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1 <?xml version="1.0"?>
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2 <tool id="seqtk_seq" name="seqtk_seq" version="@WRAPPER_VERSION@.0">
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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[seqtk seq -q $q
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10 -X $X
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11 #if $n and $n != "None" and $n is not None and $n != "":
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12 -n "$n"
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13 #end if
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14 -l $l
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15 -Q $Q
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16 -s $s
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17 -f $f
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18 #if $M and $M != "None" and $M is not None and $M != "":
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19 -M "$M"
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20 #end if
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21 -L $L
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22 $c
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23 $r
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24 $A
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25 $C
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26 $N
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27 $x1
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28 $x2
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29 $V
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30
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31 $in_file
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32 > $default]]></command>
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33 <inputs>
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34 <expand macro="in_faq"/>
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35 <param label="mask bases with quality lower than INT" help="(-q)" name="q" type="integer" value="0"/>
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36 <param label="mask bases with quality higher than INT" help="(-X)" name="X" type="integer" value="255"/>
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37 <param area="false" default="0" label="masked bases converted to CHAR; 0 for lowercase" help="(-n)" name="n" type="text"/>
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38 <param label="number of residues per line; 0 for 2^32-1" help="(-l)" name="l" type="integer" value="0"/>
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39 <param label="quality shift: ASCII-INT gives base quality" help="(-Q)" name="Q" type="integer" value="33"/>
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40 <param label="random seed" help="effective with -f (-s)" name="s" type="integer" value="11"/>
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41 <param label="sample fraction of sequences" help="(-f)" name="f" type="float" value="1"/>
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42 <param area="false" default="null" label="mask regions in BED or name list FILE" help="(-M)" name="M" type="text"/>
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43 <param label="drop sequences with length shorter than INT" help="(-L)" name="L" type="integer" value="0"/>
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44 <param checked="false" label="mask complement region" help="effective with -M (-c)" name="c" type="boolean" falsevalue="" truevalue="-c"/>
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45 <param checked="false" label="reverse complement" help="(-r)" name="r" type="boolean" falsevalue="" truevalue="-r"/>
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46 <param checked="false" label="force FASTA output (discard quality)" help="(-A)" name="A" type="boolean" falsevalue="" truevalue="-A"/>
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47 <param checked="false" label="drop comments at the header lines" help="(-C)" name="C" type="boolean" falsevalue="" truevalue="-C"/>
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48 <param checked="false" label="drop sequences containing ambiguous bases" help="(-N)" name="N" type="boolean" falsevalue="" truevalue="-N"/>
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49 <param checked="false" label="output the 2n-1 reads only" help="(-1)" name="x1" type="boolean" falsevalue="" truevalue="-1"/>
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50 <param checked="false" label="output the 2n reads only" help="(-2)" name="x2" type="boolean" falsevalue="" truevalue="-2"/>
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51 <param checked="false" label="shift quality by '(-Q) - 33' " help="(-V)" name="V" type="boolean" falsevalue="" truevalue="-V"/>
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52 </inputs>
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53 <outputs>
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54 <data format_source="in_file" hidden="false" name="default"/>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <!-- This is a sorry excuse for a test for a tool which does way more
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59 than it should, but upstream decided to put a TON of functionality
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60 into a single tool rather than using the single responsibility
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61 principle. -->
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62 <param name="in_file" value="seqtk_seq.fa"/>
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63 <param name="r" value="True"/>
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64 <param name="n" value=""/>
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65 <param name="M" value=""/>
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66 <output name="default" file="seqtk_seq_revcom.fa" ftype="fasta"/>
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67 </test>
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68 </tests>
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69 <help><![CDATA[
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70 **What it does**
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71
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72 Various utilities for transforming FASTA/Q data
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73
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74 @ATTRIBUTION@
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75 ]]></help>
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76 </tool>
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