Mercurial > repos > thanhlv > biotradis

comparison biotradis_bacteria_tradis.xml @ 7:09c1f97a5bcc draft

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"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
author thanhlv
date Fri, 06 Dec 2019 10:11:20 -0500
parents bf790f407b1b
children cbe965d49727
comparison
equal deleted inserted replaced
6:5506c4307812 7:09c1f97a5bcc
35 #if $verbose 35 #if $verbose
36 --verbose 36 --verbose
37 #end if 37 #end if
38 && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz 38 && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz
39 && tar cvzf mapped.tar.gz *mapped.bam* 39 && tar cvzf mapped.tar.gz *mapped.bam*
40 ]]></command> 40 ]]> </command>
41 <inputs> 41 <inputs>
42 <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" /> 42 <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" />
43 <param name="tag" type="text" label="Tag" help="Tag to search for" /> 43 <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" /> 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)" > 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> 46 <option value="3" selected="true">3</option>
47 <option value="5">5</option> 47 <option value="5">5</option>
48 </param> 48 </param>
49 <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" help="(optional. default = 0)" /> 49 <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" help="(optional. default = 30)" /> 50 <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" help="(optional)" /> 51 <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" />
52 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" help="(optional)" /> 52 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" />
53 <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" help="(optional. default = 0.96)" /> 53 <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" />
54 <param argument="--smalt_r" type="integer" value="-1" label="custom r parameter for SMALT" help="(optional. default = -1)" /> 54 <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)" /> 55 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" />
56 </inputs> 56 </inputs>
57 57
58 <outputs> 58 <outputs>
59 <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/> 59 <data name="insert_size_plots" format="tar.gz" label="${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 ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/> 60 <data name="mapped_bam" format="tar.gz" label="${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 ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> 61 <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/>
62 </outputs> 62 </outputs>
63 63
64 <help> 64 <help>
65 <![CDATA[ 65 <![CDATA[
66 Run a TraDIS analysis. This involves: 66 Run a TraDIS analysis. This involves:
67 1: filtering the data with tags matching that passed via -t option 67 1: filtering the data with tags matching that passed via -t option
68 2: removing the tags from the sequences 68 2: removing the tags from the sequences
69 3: mapping 69 3: mapping
70 4: creating an insertion site plot 70 4: creating an insertion site plot
86 -n : number of threads to use for SMALT and samtools sort (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) 87 -e : set defaults for essentiality experiment (smalt_r = 0, -m = 0)
88 -v : verbose debugging output 88 -v : verbose debugging output
89 89
90 Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_. 90 Documentation can be found at `site <https://github.com/sanger-pathogens/Bio-Tradis>`_.
91 ]]></help> 91 ]]> </help>
92 <expand macro="citations" />
92 93
93 </tool> 94 </tool>