Mercurial > repos > thanhlv > biotradis

comparison 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
comparison
equal deleted inserted replaced
8:99427def7645 9:cbe965d49727
21 -t $tag 21 -t $tag
22 -r $ref 22 -r $ref
23 -td $tag_dir 23 -td $tag_dir
24 -mm $mm 24 -mm $mm
25 -m $m 25 -m $m
26 #if str($smalt_k)!="" 26 #if $smalt:
27 $smalt
28 #if str($smalt_k)!=""
27 --smalt_k $smalt_k 29 --smalt_k $smalt_k
28 #end if 30 #end if
29 #if str($smalt_s)!="" 31 #if str($smalt_s)!=""
30 --smalt_s $smalt_s 32 --smalt_s $smalt_s
31 #end if 33 #end if
32 --smalt_y $smalt_y 34 --smalt_y $smalt_y
33 --smalt_r $smalt_r 35 --smalt_r $smalt_r
34 -n "\${GALAXY_SLOTS:-2}" 36 -n "\${GALAXY_SLOTS:-2}"
35 #if $verbose
36 --verbose
37 #end if 37 #end if
38 && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz 38 $verbose
39 && tar cvzf mapped.tar.gz *mapped.bam* 39 && mkdir plots bams
40 && mv *insert_site_plot.gz ./plots
41 && mv *mapped.bam* ./bams
40 ]]> </command> 42 ]]> </command>
41 <inputs> 43 <inputs>
42 <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" /> 44 <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" help="Support multiple files"/>
43 <param name="tag" type="text" optional="true" label="Tag" help="Tag to search for" /> 45 <param name="tag" type="text" optional="true" label="Tag" help="Tag to search for" />
44 <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" /> 46 <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" />
45 <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)"> 47 <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)">
46 <option value="3" selected="true">3</option> 48 <option value="3" selected="true">3</option>
47 <option value="5">5</option> 49 <option value="5">5</option>
48 </param> 50 </param>
49 <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" /> 51 <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag"/>
50 <param name="m" type="integer" value="30" label="Mapping quality cutoff score" /> 52 <param name="m" type="integer" value="30" label="Mapping quality cutoff score"/>
51 <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" /> 53 <param name="out_bam" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output mapped bam files"/>
52 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" /> 54 <param name="smalt" type="boolean" truevalue="--smalt" falsevalue="" checked="false" label="Use smalt as the mapper" help="Default mapper is bwa" />
53 <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" /> 55 <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping"/>
54 <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT" /> 56 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping"/>
57 <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT"/>
58 <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT"/>
55 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> 59 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
56 </inputs> 60 </inputs>
57 61
58 <outputs> 62 <outputs>
59 <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/> 63 <collection name="insert_plots" format="gz" type="list" label="Insert size plots">
60 <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/> 64 <discover_datasets pattern="__name_and_ext__" directory="plots" visible="true" />
65 </collection>
66 <collection name="mapped_bam" type="list" format="bam" label="Mapped bam files">
67 <filter>out_bam is True</filter>
68 <discover_datasets pattern="__name_and_ext__" directory="bams" visible="true" />
69 </collection>
61 <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> 70 <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/>
62 </outputs> 71 </outputs>
63 72
64 <help> 73 <help>
65 <![CDATA[ 74 <![CDATA[
72 81
73 Usage: bacteria_tradis [options] 82 Usage: bacteria_tradis [options]
74 83
75 Options: 84 Options:
76 -f : text file listing fastq files with tradis tags attached 85 -f : text file listing fastq files with tradis tags attached
77 -t : tag to search for 86 -t : tag to search for (optional. If not set runs bwa in tagless mode with no filtering.)
78 -r : reference genome in fasta format (.fa) 87 -r : reference genome in fasta format (.fa)
79 -td : tag direction - 3 or 5 (optional. default = 3) 88 -td : tag direction - 3 or 5 (optional. default = 3)
80 -mm : number of mismatches allowed when matching tag (optional. default = 0) 89 -mm : number of mismatches allowed when matching tag (optional. default = 0)
81 -m : mapping quality cutoff score (optional. default = 30) 90 -m : mapping quality cutoff score (optional. default = 30)
91 -k : custom k-mer value (min seed length) (optional)
92 --smalt : use smalt rather than bwa as the mapper
82 --smalt_k : custom k-mer value for SMALT mapping (optional) 93 --smalt_k : custom k-mer value for SMALT mapping (optional)
83 --smalt_s : custom step size for SMALT mapping (optional) 94 --smalt_s : custom step size for SMALT mapping (optional)
84 --smalt_y : custom y parameter for SMALT (optional. default = 0.96) 95 --smalt_y : custom y parameter for SMALT (optional. default = 0.96)
85 --smalt_r : custom r parameter for SMALT (optional. default = -1) 96 --smalt_r : custom r parameter for SMALT (optional. default = -1)
86 -n : number of threads to use for SMALT and samtools sort (optional. default = 1) 97 -n : number of threads to use for SMALT and samtools sort (optional. default = 1)