| Previous changeset 0:7e572e148175 (2018-01-11) Next changeset 2:9a4cfc910674 (2020-04-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/gffcompare_to_bed commit e5ab6444aa2f104eedfa366bee05f65edef02d82 |
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modified:
gffcompare_to_bed.xml |
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added:
static/images/GTF2Bed_workflow.png |
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| diff -r 7e572e148175 -r 0f62097d7c1a gffcompare_to_bed.xml --- a/gffcompare_to_bed.xml Thu Jan 11 11:16:51 2018 -0500 +++ b/gffcompare_to_bed.xml Fri Apr 26 14:42:31 2019 -0400 |
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| @@ -1,4 +1,4 @@ -<tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.1.0"> +<tool id="gffcompare_to_bed" name="Convert gffCompare annotated GTF to BED" version="0.2.0"> <description>for StringTie results</description> <command detect_errors="exit_code"><![CDATA[ python '$__tool_directory__/gffcompare_to_bed.py' @@ -12,6 +12,7 @@ <param name="class_codes" type="select" display="checkboxes" multiple="true" optional="true" label="filter gffCompare class_codes to convert" help="No selection implies no filtering"> <option value="=">= : Complete match of intron chain</option> + <option value="~">~ : Intron chain match or single-exon (gffcompare strict-match)</option> <option value="c">c : Contained</option> <option value="j">j : Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript</option> <option value="e">e : Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.</option> @@ -47,6 +48,12 @@ <help><![CDATA[ Convert a GFFCompare annotated GTF file to BED format. +A typical workflow: + +.. image:: GTF2Bed_workflow.png + :height: 308 + :width: 750 + usage: gffcompare_to_bed.py [-h] [-C CLASS_CODE] [-v] [-d] input output positional arguments: @@ -59,6 +66,9 @@ Restrict output to gffcompare class codes -d, --debug Debug +For class_code definitions see gffcompare documentation: +http://ccb.jhu.edu/software/stringtie/gffcompare.shtml#transfrag-class-codes + ]]></help> <citations> <citation type="doi">10.1038/nbt.1621</citation> |
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| diff -r 7e572e148175 -r 0f62097d7c1a static/images/GTF2Bed_workflow.png |
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| Binary file static/images/GTF2Bed_workflow.png has changed |
