Mercurial > repos > iuc > crossmap_bw
view crossmap_bigwig.xml @ 9:c1a0f42d6c2a draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e10d34b547557b2bd4f0be69e31204bd5703e422"
author | iuc |
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date | Thu, 20 Jan 2022 04:26:48 +0000 |
parents | cafcf7eecf44 |
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<tool id="crossmap_bw" name="CrossMap BigWig" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05"> <description>Convert genome coordinates or annotation files between genome assemblies</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ CrossMap.py bigwig '${chain_source.input_chain}' '${input}' output ]]></command> <inputs> <param name="input" type="data" format="bigwig" label="BigWig file"/> <expand macro="chain" /> </inputs> <outputs> <data name="output" format="bigwig" label="${tool.name} on ${on_string}" from_work_dir="output.bw" /> </outputs> <tests> <test> <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig"/> <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> <output name="output" file="test_bigwig_01_output_a.bw"/> </test> <test><!-- cached chain file --> <param name="input" value="test_bigwig_01_input_a.bw" ftype="bigwig" dbkey="hg18"/> <param name="index_source" value="cached"/> <output name="output" file="test_bigwig_01_output_a.bw"/> </test> </tests> <help><![CDATA[ @HELP_GENERAL@ BigWig ------ Input wiggle data can be in variableStep (for data with irregular intervals) or fixedStep (for data with regular intervals). Regardless of the input, the output will always in bedGraph format. bedGraph format is similar to wiggle format and can be converted into BigWig format using UCSC wigToBigWig tool. We export files in bedGraph because it is usually much smaller than file in wiggle format, and more importantly, CrossMap internally transforms wiggle into bedGraph to increase running speed. ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btt730</citation> </citations> </tool>