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annotate seqtk_comp.xml @ 4:ecf1c30da3a2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
author iuc
date Wed, 17 Oct 2018 05:59:21 -0400
parents bc7d99f46a5d
children a09586d5149a
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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>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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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"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
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10 seqtk comp
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11 #if $in_bed:
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12 -r '$in_bed'
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13 #end if
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14 '$in_file' | awk 'BEGIN{print "#chr\tlength\t#A\t#C\t#G\t#T\t#2\t#3\t#4\t#CpG\t#tv\t#ts\t#CpG-ts"}1'
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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15 > '$default'
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16 ]]></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" type="data" format="bed" optional="true" label="BED file"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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20 </inputs>
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21 <outputs>
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22 <data name="default" format="tabular" 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"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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27 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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28 </test>
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29 <test>
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30 <param name="in_file" value="seqtk_comp.fa.gz" ftype="fasta.gz"/>
ecf1c30da3a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit ad43df79dca3dc7c3511c6eb2ccf8589d2804eb2
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31 <output name="default" file="seqtk_comp.out" ftype="tabular"/>
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32 </test>
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33 </tests>
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34 <help><![CDATA[
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35 **What it does**
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36
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37 Reports composition of fasta/fastq sequences. For an example sequence like
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38
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39 ::
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40 >test0
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41 ACTGACTGAA
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42 >ambig_ref
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43 ACGTCGTGTTVHDBN
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44
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45 The seqtk tool will report:
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46
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47 ::
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48
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49 #chr length #A #C #G #T #2 #3 #4 #CpG #tv #ts #CpG-ts
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50 test0 11 4 2 2 2 0 0 1 0 0 0 0
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51 ambig_ref 15 1 2 3 4 0 4 1 4 0 0 0
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52
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53 @ATTRIBUTION@
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54 ]]></help>
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55 <expand macro="citation" />
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56 </tool>