Mercurial > repos > petr-novak > tidecluster
diff tidecluster.xml @ 5:af85dfc8676d draft
planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 06d2db65d620a49e796b90a37c55f89e1e275e5d
| author | petr-novak |
|---|---|
| date | Tue, 29 Aug 2023 13:06:44 +0000 |
| parents | 299f14a6050a |
| children | 971dbc97e607 |
line wrap: on
line diff
--- a/tidecluster.xml Mon Aug 28 11:08:16 2023 +0000 +++ b/tidecluster.xml Tue Aug 29 13:06:44 2023 +0000 @@ -13,8 +13,8 @@ -l '$library' #end if -m $min_length - -T ' -p $min_period -P $max_period -e $max_diverg' - -nd $no_dust + -T ' -p $min_period -P $max_period -e $max_diverg -c $min_copy' + $no_dust -c \${GALAXY_SLOTS:-1} -M $min_total_length && @@ -22,13 +22,13 @@ && cp tidecluster_clustering.gff3 '$gff3_clustering' && - cp tidecluster_tarean_report.html '$tarean_report' + if [ -f tidecluster_tarean_report.html ]; then cp tidecluster_tarean_report.html '$tarean_report'; fi && mkdir -p ${tarean_report.extra_files_path} && - cp -r tidecluster_tarean ${tarean_report.extra_files_path}/ + if [ -d tidecluster_tarean ]; then cp -r tidecluster_tarean ${tarean_report.extra_files_path}/; fi && - cp tidecluster_consensus_dimer_library.fasta ${trc_library} + if [ -f tidecluster_consensus_dimer_library.fasta ]; then cp tidecluster_consensus_dimer_library.fasta ${trc_library}; fi && zip -r output.zip * #if $library: @@ -55,10 +55,14 @@ <param type="float" name="max_diverg" value="0.25" label="Maximum allowed divergence rate between two consecutive repeats" min="0" max="1"/> + <param type="integer" name="min_copy" value="5" + label="minimum copy number of tandem repeat" min="2"/> <param type="boolean" name="no_dust" truevalue="--no_dust" falsevalue="" checked="false" label="Do not use dust filter in blastn when clustering"/> <param type="integer" name="min_total_length" value="50000" - label="Minimum combined length of tandem repeat arrays within a single cluster"/> + label="Minimum combined length of tandem repeat arrays within a single cluster" + help="Minimum combined length of tandem repeat arrays within a single cluster, required for inclusion in TAREAN analysis" + /> </inputs> <outputs> <data name="output_archive" format="zip"