# HG changeset patch
# User petr-novak
# Date 1693314404 0
# Node ID af85dfc8676d5ba3ed8c9cff54275867390100b7
# Parent  1cef42f5a11be28e588580f602e40b8e2d855928
planemo upload for repository https://github.com/kavonrtep/galaxy_packages commit 06d2db65d620a49e796b90a37c55f89e1e275e5d

diff -r 1cef42f5a11b -r af85dfc8676d macros.xml
--- a/macros.xml	Mon Aug 28 11:08:16 2023 +0000
+++ b/macros.xml	Tue Aug 29 13:06:44 2023 +0000
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.1</token>
+    <token name="@TOOL_VERSION@">1.1.1</token>
     <token name="@REQUIREMENT_VERSION@">1.0</token>
     <xml name="requirements">
         <requirements>
diff -r 1cef42f5a11b -r af85dfc8676d tidecluster.xml
--- 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"