Mercurial > repos > thanhlv > biotradis

annotate biotradis_bacteria_tradis.xml @ 9:cbe965d49727 draft

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 44b6f6a2bdcd4ba2dabc3d65c7feefcd2ff3b6db-dirty"
author thanhlv
date Fri, 17 Jan 2020 11:32:36 -0500
parents 09c1f97a5bcc
children 4e8358bc80f9
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1 <tool id="bacteria_tradis" name="bacteria tradis" version="@VERSION@">
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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>
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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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10 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
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11 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
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12 #set $named_input_files = ''
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13 #for $input_file in $input_files
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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)
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16 ln -s '${input_file}' ${_input_file} &&
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17 echo ${_input_file} >> fq.list &&
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18 #end for
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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
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26 #if $smalt:
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27 $smalt
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28 #if str($smalt_k)!=""
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29 --smalt_k $smalt_k
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30 #end if
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31 #if str($smalt_s)!=""
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32 --smalt_s $smalt_s
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33 #end if
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34 --smalt_y $smalt_y
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35 --smalt_r $smalt_r
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36 -n "\${GALAXY_SLOTS:-2}"
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37 #end if
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38 $verbose
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39 && mkdir plots bams
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40 && mv *insert_site_plot.gz ./plots
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41 && mv *mapped.bam* ./bams
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42 ]]> </command>
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43 <inputs>
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44 <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" help="Support multiple files"/>
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45 <param name="tag" type="text" optional="true" label="Tag" help="Tag to search for" />
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46 <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" />
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47 <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)">
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48 <option value="3" selected="true">3</option>
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49 <option value="5">5</option>
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50 </param>
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51 <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag"/>
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52 <param name="m" type="integer" value="30" label="Mapping quality cutoff score"/>
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53 <param name="out_bam" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output mapped bam files"/>
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54 <param name="smalt" type="boolean" truevalue="--smalt" falsevalue="" checked="false" label="Use smalt as the mapper" help="Default mapper is bwa" />
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55 <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping"/>
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56 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping"/>
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57 <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT"/>
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58 <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT"/>
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59 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
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60 </inputs>
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61
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62 <outputs>
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63 <collection name="insert_plots" format="gz" type="list" label="Insert size plots">
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64 <discover_datasets pattern="__name_and_ext__" directory="plots" visible="true" />
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65 </collection>
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66 <collection name="mapped_bam" type="list" format="bam" label="Mapped bam files">
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67 <filter>out_bam is True</filter>
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68 <discover_datasets pattern="__name_and_ext__" directory="bams" visible="true" />
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69 </collection>
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70 <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/>
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71 </outputs>
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72
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73 <help>
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74 <![CDATA[
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75 Run a TraDIS analysis. This involves:
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76 1: filtering the data with tags matching that passed via -t option
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77 2: removing the tags from the sequences
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78 3: mapping
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79 4: creating an insertion site plot
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80 5: creating a stats summary
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81
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82 Usage: bacteria_tradis [options]
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83
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84 Options:
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85 -f : text file listing fastq files with tradis tags attached
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86 -t : tag to search for (optional. If not set runs bwa in tagless mode with no filtering.)
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87 -r : reference genome in fasta format (.fa)
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88 -td : tag direction - 3 or 5 (optional. default = 3)
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89 -mm : number of mismatches allowed when matching tag (optional. default = 0)
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90 -m : mapping quality cutoff score (optional. default = 30)
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91 -k : custom k-mer value (min seed length) (optional)
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92 --smalt : use smalt rather than bwa as the mapper
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93 --smalt_k : custom k-mer value for SMALT mapping (optional)
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94 --smalt_s : custom step size for SMALT mapping (optional)
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95 --smalt_y : custom y parameter for SMALT (optional. default = 0.96)
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96 --smalt_r : custom r parameter for SMALT (optional. default = -1)
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97 -n : number of threads to use for SMALT and samtools sort (optional. default = 1)
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98 -e : set defaults for essentiality experiment (smalt_r = 0, -m = 0)
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99 -v : verbose debugging output
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100
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101 Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_.
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102 ]]> </help>
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103 <expand macro="citations" />
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104
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105 </tool>