# HG changeset patch
# User iuc
# Date 1613030458 0
# Node ID 859e0611960c2de9a746fb9dc0bb88f667a626fd
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701"
diff -r 000000000000 -r 859e0611960c jvarkit_wgscoverageplotter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/jvarkit_wgscoverageplotter.xml Thu Feb 11 08:00:58 2021 +0000
@@ -0,0 +1,232 @@
+
+ Plot read coverage across a genomic contig
+
+ 20201223
+
+
+ jvarkit-wgscoverageplotter
+ samtools
+ imagemagick
+
+ reference.dict &&
+ cat reference.dict &&
+ ln -s '$alignment_file' '$alignment_name' &&
+ ln -s '${alignment_file.metadata.bam_index}' '${alignment_name}.bai' &&
+ wgscoverageplotter.sh
+ --reference reference.fasta
+ --dimension '$dimension'
+ --output plot.svg
+ $adv.disable_paired_overlap
+ #if $include_regex
+ -I '$include_regex'
+ #end if
+ #if $exclude_regex
+ -X '$exclude_regex'
+ #end if
+ --mapq $adv.min_mapq
+ --max-depth $adv.max_depth
+ $adv.clip
+ --min-contig-length '$adv.min_contig_length'
+ --percentile $adv.percentile
+ $adv.points
+ #if str($adv.sample_filter.filter_by_sample) == "true"
+ --samples '$adv.sample_filter.samples'
+ --partition '$adv.sample_filter.partition'
+ #end if
+ '$alignment_name' &&
+ #if str($format) == "SVG"
+ mv plot.svg '$plot_output'
+ #else
+ convert plot.svg '$format:$plot_output'
+ #end if
+ ]]>
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+ [0-9,]+(bp|b|kb|k|mb|m)?$
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+ 10.6084/m9.figshare.1425030
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diff -r 000000000000 -r 859e0611960c test-data/fasta_indexes.loc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fasta_indexes.loc Thu Feb 11 08:00:58 2021 +0000
@@ -0,0 +1,1 @@
+sars-cov-2-fragment SARS-CoV-2 SARS-CoV-2 ${__HERE__}/reference.fasta
diff -r 000000000000 -r 859e0611960c test-data/reference.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fasta Thu Feb 11 08:00:58 2021 +0000
@@ -0,0 +1,35 @@
+>MN908947.3
+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCT
+GTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACT
+CACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATC
+TTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
+CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAAC
+ACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGG
+AGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG
+CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAA
+ACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACT
+CGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGG
+CGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGG
+TGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGA
+TCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGA
+ACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG
+CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTC
+ATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCG
+TGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCA
+GACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAA
+TTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAA
+GCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATG
+CAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA
+GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGA
+AGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGC
+ATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGG
+CTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTC
+TTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGG
+TTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGA
+AATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA
+GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAA
+AGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTAC
+AAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCC
+TCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCT
+TGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGG
+AATTTCACAGTATTCACTGA
diff -r 000000000000 -r 859e0611960c test-data/reference.fasta.fai
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/reference.fasta.fai Thu Feb 11 08:00:58 2021 +0000
@@ -0,0 +1,1 @@
+MN908947.3 2000 12 60 61
diff -r 000000000000 -r 859e0611960c test-data/sars_cov2_trimmed_cut.bam
Binary file test-data/sars_cov2_trimmed_cut.bam has changed
diff -r 000000000000 -r 859e0611960c tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Feb 11 08:00:58 2021 +0000
@@ -0,0 +1,12 @@
+
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+ value, dbkey, name, path
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+ value, dbkey, name, path
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\ No newline at end of file
diff -r 000000000000 -r 859e0611960c tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Thu Feb 11 08:00:58 2021 +0000
@@ -0,0 +1,7 @@
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+ value, dbkey, name, path
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+