Mercurial > repos > fubar2 > abslen_bed
comparison absval/absval.xml @ 1:aff6409d16d1 draft
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| author | fubar2 |
|---|---|
| date | Fri, 08 Dec 2023 08:47:36 +0000 |
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| 0:551c076a635c | 1:aff6409d16d1 |
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| 1 <tool name="absval" id="absval" version="1" profile="22.05"> | |
| 2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay--> | |
| 3 <!--Created by toolfactory@galaxy.org at 08/12/2023 08:31:05 using the Galaxy Tool Factory.--> | |
| 4 <description>Returns a file of absolute values from differences</description> | |
| 5 <requirements> | |
| 6 <requirement type="package">python</requirement> | |
| 7 </requirements> | |
| 8 <version_command><![CDATA[echo "1"]]></version_command> | |
| 9 <command><![CDATA[python | |
| 10 '$runme' | |
| 11 < | |
| 12 $absin | |
| 13 > | |
| 14 $absout]]></command> | |
| 15 <configfiles> | |
| 16 <configfile name="runme"><![CDATA[#raw | |
| 17 import sys | |
| 18 inp = [] | |
| 19 for line in sys.stdin: | |
| 20 if line.strip() > '': | |
| 21 ls = line.split() | |
| 22 if len(ls) > 2: | |
| 23 x = abs(int(ls[2]) - int(ls[1])) | |
| 24 ls.append((str(x))) | |
| 25 inp.append('\t'.join(ls)) | |
| 26 else: | |
| 27 break | |
| 28 sys.stdout.write('\n'.join(inp)) | |
| 29 #end raw]]></configfile> | |
| 30 </configfiles> | |
| 31 <inputs> | |
| 32 <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="csfasta,txt,tabular" multiple="false"/> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data name="absout" format="txt" hidden="false"/> | |
| 36 </outputs> | |
| 37 <tests> | |
| 38 <test> | |
| 39 <param name="absin" value="absin_sample"/> | |
| 40 <output name="absout" value="absout_sample"/> | |
| 41 </test> | |
| 42 </tests> | |
| 43 <help><![CDATA[ | |
| 44 **What it Does** | |
| 45 Takes absolute values on the input | |
| 46 | |
| 47 This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be | |
| 48 translated into Galaxy | |
| 49 | |
| 50 See https://github.com/fubar2/treeval_gal/tree/main/gap_finder | |
| 51 ]]></help> | |
| 52 <citations> | |
| 53 <citation type="doi">10.1093/bioinformatics/bts573</citation> | |
| 54 </citations> | |
| 55 </tool> | |
| 56 |