Mercurial > repos > thanhlv > biotradis
comparison biotradis_bacteria_tradis.xml @ 7:09c1f97a5bcc draft
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 1c12becfd708c0635632ab92620a846764ec4559-dirty"
author | thanhlv |
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date | Fri, 06 Dec 2019 10:11:20 -0500 |
parents | bf790f407b1b |
children | cbe965d49727 |
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6:5506c4307812 | 7:09c1f97a5bcc |
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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> |