| Previous changeset 1:ee356d7a5518 (2019-11-28) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pax2bam commit 958bbd9e30ae4d320f872f1ab5e1bacfb28b1a00" |
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modified:
bax2bam.xml |
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removed:
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 |
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| diff -r ee356d7a5518 -r 5bd67e012d54 bax2bam.xml --- a/bax2bam.xml Thu Nov 28 15:49:50 2019 -0500 +++ b/bax2bam.xml Sat Apr 17 10:41:00 2021 +0000 |
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| b'@@ -1,94 +1,133 @@\n <?xml version="1.0"?>\n-<tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+@WRAPPER_VERSION@">\n+<tool id="bax2bam" name="bax2bam" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">\n <description>converts PacBio basecall format (bax.h5) into BAM</description>\n <macros>\n- <import>macros.xml</import>\n+ <token name="@TOOL_VERSION@">0.0.11</token>\n+ <token name="@VERSION_SUFFIX@">0</token>\n </macros>\n- <expand macro="requirements"/>\n- <stdio></stdio>\n+ <edam_topics>\n+ <edam_topic>topic_3168</edam_topic> <!-- Topic - Laboratory techniques - Sequencing -->\n+ </edam_topics>\n+ <edam_operations>\n+ <edam_operation>operation_3434</edam_operation> <!-- Operation - Conversion -->\n+ </edam_operations>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">bax2bam</requirement>\n+ </requirements>\n+ <version_command><![CDATA[bax2bam --version]]></version_command>\n <command detect_errors="exit_code"><![CDATA[\n- bax2bam\n- #for $file in $files\n- \'$file\'\n- #end for\n- -o output\n- $readtype\n- #if $pulsefeatures\n- --pulsefeatures=$pulsefeatures\n- #end if\n- $losslessframes\n- $internal\n+## skipped -h/--help, --xml, -f, --output-xml, --ccs (see https://github.com/PacificBiosciences/pbbioconda/issues/215)\n+\n+## run\n+bax2bam\n+#for $file in $files\n+ \'$file\'\n+#end for\n+-o \'output\'\n+$readtype\n+#if $pulsefeatures\n+ --pulsefeatures=$pulsefeatures\n+#end if\n+$losslessframes\n+$internal\n ]]></command>\n <inputs>\n- <param name="files" type="data" format="h5" multiple="true" label="Files" help="Should be from the same movie."/>\n- <param name="readtype" type="select" label="Output read type" help="">\n- <option value="--subread">subread</option>\n- <option value="--hqregion">hqregion</option>\n- <option value="--polymeraseread">polymeraseread</option>\n+ <param name="files" type="data" format="h5" multiple="true" label="Select files" help="Should be from the same movie."/>\n+ <param name="readtype" type="select" label="Select output read type">\n+ <option value="--hqregion">Hqregion</option>\n+ <option value="--polymeraseread">Polymeraseread</option>\n+ <option value="--subread">Subread</option>\n </param>\n- <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in the output BAM." help="">\n+ <param argument="--pulsefeatures" type="select" multiple="true" label="Select pulse features in output BAM">\n <option value="DeletionQV" selected="true">dq - DeletionQV</option>\n <option value="DeletionTag" selected="true">dt - DeletionTag</option>\n <option value="InsertionQV" selected="true">iq - InsertionQV</option>\n <option value="IPD" selected="true">ip - IPD</option>\n+ <option value="MergeQV" selected="true">mq - MergeQV</option>\n <option value="PulseWidth" selected="true">pw - PulseWidth</option>\n- <option value="MergeQV" selected="true">mq - MergeQV</option>\n <option value="SubstitutionQV" selected="true">sq - SubstitutionQV</option>\n <option value="SubstitutionTag" selected="false">st - SubstitutionTag</option>\n </param>\n- <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."/>\n- <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."/>\n+ <param argument="--losslessframes" type="boole'..b'scrap" file="scraps.bam" compare="sim_size" delta="100"/>\n- <output name="output_subread" file="subreads.bam" compare="sim_size" delta="100"/>\n+ <output name="output_scrap">\n+ <assert_contents>\n+ <has_size value="113578" delta="100"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_subread">\n+ <assert_contents>\n+ <has_size value="242552" delta="100"/>\n+ </assert_contents>\n+ </output>\n </test>\n- <!-- #2: read type: hqregion -->\n- <test>\n+ <!-- #2 hqregion, default -->\n+ <test expect_num_outputs="2">\n <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>\n <param name="readtype" value="--hqregion"/>\n- <output name="output_hqregion" file="hqregions.bam" compare="sim_size" delta="100"/>\n- <output name="output_hqregion" file="lqregions.bam" compare="sim_size" delta="100"/>\n+ <output name="output_hqregion">\n+ <assert_contents>\n+ <has_size value="232342" delta="100"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_hqregion">\n+ <assert_contents>\n+ <has_size value="232342" delta="100"/>\n+ </assert_contents>\n+ </output>\n </test>\n- <!-- #3: read type: polymeraseread -->\n- <test>\n+ <!-- #3 polymeraseread, default -->\n+ <test expect_num_outputs="1">\n <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>\n <param name="readtype" value="--polymeraseread"/>\n- <output name="output_polymeraseread" file="polymerase.bam" compare="sim_size" delta="100"/>\n+ <output name="output_polymeraseread">\n+ <assert_contents>\n+ <has_size value="333195" delta="100"/>\n+ </assert_contents>\n+ </output>\n </test>\n- <!-- #4: read type: subread, custom parameters -->\n- <test>\n+ <!-- #4 subread, custom -->\n+ <test expect_num_outputs="2">\n <param name="files" value="set.3.bax.h5,set.2.bax.h5,set.1.bax.h5"/>\n <param name="readtype" value="--subread"/>\n <param name="pulsefeatures" value="SubstitutionTag"/>\n <param name="losslessframes" value="true"/>\n <param name="internal" value="true"/>\n- <output name="output_scrap" file="scraps_custom.bam" compare="sim_size" delta="100"/>\n- <output name="output_subread" file="subreads_custom.bam" compare="sim_size" delta="100"/>\n+ <output name="output_scrap">\n+ <assert_contents>\n+ <has_size value="23497" delta="100"/>\n+ </assert_contents>\n+ </output>\n+ <output name="output_subread">\n+ <assert_contents>\n+ <has_size value="45147" delta="100"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n@@ -101,17 +140,17 @@\n \n **Input**\n \n-bax.h5 files that should be from the same movie.\n+- Sample files that should be from the same movie (bax.h5)\n \n **Output**\n \n-A single BAM file. \n+- Converted sample (BAM) \n \n .. class:: infomark\n \n **References**\n \n- More information can be found on the github repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_.\n+ More information can be found on the GitHub repositories `bax2bam <https://github.com/pacificbiosciences/bax2bam/>`_ and `PacBio Bioconda <https://github.com/PacificBiosciences/pbbioconda>`_.\n ]]></help>\n <citations>\n <citation type="bibtex">\n@@ -125,4 +164,4 @@\n }\n </citation>\n </citations>\n-</tool>\n+</tool>\n\\ No newline at end of file\n' |
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| diff -r ee356d7a5518 -r 5bd67e012d54 macros.xml --- a/macros.xml Thu Nov 28 15:49:50 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 |
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| diff -r ee356d7a5518 -r 5bd67e012d54 test-data/hqregions.bam |
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| Binary file test-data/hqregions.bam has changed |
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| diff -r ee356d7a5518 -r 5bd67e012d54 test-data/lqregions.bam |
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| Binary file test-data/lqregions.bam has changed |
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| diff -r ee356d7a5518 -r 5bd67e012d54 test-data/polymerase.bam |
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| Binary file test-data/polymerase.bam has changed |
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| diff -r ee356d7a5518 -r 5bd67e012d54 test-data/scraps.bam |
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| Binary file test-data/scraps.bam has changed |
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| diff -r ee356d7a5518 -r 5bd67e012d54 test-data/scraps_custom.bam |
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| Binary file test-data/scraps_custom.bam has changed |
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| diff -r ee356d7a5518 -r 5bd67e012d54 test-data/subreads.bam |
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| Binary file test-data/subreads.bam has changed |
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| diff -r ee356d7a5518 -r 5bd67e012d54 test-data/subreads_custom.bam |
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| Binary file test-data/subreads_custom.bam has changed |