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annotate seqtk_seq.xml @ 3:bc7d99f46a5d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
author iuc
date Mon, 05 Jun 2017 13:27:11 -0400
parents f73729b62b51
children ecf1c30da3a2
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1 <?xml version="1.0"?>
3
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2 <tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.2">
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3 <description>common transformation 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[
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10 seqtk seq -q $q
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11 -X $X
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12 #if $n:
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13 -n '$n'
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14 #end if
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15 -l $l
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16 -Q $Q
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17 -s $s
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18 -f $f
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19 #if $M:
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20 -M '$M'
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21 #end if
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22 -L $L
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23 $c
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24 $r
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25 $A
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26 $C
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27 $N
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28 $x1
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29 $x2
3
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30 #if $in_file.is_of_type('fastqillumina')
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31 -V
2
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32 #end if
3
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33 '$in_file'
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34 > '$default'
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35 ]]></command>
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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36 <inputs>
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37 <expand macro="in_faq"/>
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38 <param argument="-q" type="integer" value="0" label="Mask bases with quality lower than INT" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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39 <param argument="-X" type="integer" value="255" label="Mask bases with quality higher than INT" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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40 <param argument="-n" type="text" value="0" label="Masked bases converted to CHAR; 0 for lowercase" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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41 <param argument="-l" type="integer" value="0" label="Number of residues per line; 0 for 2^32-1" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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42 <param argument="-Q" type="integer" value="33" label="Quality shift: ASCII-INT gives base quality" />
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43 <param argument="-s" type="integer" value="11" label="Random seed" help="Effective with -f" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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44 <param argument="-f" type="float" value="1" label="Sample fraction of sequences" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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45 <param argument="-M" type="data" format="bed,txt" optional="true" label="Mask regions in BED or name list file" />
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46 <param argument="-L" type="integer" value="0" label="Drop sequences with length shorter than INT" />
bc7d99f46a5d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqtk commit 7379d9f8823d3c639c8119b116e141d0a736ca1d
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47 <param argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" label="Mask complement region" help="Effective with -M" />
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48 <param argument="-r" type="boolean" truevalue="-r" falsevalue="" checked="false" label="Reverse complement" />
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49 <param argument="-A" type="boolean" truevalue="-A" falsevalue="" checked="false" label="Force FASTA output (discard quality)" />
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50 <param argument="-C" type="boolean" truevalue="-C" falsevalue="" checked="false" label="Drop comments at the header lines" />
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51 <param argument="-N" type="boolean" truevalue="-N" falsevalue="" checked="false" label="Drop sequences containing ambiguous bases" />
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52 <param name="x1" argument="-1" type="boolean" truevalue="-1" falsevalue="" checked="false" label="Output the 2n-1 reads only" />
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53 <param name="x2" argument="-2" type="boolean" truevalue="-2" falsevalue="" checked="false" label="Output the 2n reads only" />
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54 </inputs>
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55 <outputs>
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56 <data name="default" format_source="in_file" />
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57 </outputs>
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58 <tests>
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59 <!-- This is a sorry excuse for a test for a tool which does way more
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60 than it should, but upstream decided to put a TON of functionality
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61 into a single tool rather than using the single responsibility
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62 principle. -->
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63 <test>
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64 <param name="in_file" value="seqtk_seq.fa"/>
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65 <param name="r" value="True"/>
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66 <param name="n" value=""/>
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67 <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 **What it does**
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72
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73 Various utilities for transforming FASTA/Q data
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74
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75 @ATTRIBUTION@
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76 ]]></help>
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77 <expand macro="citation" />
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78 </tool>