Mercurial > repos > thanhlv > biotradis
diff 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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--- a/biotradis_bacteria_tradis.xml Fri Jan 17 11:32:36 2020 -0500 +++ b/biotradis_bacteria_tradis.xml Fri Jan 17 12:16:55 2020 -0500 @@ -25,14 +25,14 @@ -m $m #if $smalt: $smalt - #if str($smalt_k)!="" - --smalt_k $smalt_k + #if str($smalt_settings.smalt_k)!="" + --smalt_k $smalt_settings.smalt_k #end if - #if str($smalt_s)!="" - --smalt_s $smalt_s + #if str($smalt_settings.smalt_s)!="" + --smalt_s $smalt_settings.smalt_s #end if - --smalt_y $smalt_y - --smalt_r $smalt_r + --smalt_y $smalt_settings.smalt_y + --smalt_r $smalt_settings.smalt_r -n "\${GALAXY_SLOTS:-2}" #end if $verbose @@ -52,10 +52,12 @@ <param name="m" type="integer" value="30" label="Mapping quality cutoff score"/> <param name="out_bam" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output mapped bam files"/> <param name="smalt" type="boolean" truevalue="--smalt" falsevalue="" checked="false" label="Use smalt as the mapper" help="Default mapper is bwa" /> - <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping"/> - <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping"/> - <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT"/> - <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT"/> + <section name="smalt_settings" title="Optional setting for SMALT" expanded="False"> + <param argument="--smalt_k" type="integer" value="" optional="True" label="Custom k-mer value for SMALT mapping"/> + <param argument="--smalt_s" type="integer" value="" optional="True" label="Custom step size for SMALT mapping"/> + <param argument="--smalt_y" type="float" value="0.96" label="Custom y parameter for SMALT"/> + <param argument="--smalt_r" type="integer" value="-1" label="Custom r parameter for SMALT"/> + </section> <param argument="--verbose" type="boolean" truevalue="-v" falsevalue="" checked="false" label="verbose debugging output" help="(Default:No)" /> </inputs> @@ -67,7 +69,7 @@ <filter>out_bam is True</filter> <discover_datasets pattern="__name_and_ext__" directory="bams" visible="true" /> </collection> - <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fastqs.stats"/> + <data name="fastq_stats" format="txt" label="${tool.name} on ${on_string}: Fastq Stats" from_work_dir="fq.stats"/> </outputs> <help>