Mercurial > repos > iuc > seqkit_head

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 76c1a289f15cc9a9a7d9a49dc132af62cc1d5af2
author iuc
date Fri, 26 Sep 2025 16:49:43 +0000
parents 3c0120a0e35c
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3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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1 <tool id="seqkit_head" name="SeqKit Head" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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2 <description>Displays N records of a FASTA or FASTQ file</description>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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3 <macros>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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4 <import>macros.xml</import>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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5 </macros>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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6 <expand macro="bio_tools"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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7 <expand macro="requirements"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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8 <command detect_errors="exit_code"><![CDATA[
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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9 #set $input_fn='input.' + str($input.ext)
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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10 #set $output_fn='seqkithead_output.' + str($output.ext)
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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11 ln -s '$input' '$input_fn'
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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12 && seqkit head
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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13 '$input_fn'
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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14 --number '$number'
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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15 -o '$output_fn'
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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16 --threads \${GALAXY_SLOTS:-4}
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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17
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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18 ]]></command>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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19 <inputs>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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20 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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21 <param argument="--number" type="integer" value="10" label="Output first N FASTA/Q records"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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22 </inputs>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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23 <outputs>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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24 <data name="output" format_source="input" from_work_dir="seqkithead_output.*" label="${input.name} Head (${tool.name})"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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25 </outputs>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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26 <tests>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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27 <!-- 1. fastq.gz -->
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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28 <test expect_num_outputs="1">
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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29 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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30 <param name="number" value="10"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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31 <output name="output" file="head_output1.fastq.gz" ftype="fastqsanger.gz"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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32 </test>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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33 <!-- 2. fasta.gz -->
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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34 <test expect_num_outputs="1">
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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35 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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36 <param name="number" value="10"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
iuc
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37 <output name="output" file="head_output2.fasta.gz" ftype="fasta.gz"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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38 </test>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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39 </tests>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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40 <help>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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41 **What it does**
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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42
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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43 Prints first N FASTA/Q records,
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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44
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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45 </help>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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46 <expand macro="citations"/>
3c0120a0e35c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit f38872ceb6fdf153a7a370846d7097f5a40d9f92
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47 </tool>