Mercurial > repos > iuc > seqkit_fx2tab

annotate seqkit_fx2tab.xml @ 2:4cf00d20acab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 202bb1229cb0b8e8040a87d140edb6fdf7654628
author iuc
date Thu, 03 Nov 2022 19:36:37 +0000
parents c1aa9a90b4c4
children 1dc73570fd5a
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c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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1 <tool id="seqkit_fx2tab" name="SeqKit fx2tab" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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2 <description>convert FASTA/Q to tabular</description>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="bio_tools"/>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
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9 #import re
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10
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11 #set input_identifier = re.sub('[^\s\w\-]', '_', str($input.element_identifier))
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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12 ln -s '${input}' '${input_identifier}' &&
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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13
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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14 seqkit fx2tab
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15 '${input_identifier}'
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16 $alphabet
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17 $avg_qual
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18 $gc
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19 $gc_skew
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20 $header_line
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21 $length
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22 $name
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23 $no_qual
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24 $only_id
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25 #if str($input.ext) in ['fastqsanger', 'fastqsanger.gz']:
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26 --qual-ascii-base 33
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27 #end if
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28 $seq_hash
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29 > '$output'
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30 ]]></command>
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31 <inputs>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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32 <param name="input" type="data" format="fasta,fasta.gz,fastqsanger,fastqsanger.gz" label="Input file"/>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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33 <param argument="--alphabet" type="boolean" truevalue="--alphabet" falsevalue="" checked="false" label="Output alphabet letters?"/>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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34 <param argument="--avg_qual" type="boolean" truevalue="--avg-qual" falsevalue="" checked="false" label="Output average quality of the read?"/>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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35 <param argument="--gc" type="boolean" truevalue="--gc" falsevalue="" checked="false" label="Output GC content?"/>
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36 <param argument="--gc_skew" type="boolean" truevalue="--gc-skew" falsevalue="" checked="false" label="Output GC-Skew?"/>
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37 <param argument="--header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="false" label="Output header line?"/>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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38 <param argument="--length" type="boolean" truevalue="--length" falsevalue="" checked="false" label="Output sequence length?"/>
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39 <param argument="--name" type="boolean" truevalue="--name" falsevalue="" checked="false" label="Output only names (no sequences and qualities)?"/>
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40 <param argument="--no_qual" type="boolean" truevalue="--no-qual" falsevalue="" checked="false" label="Eliminate qualities from output?"/>
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41 <param argument="--only_id" type="boolean" truevalue="--only-id" falsevalue="" checked="false" label="Output id instead of full head?"/>
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42 <param argument="--seq_hash" type="boolean" truevalue="--seq-hash" falsevalue="" checked="false" label="Output md5 hash of sequence?"/>
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43 </inputs>
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44 <outputs>
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45 <data name="output" format="tabular"/>
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46 </outputs>
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47 <tests>
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48 <test expect_num_outputs="1">
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49 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
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50 <output name="output" file="fx2tab_output1.tabular" ftype="tabular"/>
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51 </test>
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52 <test expect_num_outputs="1">
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53 <param name="input" value="input1.fastq.gz" ftype="fastqsanger.gz"/>
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54 <param name="avg_qual" value="--avg-qual"/>
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55 <param name="header_line" value="--header-line"/>
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56 <param name="length" value="--length"/>
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57 <param name="name" value="--name"/>
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58 <param name="only_id" value="--only-id"/>
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59 <output name="output" file="fx2tab_output2.tabular" ftype="tabular"/>
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60 </test>
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61 <test expect_num_outputs="1">
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62 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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63 <output name="output" file="fx2tab_output3.tabular" ftype="tabular"/>
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64 </test>
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65 <test expect_num_outputs="1">
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66 <param name="input" value="input1.fasta.gz" ftype="fasta.gz"/>
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67 <param name="alphabet" value="--alphabet"/>
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68 <param name="avg_qual" value="--avg-qual"/>
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69 <param name="gc" value="--gc"/>
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70 <param name="gc_skew" value="--gc-skew"/>
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71 <param name="header_line" value="--header-line"/>
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72 <param name="length" value="--length"/>
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73 <param name="name" value="--name"/>
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74 <param name="no_qual" value="--no-qual"/>
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75 <param name="only_id" value="--only-id"/>
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76 <param name="seq_hash" value="--seq-hash"/>
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77 <output name="output" file="fx2tab_output4.tabular" ftype="tabular"/>
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78 </test>
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79 </tests>
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80 <help>
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81 **What it does**
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82
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83 Converts FASTA/Q to tabular format and adds columns for sequence length and GC content/GC skew. The output
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84 consists of 3 columns; id, sequence and quality unless one of the options to output only names or to eliminate
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85 qualities is selected or additional columns (e.g., md5 sequence hash) are requested.
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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86 </help>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
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87 <expand macro="citations"/>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
iuc
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88 </tool>
c1aa9a90b4c4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seqkit commit 15c99d80da6739b94a911a2744b523a2112cc55c
iuc
parents:
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89