Mercurial > repos > iuc > seqtk
comparison seqtk_cutN.xml @ 9:4b494533146a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 2f75805e2e6cfa2af15076e6f4929b87631360a6
author | iuc |
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date | Sat, 09 Dec 2023 11:14:21 +0000 |
parents | 3da72230c066 |
children |
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8:3da72230c066 | 9:4b494533146a |
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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"/> |