Mercurial > repos > jpayne > gtsubsampler
diff reads_subsampler.xml @ 5:3852b3edc8a4 tip
"planemo upload for repository https://toolrepo.galaxytrakr.org/"
| author | jpayne |
|---|---|
| date | Fri, 19 Feb 2021 17:51:59 -0500 |
| parents | 504004e78363 |
| children |
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--- a/reads_subsampler.xml Fri Feb 19 15:28:20 2021 -0500 +++ b/reads_subsampler.xml Fri Feb 19 17:51:59 2021 -0500 @@ -6,12 +6,10 @@ <command detect_errors="exit_code"><![CDATA[ #if $reads.reads_select == 'collection' python3 ${__tool_directory__}/subsamplr.py '$reads.coll.forward' '$reads.coll.reverse' '$downsampled.forward' '$downsampled.reverse' $coverage $genome_size '$seed' - #else - #if $reverse - python3 ${__tool_directory__}/subsamplr.py '$forward' '$reverse' $forward_out $reverse_out $coverage $genome_size '$seed' - #else - python3 ${__tool_directory__}/subsamplr.py '$forward' '$forward_out' $coverage $genome_size '$seed' - #end if + #elif $reads.reads_select == 'single' + python3 ${__tool_directory__}/subsamplr.py '$forward' '$forward_out' $coverage $genome_size '$seed' + #else + python3 ${__tool_directory__}/subsamplr.py '$forward' '$reverse' $forward_out $reverse_out $coverage $genome_size '$seed' #end if ]]></command> <inputs> @@ -34,8 +32,10 @@ </conditional> <param name="coverage" type="integer" label="Maximum Coverage" value="200" /> <param name="genome_size" type="select" label="Assumed Genome Size"> - <option value="4500000">Salmonella, E. Coli (4500000)</option> + <option value="5000000">Salmonella, E. Coli, Vibrio p. (5000000)</option> + <option value="4000000">Vibrio cholerae (4000000)</option> <option value="2700000">Listeria (2700000)</option> + <option value="1600000">Campylobacter (1600000)</option> <option value="29900">SARS-CoV-2 (29900)</option> </param> <param name="seed" type="text" value="ed2b99d842cddc1ac81d7c01a0bf0555" label="Random seed (you don't have to change this)"/> @@ -56,6 +56,15 @@ <tests> <test> <conditional name="reads"> + <param name="reads_select" value="single" /> + <param name="forward" value="forward.fastq" /> + </conditional> + <param name="coverage" value="20" /> + <param name="genome_size" value="29900" /> + <output name="forward_out" value="forward_out.fastq" /> + </test> + <test> + <conditional name="reads"> <param name="reads_select" value="collection" /> <param name="coll"> <collection type="paired">