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annotate seqtk_comp.xml @ 22:f2a792351212 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 75d5141110314addc160504e0a1f9cd66443de66
author iuc
date Wed, 16 Oct 2024 09:08:17 +0000
parents 8f26884c60b6
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1 <?xml version="1.0"?>
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2 <tool id="seqtk_comp" name="seqtk_comp" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="22.05">
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3 <description>get the nucleotide composition of FASTA/Q</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="bio_tools"/>
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8 <expand macro="requirements">
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9 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
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10 </expand>
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11 <expand macro="stdio"/>
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12 <command><![CDATA[
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13 seqtk comp
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14 #if $in_bed:
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15 -r '$in_bed'
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16 #end if
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17 '$in_file' | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'
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18 > '$default'
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19 ]]></command>
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20 <inputs>
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21 <expand macro="in_faq"/>
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22 <param name="in_bed" type="data" format="bed" optional="true" label="BED file"/>
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23 </inputs>
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24 <outputs>
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25 <data name="default" format="tabular" label="${tool.name} on ${on_string}: Nucleotide composition"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
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30 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
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31 </test>
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32 <test>
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33 <param name="in_file" value="seqtk_comp.fa.gz" ftype="fasta.gz"/>
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34 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 **What it does**
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39
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40 Reports composition of fasta/fastq sequences. For an example sequence like
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41
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42 ::
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43 >test0
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44 ACTGACTGAA
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45 >ambig_ref
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46 ACGTCGTGTTVHDBN
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47
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48 The seqtk tool will report:
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49
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50 ::
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51
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52 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
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53 test0 11 4 2 2 2 0 0 1 0 0 0 0
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54 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
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55
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56 @ATTRIBUTION@
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57 ]]></help>
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58 <expand macro="citation" />
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59 </tool>