Mercurial > repos > thanhlv > biotradis
changeset 9:cbe965d49727 draft
"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 | 99427def7645 |
| children | 4e8358bc80f9 |
| files | biotradis_bacteria_tradis.xml |
| diffstat | 1 files changed, 30 insertions(+), 19 deletions(-) [+] |
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--- a/biotradis_bacteria_tradis.xml Fri Dec 06 10:15:14 2019 -0500 +++ b/biotradis_bacteria_tradis.xml Fri Jan 17 11:32:36 2020 -0500 @@ -23,41 +23,50 @@ -td $tag_dir -mm $mm -m $m - #if str($smalt_k)!="" + #if $smalt: + $smalt + #if str($smalt_k)!="" --smalt_k $smalt_k - #end if - #if str($smalt_s)!="" - --smalt_s $smalt_s - #end if + #end if + #if str($smalt_s)!="" + --smalt_s $smalt_s + #end if --smalt_y $smalt_y --smalt_r $smalt_r -n "\${GALAXY_SLOTS:-2}" - #if $verbose - --verbose #end if - && tar cvzf insert_site_plot.tar.gz *insert_site_plot.gz - && tar cvzf mapped.tar.gz *mapped.bam* + $verbose + && mkdir plots bams + && mv *insert_site_plot.gz ./plots + && mv *mapped.bam* ./bams ]]> </command> <inputs> - <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" /> + <param name="input_files" type="data" format="fastqsanger,fastqsanger.gz,fastqsanger.bz2" multiple="true" label="Input files" help="Support multiple files"/> <param name="tag" type="text" optional="true" label="Tag" help="Tag to search for" /> <param name="ref" type="data" format="fasta" label="Reference geome" help="Fasta format" /> <param name="tag_dir" type="select" label="Tag direction" help="3 or 5(optional. default = 3)"> <option value="3" selected="true">3</option> <option value="5">5</option> </param> - <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag" /> - <param name="m" type="integer" value="30" label="Mapping quality cutoff score" /> - <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping" /> - <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping" /> - <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT" /> - <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT" /> + <param name="mm" type="integer" value="0" label="Number of mismatches allowed when matching tag"/> + <param name="m" type="integer" value="30" label="Mapping quality cutoff score"/> + <param name="out_bam" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output mapped bam files"/> + <param name="smalt" type="boolean" truevalue="--smalt" falsevalue="" checked="false" label="Use smalt as the mapper" help="Default mapper is bwa" /> + <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping"/> + <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping"/> + <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT"/> + <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT"/> <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> </inputs> <outputs> - <data name="insert_size_plots" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="insert_site_plot.tar.gz"/> - <data name="mapped_bam" format="tar.gz" label="${tool.name} on ${on_string}: Insert size plot" from_work_dir="mapped.tar.gz"/> + <collection name="insert_plots" format="gz" type="list" label="Insert size plots"> + <discover_datasets pattern="__name_and_ext__" directory="plots" visible="true" /> + </collection> + <collection name="mapped_bam" type="list" format="bam" label="Mapped bam files"> + <filter>out_bam is True</filter> + <discover_datasets pattern="__name_and_ext__" directory="bams" visible="true" /> + </collection> <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> </outputs> @@ -74,11 +83,13 @@ Options: -f : text file listing fastq files with tradis tags attached - -t : tag to search for + -t : tag to search for (optional. If not set runs bwa in tagless mode with no filtering.) -r : reference genome in fasta format (.fa) -td : tag direction - 3 or 5 (optional. default = 3) -mm : number of mismatches allowed when matching tag (optional. default = 0) -m : mapping quality cutoff score (optional. default = 30) + -k : custom k-mer value (min seed length) (optional) + --smalt : use smalt rather than bwa as the mapper --smalt_k : custom k-mer value for SMALT mapping (optional) --smalt_s : custom step size for SMALT mapping (optional) --smalt_y : custom y parameter for SMALT (optional. default = 0.96)