Mercurial > repos > iuc > crossmap_wig
view crossmap_wig.xml @ 2:d0e7cc22351f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 39a5f30a013c6d71ea84807b72511e3aa4bab147
author | iuc |
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date | Fri, 20 Oct 2017 11:33:40 -0400 |
parents | 81986a56b281 |
children | 8c26026e7ad9 |
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<tool id="crossmap_wig" name="CrossMap Wig" version="@WRAPPER_VERSION@-0"> <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 wig '${chain_source.input_chain}' '${input}' '${output}' && mv '${output}.bw' '${output}' && mv '${output}.sorted.bgr' '${output2}' ]]></command> <inputs> <param name="input" type="data" format="wig" label="Wiggle file"/> <expand macro="chain" /> </inputs> <outputs> <data name="output" format="wig" label="${tool.name} on ${on_string}" /> <data name="output2" format="bedgraph" label="${tool.name} (bedgraph) on ${on_string}" /> </outputs> <tests> <!-- WIG - Doesn't understand fixedStep --> <test> <param name="input" value="test_wig_01_input_a.wig" ftype="wig"/> <param name="index_source" value="history"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> <output name="output" file="test_wig_01_output_a.bw"/> <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> </test> <test><!-- cached reference genome --> <param name="input" value="test_wig_01_input_a.wig" ftype="wig" dbkey="hg18" /> <param name="index_source" value="cached"/> <output name="output" file="test_wig_01_output_a.bw"/> <output name="output2" file="test_wig_01_output_a.sorted.bgr"/> </test> </tests> <help><![CDATA[ @HELP_GENERAL@ Wig --- 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>