# HG changeset patch
# User iuc
# Date 1630482048 0
# Node ID 994e1ce9f4d56d2298c7805bbbb2ea99093ce847
# Parent 07f0df25bd0ca1bd59755942cdfbcc798a85d8d7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mitos commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
diff -r 07f0df25bd0c -r 994e1ce9f4d5 mitos.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mitos.xml.orig Wed Sep 01 07:40:48 2021 +0000
@@ -0,0 +1,259 @@
+<<<<<<< HEAD
+
+ de-novo annotation of metazoan mitochondrial genomes
+
+ mitos
+
+
+ macros.xml
+ MITOS
+ 1.0.5
+ 1
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+
+ mitos
+ zip
+
+ python -c "import mitos; print(mitos.__version__)"
+
+ de-novo annotation of metazoan mitochondrial genomes
+
+ mitos
+
+
+ macros.xml
+ MITOS
+ 1.0.5
+
+
+ mitos
+ zip
+
+ python -c "import mitos; print(mitos.__version__)"
+ >>>>>> 9b5f70762 (Use double quotes)
+mkdir outdir &&
+
+runmitos.py
+--input '$input'
+--code $code
+--outdir outdir
+--refdir '$refdir.fields.path'
+#for tpe in ["prot", "trna", "rrna"]
+ #if not $tpe in str($advanced.featuretypes).split(',')
+ --no$tpe
+ #end if
+#end for
+--finovl $advanced.finovl
+--evalue $advanced_prot.evalue
+--cutoff $advanced_prot.cutoff
+#set maxovl=float($advanced_prot.maxovl)/100.0
+--maxovl $maxovl
+--clipfac $advanced_prot.clipfac
+#set fragovl=float($advanced_prot.fragovl)/100.0
+--fragovl $fragovl
+--fragfac $advanced_prot.fragfac
+--ststrange $advanced_prot.ststrange
+
+#if "raw" in str($addoutputs).split(','):
+ && zip -9 -y -r output.zip outdir/ > /dev/null
+#end if
+ ]]>
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+ "bed" in str(addoutputs)
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+ "mito" in str(addoutputs)
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+ "gff" in str(addoutputs)
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+ "seq" in str(addoutputs)
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+ "fas" in str(addoutputs)
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+ "faa" in str(addoutputs)
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+ "geneorder" in str(addoutputs)
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+ "protein_plot" in str(addoutputs)
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+ "protein_plot" in str(addoutputs)
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+ "ncRNA_structure_svg_plots" in str(addoutputs)
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+ "raw" in str(addoutputs)
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+ @COMMON_HELP@
+
+
+ 10.1016/j.ympev.2012.08.023
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+
+
diff -r 07f0df25bd0c -r 994e1ce9f4d5 mitos2.xml
--- a/mitos2.xml Wed Jun 02 18:37:31 2021 +0000
+++ b/mitos2.xml Wed Sep 01 07:40:48 2021 +0000
@@ -1,5 +1,8 @@
de-novo annotation of metazoan mitochondrial genomes
+
+ mitos
+
macros.xml
MITOS2
diff -r 07f0df25bd0c -r 994e1ce9f4d5 mitos2.xml.orig
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/mitos2.xml.orig Wed Sep 01 07:40:48 2021 +0000
@@ -0,0 +1,384 @@
+<<<<<<< HEAD
+
+ de-novo annotation of metazoan mitochondrial genomes
+
+ mitos
+
+
+ macros.xml
+ MITOS2
+ 2.0.6
+ 1
+
+
+ mitos
+ zip
+
+ python -c "import mitos; print(mitos.__version__)"
+
+ de-novo annotation of metazoan mitochondrial genomes
+
+ mitos
+
+
+ macros.xml
+ MITOS2
+ 2.0.6
+
+
+ mitos
+ zip
+
+ python -c "import mitos; print(mitos.__version__)"
+ >>>>>> 9b5f70762 (Use double quotes)
+mkdir outdir &&
+
+runmitos.py
+--input '$input'
+--code $code
+--outdir outdir
+--refdir '/'
+--refseqver '$refseqver.fields.path'
+$linear
+#for tpe in ["prot", "trna", "rrna", "intron", "oril", "orih"]
+ #if not $tpe in str($advanced.featuretypes).split(',')
+ --$tpe 0
+ #end if
+#end for
+--finovl $advanced.finovl
+$advanced.best
+#set fragovl=float($advanced.fragovl)/100.0
+--fragovl $fragovl
+--fragfac $advanced.fragfac
+
+--evalue $advanced_prot.evalue
+#set cutoff=float($advanced_prot.cutoff)/100.0
+--cutoff $cutoff
+--clipfac $advanced_prot.clipfac
+$advanced_prot.ncbicode
+$advanced_prot.alarab
+$advanced_prot.oldstst
+$advanced_ncrna.locandgloc
+--ncev $advanced_ncrna.ncev
+$advanced_ncrna.sensitive
+--maxtrnaovl $advanced_ncrna.maxtrnaovl
+--maxrrnaovl $advanced_ncrna.maxrrnaovl
+
+#if not ("protein_plot" in str($addoutputs).split(',') or "ncRNA_plot" in str($addoutputs).split(',')):
+ --noplots
+#end if
+
+#if "raw" in str($addoutputs).split(','):
+ && zip -9 -y -r output.zip outdir/ > /dev/null
+#end if
+ ]]>
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+ "bed" in str(addoutputs)
+
+
+ "mito" in str(addoutputs)
+
+
+ "gff" in str(addoutputs)
+
+
+ "seq" in str(addoutputs)
+
+
+ "faa" in str(addoutputs)
+
+
+ "fas" in str(addoutputs)
+
+
+ "geneorder" in str(addoutputs)
+
+
+ "protein_plot" in str(addoutputs)
+
+
+ "ncRNA_plot" in str(addoutputs)
+
+
+
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+ "ncRNA_structure_svg_plots" in str(addoutputs)
+
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+ "raw" in str(addoutputs)
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+
+
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+
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+ @COMMON_HELP@
+
+
+ 10.1093/nar/gkz833
+ 10.1016/j.ympev.2016.09.024
+
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+