="true">ip - IPD</option> + <option value="PulseWidth" selected="true">pw - PulseWidth</option> + <option value="MergeQV" selected="true">mq - MergeQV</option> + <option value="SubstitutionQV" selected="true">sq - SubstitutionQV</option> + <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option> + </param> + <param argument="--losslessframes" type="boolean" truevalue="--losslessframes" falsevalue="" checked="false" label="Store full, 16-bit IPD/PulseWidth data" help="Instead of (default) downsampled, 8-bit encoding."/> + <param argument="--internal" type="boolean" truevalue="--internal" falsevalue="" checked="false" label="Output BAMs in internal mode." help="Currently this indicates that non-sequencing ZMWs should be included in the output scraps BAM file, if applicable."/> + </inputs> + + <outputs> + <data name="output_scrap" from_work_dir="output.scraps.bam" format="bam" label="${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> + <!-- source of test data: https://github.com/PacificBiosciences/PacBioTestData/tree/master/data/HdfSubreadSet/Analysis_Results/ --> + <!-- #1: read type: subread --> + <test> + <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"/> + </test> + <!-- #2: read type: hqregion --> + <test> + <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"/> + </test> + <!-- #3: read type: polymeraseread --> + <test> + <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/> + <param name="readtype" value="--polymeraseread" compare="sim_size" delta="100"/> + <output name="output_polymeraseread" file="polymerase.bam" compare="sim_size" delta="100"/> + </test> + <!-- #4: read type: subread, custom parameters --> + <test> + <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"/> + </test> + </tests> + <help><![CDATA[ + +.. class:: infomark + +**What it does** + +bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAM basecall format. + +**Input** + +bax.h5 files that should be from the same movie. + +**Output** + +A single BAM file. + +.. 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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Sat Oct 12 06:50:34 2019 -0400 @@ -0,0 +1,12 @@ +<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