# HG changeset patch
# User bvalot
# Date 1655383050 0
# Node ID 349c2fbd38a0382816cdd9d247d1fae1ee7e9da9
"planemo upload for repository https://github.com/bvalot/panISa commit 13edfab02a5da9e374c38ecbd0e229ec0f8d53bb"
diff -r 000000000000 -r 349c2fbd38a0 isfinder_search.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/isfinder_search.xml Thu Jun 16 12:37:30 2022 +0000
@@ -0,0 +1,87 @@
+
+ Search IS homology in ISFinder from panISa output
+
+ panisa
+
+
+
+
+ ISFinder_search.py -v
+
+ ISFinder_search.py
+ -r ' '
+ #if str($length)
+ -l $length
+ #end if
+ #if str($identity)
+ -i $identity
+ #end if
+ #if str($evalue)
+ -e $evalue
+ #end if
+ #if str($alignment)
+ -a $alignment
+ #end if
+ #for $panisa in $panisa_list:
+ #if $panisa:
+ '$panisa'
+ #end if
+ #end for
+ #for $panisa in $panisa_list:
+ #if $panisa:
+ | sed -e "~s/`echo $panisa.file_name | sed -e
+ '~s/.*\///'`/$panisa.name.replace('panISa on ', '')/"
+ #end if
+ #end for
+ > '$output'
+ 2> /dev/null
+
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+**What it does**
+
+Automate search integrative element (IS) homology in ISFinder from panISa output.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`.
+
+PanISa program was publised recently:
+
+Treepong, P., Guyeux, C., Meunier, A., Couchoud, C., Hocquet, D. et Valot, B. (2018). PanISa : Ab initio detection of insertion sequences in bacterial genomes from short read sequence
+data. Bioinformatics.
+
+
+ 10.1093/bioinformatics/bty479
+
+
diff -r 000000000000 -r 349c2fbd38a0 panisa.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/panisa.xml Thu Jun 16 12:37:30 2022 +0000
@@ -0,0 +1,74 @@
+
+ Search integrative element (IS) insertion on a genome using BAM alignment
+
+ panisa
+
+
+
+
+ panISa.py -v
+
+ panISa.py
+ #if str($quality)
+ -q $quality
+ #end if
+ #if str($minimun)
+ -m $minimun
+ #end if
+ #if str($size)
+ -s $size
+ #end if
+ #if str($percentage)
+ -p $percentage
+ #end if
+ '$bam' > '$output'
+
+
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+
+
+
+
+
+
+
+
+**What it does**
+
+Search integrative element (IS) insertion on a genome using BAM alignment.
+
+**License and citation**
+
+This Galaxy tool is Copyright © 2018 `B. Valot` and is released under the `GPL3 license`.
+
+PanISa program was publised :
+
+Treepong, P., Guyeux, C., Meunier, A., Couchoud, C., Hocquet, D. et Valot, B. (2018). PanISa : Ab initio detection of insertion sequences in bacterial genomes from short read sequence
+data. Bioinformatics.
+
+
+ 10.1093/bioinformatics/bty479
+
+
diff -r 000000000000 -r 349c2fbd38a0 test-data/input.bam
Binary file test-data/input.bam has changed
diff -r 000000000000 -r 349c2fbd38a0 test-data/isfinder.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/isfinder.txt Thu Jun 16 12:37:30 2022 +0000
@@ -0,0 +1,2 @@
+Sample Chromosome Start_Position Stop_Position Potential_sequence Potential_IS Alignment
+panisa.txt contig-2000003 334442 334451 CAATGTCATCAACTTTGGAAATTATCCATA-GCAGGGCTGCAGCTTAGGTTGATGACATTG ISPa1635 two side
diff -r 000000000000 -r 349c2fbd38a0 test-data/panisa.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/panisa.txt Thu Jun 16 12:37:30 2022 +0000
@@ -0,0 +1,2 @@
+Chromosome End position End clipped reads Direct repeats Start position Start clipped reads Inverted repeats Left sequence Right sequence
+contig-2000003 334451 59 GTCCTGGAGC 334442 40 No IR CAATGTCATCAACTTTGGAAATTATCCATAAATATCATATAATTAGCGCTCAAATCAGTGCATGGGAGNNGNC NNNNNGGCCATGGCGGCTGGCTGCTTCGGGGGGCTTGCCTTGGGCAGGGCTGCAGCTTAGGTTGATGACATTG