Mercurial > repos > thanhlv > biotradis
comparison biotradis_bacteria_tradis.xml @ 10:4e8358bc80f9 draft
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/biotradis commit 35e807998700f046b29e0b8100416cf6ea0f930b-dirty"
| author | thanhlv |
|---|---|
| date | Fri, 17 Jan 2020 12:16:55 -0500 |
| parents | cbe965d49727 |
| children | 47269fae5647 |
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| 9:cbe965d49727 | 10:4e8358bc80f9 |
|---|---|
| 23 -td $tag_dir | 23 -td $tag_dir |
| 24 -mm $mm | 24 -mm $mm |
| 25 -m $m | 25 -m $m |
| 26 #if $smalt: | 26 #if $smalt: |
| 27 $smalt | 27 $smalt |
| 28 #if str($smalt_k)!="" | 28 #if str($smalt_settings.smalt_k)!="" |
| 29 --smalt_k $smalt_k | 29 --smalt_k $smalt_settings.smalt_k |
| 30 #end if | 30 #end if |
| 31 #if str($smalt_s)!="" | 31 #if str($smalt_settings.smalt_s)!="" |
| 32 --smalt_s $smalt_s | 32 --smalt_s $smalt_settings.smalt_s |
| 33 #end if | 33 #end if |
| 34 --smalt_y $smalt_y | 34 --smalt_y $smalt_settings.smalt_y |
| 35 --smalt_r $smalt_r | 35 --smalt_r $smalt_settings.smalt_r |
| 36 -n "\${GALAXY_SLOTS:-2}" | 36 -n "\${GALAXY_SLOTS:-2}" |
| 37 #end if | 37 #end if |
| 38 $verbose | 38 $verbose |
| 39 && mkdir plots bams | 39 && mkdir plots bams |
| 40 && mv *insert_site_plot.gz ./plots | 40 && mv *insert_site_plot.gz ./plots |
| 50 </param> | 50 </param> |
| 51 <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"/> |
| 52 <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"/> |
| 53 <param name="out_bam" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output mapped bam files"/> | 53 <param name="out_bam" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output mapped bam files"/> |
| 54 <param name="smalt" type="boolean" truevalue="--smalt" falsevalue="" checked="false" label="Use smalt as the mapper" help="Default mapper is bwa" /> | 54 <param name="smalt" type="boolean" truevalue="--smalt" falsevalue="" checked="false" label="Use smalt as the mapper" help="Default mapper is bwa" /> |
| 55 <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping"/> | 55 <section name="smalt_settings" title="Optional setting for SMALT" expanded="False"> |
| 56 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping"/> | 56 <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping"/> |
| 57 <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT"/> | 57 <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping"/> |
| 58 <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT"/> | 58 <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT"/> |
| 59 <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT"/> | |
| 60 </section> | |
| 59 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> | 61 <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> |
| 60 </inputs> | 62 </inputs> |
| 61 | 63 |
| 62 <outputs> | 64 <outputs> |
| 63 <collection name="insert_plots" format="gz" type="list" label="Insert size plots"> | 65 <collection name="insert_plots" format="gz" type="list" label="Insert size plots"> |
| 65 </collection> | 67 </collection> |
| 66 <collection name="mapped_bam" type="list" format="bam" label="Mapped bam files"> | 68 <collection name="mapped_bam" type="list" format="bam" label="Mapped bam files"> |
| 67 <filter>out_bam is True</filter> | 69 <filter>out_bam is True</filter> |
| 68 <discover_datasets pattern="__name_and_ext__" directory="bams" visible="true" /> | 70 <discover_datasets pattern="__name_and_ext__" directory="bams" visible="true" /> |
| 69 </collection> | 71 </collection> |
| 70 <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> | 72 <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fq.stats"/> |
| 71 </outputs> | 73 </outputs> |
| 72 | 74 |
| 73 <help> | 75 <help> |
| 74 <![CDATA[ | 76 <![CDATA[ |
| 75 Run a TraDIS analysis. This involves: | 77 Run a TraDIS analysis. This involves: |