Mercurial > repos > thanhlv > biotradis

annotate biotradis_bacteria_tradis.xml @ 5:bf790f407b1b draft

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author thanhlv
date Thu, 25 Jul 2019 06:28:00 -0400
parents 7366ea56a6f3
children 09c1f97a5bcc
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1 <tool id="bacteria_tradis" name="bacteria tradis" version="@VERSION@">
4
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2 <description>Generates a BAM file with tags added to read strings</description>
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3 <macros>
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4 <import>macros.xml</import>
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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5 </macros>
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6 <expand macro="requirements" />
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7 <command detect_errors="exit_code"><![CDATA[
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8 #import re
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9
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10 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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11 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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12 #set $named_input_files = ''
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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13 #for $input_file in $input_files
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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14 ## Add single quotes around each input file identifier
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15 #set $_input_file = "'{}'".format($input_file.element_identifier)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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16 ln -s '${input_file}' ${_input_file} &&
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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17 echo ${_input_file} >> fq.list &&
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18 #end for
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19
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20 bacteria_tradis -f fq.list
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21 -t $tag
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22 -r $ref
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23 -td $tag_dir
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24 -mm $mm
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25 -m $m
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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26 #if str($smalt_k)!=""
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27 --smalt_k $smalt_k
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28 #end if
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29 #if str($smalt_s)!=""
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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30 --smalt_s $smalt_s
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31 #end if
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32 --smalt_y $smalt_y
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33 --smalt_r $smalt_r
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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34 -n "\${GALAXY_SLOTS:-2}"
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35 #if $verbose
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36 --verbose
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37 #end if
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38 && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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39 && tar cvzf mapped.tar.gz *mapped.bam*
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40 ]]></command>
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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41 <inputs>
5
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42 <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" />
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43 <param name="tag" type="text" label="Tag" help="Tag to search for" />
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44 <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" />
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45 <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)" >
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46 <option value="3" selected="true">3</option>
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47 <option value="5">5</option>
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48 </param>
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49 <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" help="(optional. default = 0)" />
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50 <param name="m" type="integer" value="30" label="Mapping quality cutoff score" help="(optional. default = 30)" />
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51 <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" help="(optional)" />
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52 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" help="(optional)" />
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53 <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" help="(optional. default = 0.96)" />
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54 <param argument="--smalt_r" type="integer" value="-1" label="custom r parameter for SMALT" help="(optional. default = -1)" />
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55 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
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56 </inputs>
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57
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58 <outputs>
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59 <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/>
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60 <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/>
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61 <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/>
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62 </outputs>
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63
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64 <help>
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65 <![CDATA[
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66 Run a TraDIS analysis. This involves:
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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67 1: filtering the data with tags matching that passed via -t option
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68 2: removing the tags from the sequences
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69 3: mapping
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70 4: creating an insertion site plot
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71 5: creating a stats summary
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72
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73 Usage: bacteria_tradis [options]
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74
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75 Options:
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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76 -f : text file listing fastq files with tradis tags attached
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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77 -t : tag to search for
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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78 -r : reference genome in fasta format (.fa)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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79 -td : tag direction - 3 or 5 (optional. default = 3)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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80 -mm : number of mismatches allowed when matching tag (optional. default = 0)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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81 -m : mapping quality cutoff score (optional. default = 30)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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82 --smalt_k : custom k-mer value for SMALT mapping (optional)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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83 --smalt_s : custom step size for SMALT mapping (optional)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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84 --smalt_y : custom y parameter for SMALT (optional. default = 0.96)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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85 --smalt_r : custom r parameter for SMALT (optional. default = -1)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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86 -n : number of threads to use for SMALT and samtools sort (optional. default = 1)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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87 -e : set defaults for essentiality experiment (smalt_r = 0, -m = 0)
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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88 -v : verbose debugging output
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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89
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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90 Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_.
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91 ]]></help>
d44c3626166e planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
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92
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93 </tool>