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comparison biotradis_bacteria_tradis.xml @ 3:d44c3626166e draft

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 2e1b1f737f3a3d7cfc6350c6936fbb0bd84a5dad-dirty
author thanhlv
date Thu, 25 Jul 2019 06:09:36 -0400
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children 7366ea56a6f3
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2:0cfaf8b3049f 3:d44c3626166e
1 <tool id="bacteria_tradis" name="bacteria tradis" version="@VERSION@">
2 <description>Generates a BAM file with tags added to read strings.</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements" />
7 <command detect_errors="exit_code"><![CDATA[
8 #import re
9
10 ## Creates symlinks for each input file based on the Galaxy 'element_identifier'
11 ## Used so that a human-readable name appears in the output table (instead of 'dataset_xyz.dat')
12 #set $named_input_files = ''
13 #for $input_file in $input_files
14 ## Add single quotes around each input file identifier
15 #set $_input_file = "'{}'".format($input_file.element_identifier)
16 ln -s '${input_file}' ${_input_file} &&
17 echo ${_input_file} >> fq.list &&
18 #end for
19
20 bacteria_tradis -f fq.list
21 -t $tag
22 -r $ref
23 -td $tag_dir
24 -mm $mm
25 -m $m
26 #if str($smalt_k)!=""
27 --smalt_k $smalt_k
28 #end if
29 #if str($smalt_s)!=""
30 --smalt_s $smalt_s
31 #end if
32 --smalt_y $smalt_y
33 --smalt_r $smalt_r
34 -n "\${GALAXY_SLOTS:-2}"
35 #if $verbose
36 --verbose
37 #end if
38 && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz
39 && tar cvzf mapped.tar.gz *mapped.bam*
40 ]]></command>
41 <inputs>
42 <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" />
43 <param name="tag" type="text" label="Tag" help="Tag to search for" />
44 <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" />
45 <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)" >
46 <option value="3" selected="true">3</option>
47 <option value="5">5</option>
48 </param>
49 <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" help="(optional. default = 0)" />
50 <param name="m" type="integer" value="30" label="Mapping quality cutoff score" help="(optional. default = 30)" />
51 <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" help="(optional)" />
52 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" help="(optional)" />
53 <param argument="--smalt_y" type="integer" value="0.96" label="Custom y parameter for SMALT" help="(optional. default = 0.96)" />
54 <param argument="--smalt_r" type="integer" value="-1" label="custom r parameter for SMALT" help="(optional. default = -1)" />
55 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
56 </inputs>
57
58 <outputs>
59 <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/>
60 <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/>
61 <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/>
62 </outputs>
63
64 <help>
65 <![CDATA[
66 Run a TraDIS analysis. This involves:
67 1: filtering the data with tags matching that passed via -t option
68 2: removing the tags from the sequences
69 3: mapping
70 4: creating an insertion site plot
71 5: creating a stats summary
72
73 Usage: bacteria_tradis [options]
74
75 Options:
76 -f : text file listing fastq files with tradis tags attached
77 -t : tag to search for
78 -r : reference genome in fasta format (.fa)
79 -td : tag direction - 3 or 5 (optional. default = 3)
80 -mm : number of mismatches allowed when matching tag (optional. default = 0)
81 -m : mapping quality cutoff score (optional. default = 30)
82 --smalt_k : custom k-mer value for SMALT mapping (optional)
83 --smalt_s : custom step size for SMALT mapping (optional)
84 --smalt_y : custom y parameter for SMALT (optional. default = 0.96)
85 --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)
87 -e : set defaults for essentiality experiment (smalt_r = 0, -m = 0)
88 -v : verbose debugging output
89
90 Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_.
91 ]]></help>
92
93 </tool>