Mercurial > repos > iuc > crossmap_gff
changeset 15:75a08e10cc76 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568
author | iuc |
---|---|
date | Mon, 02 Sep 2024 12:02:06 +0000 |
parents | 42b239a32349 |
children | |
files | crossmap_gff.xml macros.xml |
diffstat | 2 files changed, 7 insertions(+), 17 deletions(-) [+] |
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--- a/crossmap_gff.xml Thu Jan 20 04:32:52 2022 +0000 +++ b/crossmap_gff.xml Mon Sep 02 12:02:06 2024 +0000 @@ -6,9 +6,8 @@ <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> - <command><![CDATA[ -CrossMap.py gff +CrossMap gff '${chain_source.input_chain}' '${input}' @@ -18,26 +17,20 @@ output ]]></command> - <inputs> <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/> - - <expand macro="chain" /> - + <expand macro="chain"/> <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/> </inputs> - <outputs> - <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output" /> + <data name="output" format="gff" label="${tool.name} on ${on_string}" from_work_dir="output"/> </outputs> - <tests> <test> <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> <param name="include_fails" value="False"/> - <output name="output" file="test_gff_01_output_a__only-matches.gtf"/> </test> <test> @@ -45,14 +38,13 @@ <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> <param name="include_fails" value="True"/> - <output name="output" file="test_gff_01_output_a__all.gtf"/> </test> - <test><!-- cached chain file --> + <test> + <!-- cached chain file --> <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf" dbkey="hg18"/> <param name="index_source" value="cached"/> <param name="include_fails" value="True"/> - <output name="output" file="test_gff_01_output_a__all.gtf"/> </test> </tests> @@ -75,7 +67,6 @@ the same gene were converted into the same gene. - If user want to liftover gene annotation files, use BED12 format. ]]></help> - <citations> <citation type="doi">10.1093/bioinformatics/btt730</citation> </citations>
--- a/macros.xml Thu Jan 20 04:32:52 2022 +0000 +++ b/macros.xml Mon Sep 02 12:02:06 2024 +0000 @@ -1,4 +1,3 @@ -<?xml version="1.0"?> <macros> <xml name="requirements"> <requirements> @@ -6,7 +5,7 @@ <yield/> </requirements> </xml> - <token name="@TOOL_VERSION@">0.6.1</token> + <token name="@TOOL_VERSION@">0.7.0</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="stdio"> <stdio> @@ -17,7 +16,7 @@ </xml> <xml name="version_command"> <version_command><![CDATA[ -CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' +CrossMap 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' ]]></version_command> </xml> <xml name="chain">