Mercurial > repos > iuc > poretools_extract

annotate poretools_extract.xml @ 2:263124f77b6f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:04:46 +0000
parents f97175ea170d
children 30817f9dd63a
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f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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1 <?xml version="1.0"?>
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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2 <tool id="poretools_extract" name="Extract reads" version="@VERSION@.0">
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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3 <description>in FASTA or FASTQ format from nanopore files</description>
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263124f77b6f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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4 <expand macro="bio_tools"/>
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5 <macros>
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6 <import>macros.xml</import>
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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7 </macros>
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8 <expand macro="requirements" />
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9 <command detect_errors="aggressive">
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10 <![CDATA[
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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11 poretools $output_format --type $type --min-length $min_length --max-length $max_length
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12 $quality
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13 #if $group:
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14 --group '$group'
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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15 #end if
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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16 #if $start:
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17 --start '$start'
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18 #end if
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19 #if $end:
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20 --end '$end'
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21 #end if
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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22 '$input' > '$output'
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23 ]]>
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24 </command>
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25 <inputs>
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26 <param name="input" type="data" format="h5,fast5.tar,fast5.tar.gz,fast5.tar.bz2" label="Input fast5 or archive of fast5 files" />
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27 <param name="output_format" type="select" label="Output format">
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28 <option value="fastq">FASTQ</option>
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29 <option value="fasta">FASTA</option>
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30 </param>
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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31 <expand macro="length_options" />
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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32 <param argument="--type" type="select" label="FASTQ Type">
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33 <option value="all">All</option>
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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34 <option value="fwd">Forward</option>
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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35 <option value="rev">Reverse</option>
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36 <option value="2D">2D</option>
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37 <option value="fwd,rev">Forward and reverse</option>
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38 <option value="best">Best</option>
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39 </param>
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40 <param name="quality" type="select" label="Filter by complement events">
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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41 <option value="">Do not filter</option>
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42 <option value="--high-quality">Only report reads with more</option>
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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43 <option value="--normal-quality">Only report reads with fewer</option>
f97175ea170d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/poretools commit aee00b3755588862ab34c199c28578706c004a34
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44 </param>
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45 <param argument="--group" type="integer" optional="True" label="Base calling group serial number to extract" />
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46 <param argument="--start" type="integer" optional="True" label="Start timestamp" />
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47 <param argument="--end" type="integer" optional="True" label="End timestamp" />
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48 </inputs>
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49 <outputs>
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50 <data name="output" format="fastq">
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51 <change_format>
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52 <when input="output_format" value="fasta" format="fasta" />
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53 </change_format>
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54 </data>
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55 </outputs>
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56 <tests>
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57 <test>
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58 <expand macro="test_input" />
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59 <param name="output_format" value="fastq" />
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60 <output name="output" file="poretools-extract-out1.fastq" ftype="fastq" />
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61 </test>
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62 <test>
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63 <expand macro="test_input" />
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64 <param name="output_format" value="fasta" />
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65 <output name="output" file="poretools-extract-out1.fasta" ftype="fasta" />
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66 </test>
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67 </tests>
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68 <help>
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69 Extract sequences from fast5 files generated by the Oxford Nanopore sequencing technology.
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70 </help>
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71 <expand macro="citations" />
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72 </tool>