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1 <?xml version="1.0"?>
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2 <tool id="seqtk_comp" name="seqtk_comp" version="@WRAPPER_VERSION@.0">
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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 <expand macro="stdio"/>
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9 <command><![CDATA[seqtk comp
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10 #if $in_bed:
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11 -r $in_bed
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12 #end if
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13
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14 $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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15
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16 > $default]]></command>
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17 <inputs>
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18 <expand macro="in_faq"/>
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19 <param name="in_bed" optional="True" type="data" format="bed" label="bed file"/>
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20 </inputs>
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21 <outputs>
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22 <data format="tabular" hidden="false" name="default" label="Nucleotide composition of $in_file.name"/>
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23 </outputs>
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24 <tests>
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25 <test>
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26 <param name="in_file" value="seqtk_comp.fa" ftype="fasta"/>
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27 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
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28 </test>
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29 </tests>
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30 <help><![CDATA[
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31 **What it does**
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32
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33 Reports composition of fasta/fastq sequences. For an example sequence like
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34
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35 ::
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36 >test0
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37 ACTGACTGAA
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38 >ambig_ref
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39 ACGTCGTGTTVHDBN
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40
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41 The seqtk tool will report:
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42
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43 ::
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44
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45 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
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46 test0 11 4 2 2 2 0 0 1 0 0 0 0
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47 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
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48
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49
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50 @ATTRIBUTION@
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51 ]]></help>
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52 </tool>
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