| Previous changeset 8:cb20f99fd45b (2020-02-20) Next changeset 10:108db6635177 (2023-01-13) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/bamtools/bamtools_filter commit 1cacd14cfb2429fefa91fdd05c82d2e36d23283a" |
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modified:
bamtools-filter.xml macros.xml |
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| diff -r cb20f99fd45b -r 1dfd95ee241e bamtools-filter.xml --- a/bamtools-filter.xml Thu Feb 20 17:23:24 2020 -0500 +++ b/bamtools-filter.xml Sat Nov 27 10:02:24 2021 +0000 |
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| @@ -1,4 +1,4 @@ -<tool id="bamFilter" name="Filter" version="2.4.1"> +<tool id="bamFilter" name="Filter" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@"> <description>BAM datasets on a variety of attributes</description> <macros> <import>macros.xml</import> @@ -41,28 +41,28 @@ <repeat name="filters" title="Filter" min="1"> <conditional name="bam_property"> <param name="bam_property_selector" type="select" label="Select BAM property to filter on"> - <option value="alignmentFlag"/> - <option value="cigar"/> - <option value="insertSize"/> - <option value="isDuplicate"/> - <option value="isFailedQC"/> - <option value="isFirstMate"/> - <option value="isMapped"/> - <option value="isMateMapped"/> - <option value="isMateReverseStrand"/> - <option value="isPaired"/> - <option value="isPrimaryAlignment"/> - <option value="isProperPair"/> - <option value="isReverseStrand"/> - <option value="isSecondMate"/> - <option selected="True" value="mapQuality"/> - <option value="matePosition"/> - <option value="mateReference"/> - <option value="name"/> - <option value="position"/> - <option value="queryBases"/> - <option value="reference"/> - <option value="tag"/> + <option value="alignmentFlag">Alignment flag</option> + <option value="cigar">CIGAR string</option> + <option value="insertSize">Insert size</option> + <option value="isDuplicate">Duplicate</option> + <option value="isFailedQC">Quality check</option> + <option value="isFirstMate">First mate</option> + <option value="isMapped">Mapped</option> + <option value="isMateMapped">Mate mapped</option> + <option value="isMateReverseStrand">Mate is on reverse strand</option> + <option value="isPaired">Paired</option> + <option value="isPrimaryAlignment">Primary alignment</option> + <option value="isProperPair">Proper pair</option> + <option value="isReverseStrand">Reverse strand</option> + <option value="isSecondMate">Second mate</option> + <option selected="true" value="mapQuality">Mapping quality</option> + <option value="matePosition">Position of the mate</option> + <option value="mateReference">Reference name of the mate</option> + <option value="name">Read name</option> + <option value="position">Position of the read</option> + <option value="queryBases">Sequence motif</option> + <option value="reference">Reference name of the read</option> + <option value="tag">Tag</option> </param> <!-- would be fanstastic to have AND and OR constructs in when statements --> <when value="alignmentFlag"> @@ -79,7 +79,7 @@ </param> </when> <when value="isDuplicate"> - <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads makwed as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" /> + <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads marked as duplicates" help="Checked = Read IS Duplicate, Empty = Read is NOT Duplicate" /> </when> <when value="isFailedQC"> <param name="bam_property_value" type="boolean" truevalue="true" falsevalue="false" label="Select reads failing QC" help="Checked = Failed QC, Empty = Passed QC"/> |
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| diff -r cb20f99fd45b -r 1dfd95ee241e macros.xml --- a/macros.xml Thu Feb 20 17:23:24 2020 -0500 +++ b/macros.xml Sat Nov 27 10:02:24 2021 +0000 |
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| @@ -1,9 +1,10 @@ <?xml version="1.0"?> <macros> - <token name="@VERSION@">2.4.0</token> + <token name="@TOOL_VERSION@">2.5.1</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> - <requirement type="package" version="@VERSION@">bamtools</requirement> + <requirement type="package" version="@TOOL_VERSION@">bamtools</requirement> <requirement type="package" version="1.4.1">samtools</requirement> </requirements> </xml> |