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1 <tool name="abslen_bed" id="abslen_bed" version="1" profile="22.05">
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2 <!--Source in git at: https://github.com/fubar2/galaxy_tf_overlay-->
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3 <!--Created by toolfactory@galaxy.org at 10/12/2023 11:37:03 using the Galaxy Tool Factory.-->
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4 <description>Returns a file of absolute values from differences</description>
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5 <requirements>
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6 <requirement type="package">python</requirement>
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7 </requirements>
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8 <version_command><![CDATA[echo "1"]]></version_command>
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9 <command><![CDATA[python
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10 '$runme'
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11 <
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12 $absin
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13 >
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14 $absout]]></command>
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15 <configfiles>
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16 <configfile name="runme"><![CDATA[#raw
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17 import sys
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18 inp = []
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19 for line in sys.stdin:
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20 if line.strip() > '':
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21 ls = line.split()
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22 if len(ls) > 2:
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23 x = abs(int(ls[2]) - int(ls[1]))
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24 ls.append((str(x)))
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25 inp.append('\t'.join(ls))
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26 else:
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27 break
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28 sys.stdout.write('\n'.join(inp))
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29 #end raw]]></configfile>
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30 </configfiles>
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31 <inputs>
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32 <param name="absin" type="data" optional="false" label="absin" help="Input file to be converted using abs()" format="csfasta,txt,tabular" multiple="false"/>
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33 </inputs>
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34 <outputs>
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35 <data name="absout" format="bed" hidden="false"/>
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36 </outputs>
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37 <tests>
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38 <test>
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39 <param name="absin" value="absin_sample"/>
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40 <output name="absout" value="absout_sample"/>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 **What it Does**
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45 Takes absolute values on the input
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46
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47 This tool is a temporary step to enable the Sanger TreeVal NF gap_finder workflow to be
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48 translated into Galaxy
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49
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50 See https://github.com/fubar2/treeval_gal/tree/main/gap_finder
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51 ]]></help>
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52 <citations>
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53 <citation type="doi">10.1093/bioinformatics/bts573</citation>
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54 </citations>
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55 </tool>
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56
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