Mercurial > repos > iuc > seqtk

annotate seqtk_comp.xml @ 18:1d63dbcecb10 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 50a0bd6d783a69e7303363a31130134767493e66"
author iuc
date Fri, 06 Sep 2019 09:09:35 -0400
parents 069c8f0695ee
children 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@.1">
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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="requirements">
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8 <requirement type="package" version="@AWK_VERSION@">gawk</requirement>
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9 </expand>
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10 <expand macro="stdio"/>
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11 <command><![CDATA[
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12 seqtk comp
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13 #if $in_bed:
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14 -r '$in_bed'
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15 #end if
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16 '$in_file' | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'
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17 > '$default'
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18 ]]></command>
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19 <inputs>
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20 <expand macro="in_faq"/>
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21 <param name="in_bed" type="data" format="bed" optional="true" label="BED file"/>
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22 </inputs>
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23 <outputs>
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24 <data name="default" format="tabular" label="Nucleotide composition of $in_file.name"/>
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25 </outputs>
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26 <tests>
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27 <test>
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28 <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
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29 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
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30 </test>
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31 <test>
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32 <param name="in_file" value="seqtk_comp.fa.gz" ftype="fasta.gz"/>
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33 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
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34 </test>
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35 </tests>
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36 <help><![CDATA[
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37 **What it does**
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38
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39 Reports composition of fasta/fastq sequences. For an example sequence like
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40
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41 ::
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42 >test0
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43 ACTGACTGAA
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44 >ambig_ref
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45 ACGTCGTGTTVHDBN
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46
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47 The seqtk tool will report:
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48
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49 ::
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50
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51 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
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52 test0 11 4 2 2 2 0 0 1 0 0 0 0
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53 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
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54
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55 @ATTRIBUTION@
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56 ]]></help>
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57 <expand macro="citation" />
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58 </tool>