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author | fubar |
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date | Thu, 22 Feb 2024 10:48:01 +0000 |
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<tool name="abslen_bed" id="abslen_bed" version="1" profile="22.05"> <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> <!--Created by toolfactory@galaxy.org at 10/12/2023 11:37:03 using the Galaxy Tool Factory.--> <description>Returns a file of absolute values from differences</description> <requirements> <requirement type="package">python</requirement> </requirements> <version_command><![CDATA[echo "1"]]></version_command> <command><![CDATA[python '$runme' < $absin > $absout]]></command> <configfiles> <configfile name="runme"><![CDATA[#raw import sys inp = [] for line in sys.stdin: if line.strip() > '': ls = line.split() if len(ls) > 2: x = abs(int(ls[2]) - int(ls[1])) ls.append((str(x))) inp.append('\t'.join(ls)) else: break sys.stdout.write('\n'.join(inp)) #end raw]]></configfile> </configfiles> <inputs> <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="csfasta,txt,tabular" multiple="false"/> </inputs> <outputs> <data name="absout" format="bed" hidden="false"/> </outputs> <tests> <test> <param name="absin" value="absin_sample"/> <output name="absout" value="absout_sample"/> </test> </tests> <help><![CDATA[ **What it Does** Takes absolute values on the input This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be translated into Galaxy See https://github.com/fubar2/treeval_gal/tree/main/gap_finder ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/bts573</citation> </citations> </tool>