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comparison seqtk_cutN.xml @ 9:4b494533146a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6
author iuc
date Sat, 09 Dec 2023 11:14:21 +0000
parents 3da72230c066
children
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8:3da72230c066 9:4b494533146a
1 <?xml version="1.0"?> 1 <tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
2 <tool id="seqtk_cutN" name="seqtk_cutN" version="@TOOL_VERSION@.1">
3 <description>cut sequence at long N</description> 2 <description>cut sequence at long N</description>
4 <expand macro="bio_tools"/>
5 <macros> 3 <macros>
6 <import>macros.xml</import> 4 <import>macros.xml</import>
7 </macros> 5 </macros>
6 <expand macro="bio_tools"/>
8 <expand macro="requirements"/> 7 <expand macro="requirements"/>
9 <expand macro="stdio"/> 8 <expand macro="stdio"/>
10 <command><![CDATA[ 9 <command><![CDATA[
11 seqtk cutN 10 seqtk cutN
12 -n $n 11 -n $n
20 <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" /> 19 <param argument="-n" type="integer" value="1000" label="Minimum size of N tract" />
21 <param argument="-p" type="integer" value="10" label="Penalty for a non-N" /> 20 <param argument="-p" type="integer" value="10" label="Penalty for a non-N" />
22 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" /> 21 <param argument="-g" type="boolean" truevalue="-g" falsevalue="" checked="false" label="Print gaps only, no sequence" />
23 </inputs> 22 </inputs>
24 <outputs> 23 <outputs>
25 <data name="default" format_source="in_file" label="$in_file.name split on N runs longer than $n"/> 24 <data name="default" format_source="in_file" label="${tool.name} on ${on_string}: split on N runs longer than $n">
25 <change_format>
26 <when input="g" value="-g" format="bed" />
27 </change_format>
28 </data>
26 </outputs> 29 </outputs>
27 <tests> 30 <tests>
28 <test> 31 <test>
29 <param name="in_file" value="seqtk_cutn.fa"/> 32 <param name="in_file" value="seqtk_cutn.fa"/>
30 <param name="n" value="1"/> 33 <param name="n" value="1"/>