| Next changeset 1:364b8ee3a3e4 (2021-02-11) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/jvarkit commit ee258cf884aa478b4ce4f978c4239f237c813701" |
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added:
jvarkit_wgscoverageplotter.xml test-data/fasta_indexes.loc test-data/reference.fasta test-data/reference.fasta.fai test-data/sars_cov2_trimmed_cut.bam tool_data_table_conf.xml.sample tool_data_table_conf.xml.test |
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| 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 |
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| b'@@ -0,0 +1,232 @@\n+<tool id="jvarkit_wgscoverageplotter" name="BAM Coverage Plotter" version="@TOOL_VERSION@+galaxy0">\n+ <description>Plot read coverage across a genomic contig</description>\n+ <macros>\n+ <token name="@TOOL_VERSION@">20201223</token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@TOOL_VERSION@">jvarkit-wgscoverageplotter</requirement>\n+ <requirement type="package" version="1.11">samtools</requirement>\n+ <requirement type="package" version="7.0.10_62">imagemagick</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ #set include_regex = str($adv.include_contig_regex).strip()\n+ #set exclude_regex = str($adv.skip_contig_regex).strip()\n+ #set alignment_name = str($alignment_file.element_identifier)\n+ #if str($reference.source) == "history"\n+ ln -s \'$reference.hist_genome\' reference.fasta &&\n+ samtools faidx reference.fasta &&\n+ #else\n+ #set ref_path = str($reference.cached_genome.fields.path)\n+ #set ref_index_path = str($reference.cached_genome.fields.path) + \'.fai\'\n+ ln -s \'$ref_path\' reference.fasta &&\n+ ln -s \'$ref_index_path\' reference.fasta.fai &&\n+ #end if\n+ samtools view -H \'$alignment_file\' |grep -E \'^(@HD|@SQ)\' >reference.dict &&\n+ cat reference.dict &&\n+ ln -s \'$alignment_file\' \'$alignment_name\' &&\n+ ln -s \'${alignment_file.metadata.bam_index}\' \'${alignment_name}.bai\' &&\n+ wgscoverageplotter.sh \n+ --reference reference.fasta\n+ --dimension \'$dimension\'\n+ --output plot.svg\n+ $adv.disable_paired_overlap\n+ #if $include_regex\n+ -I \'$include_regex\'\n+ #end if\n+ #if $exclude_regex\n+ -X \'$exclude_regex\'\n+ #end if\n+ --mapq $adv.min_mapq\n+ --max-depth $adv.max_depth\n+ $adv.clip\n+ --min-contig-length \'$adv.min_contig_length\'\n+ --percentile $adv.percentile\n+ $adv.points\n+ #if str($adv.sample_filter.filter_by_sample) == "true"\n+ --samples \'$adv.sample_filter.samples\'\n+ --partition \'$adv.sample_filter.partition\'\n+ #end if\n+ \'$alignment_name\' &&\n+ #if str($format) == "SVG"\n+ mv plot.svg \'$plot_output\'\n+ #else\n+ convert plot.svg \'$format:$plot_output\'\n+ #end if\n+ ]]>\n+ </command>\n+ <inputs>\n+ <conditional name="reference">\n+ <param name="source" type="select"\n+ label="Will you select a reference genome from your history or use a built-in genome?">\n+ <option value="cached">Use a built-in genome</option>\n+ <option value="history" selected="true">Use a genome from my history</option>\n+ </param>\n+ <when value="cached">\n+ <!-- NOTE: wgscoverageplotter requires the genome to be both indexed (with samtools index)\n+ and also have a dictionary (from picard CreateSequenceDictionary). since there is no\n+ way to specify both of these requirements, we take the indexed genome and build a dictionary -->\n+ <param name="cached_genome" type="select"\n+ label="Reference genome"\n+ help="The FASTA reference genome that reads were mapped against.">\n+ <options from_data_table="fasta_indexes" />\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="hist_genome" type="data" format="fasta"\n+ label="Reference genome"\n+ help="The FASTA reference genome that reads were mapped against."/>\n+ </when>\n+ </conditional>\n+ <param name="alignment_file" type="data" format="bam" label="BAM alignment" />\n+ <param argument="--dimension" value="1000x500" type="text" label="Image dimensions" />\n+ <'..b'rtitions are modelled on the GATK logic as described here: https://gatk.broadinstitute.org/hc/en-us/articles/360051307491-DepthOfCoverage-BETA-#--partition-type">\n+ <option value="sample" selected="true">sample</option>\n+ <option value="readgroup">readgroup</option>\n+ <option value="library">library</option>\n+ <option value="platform">platform</option>\n+ <option value="sample_by_platform">sample_by_platform</option>\n+ <option value="sample_by_platform_by_center">sample_by_platform_by_center</option>\n+ <option value="any">any</option>\n+ </param>\n+ </when>\n+ <when value="false">\n+ </when>\n+ </conditional>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data format="png" name="plot_output">\n+ <change_format>\n+ <when input="format" value="SVG" format="svg" />\n+ </change_format>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <conditional name="reference">\n+ <param name="source" value="history" />\n+ <param name="hist_genome" ftype="fasta" value="reference.fasta" />\n+ </conditional>\n+ <param name="alignment_file" ftype="bam" value="sars_cov2_trimmed_cut.bam" />\n+ <output name="plot_output">\n+ <assert_contents>\n+ <has_size value="26303" delta="15000" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="reference">\n+ <param name="source" value="history" />\n+ <param name="hist_genome" ftype="fasta" value="reference.fasta" />\n+ </conditional>\n+ <param name="alignment_file" ftype="bam" value="sars_cov2_trimmed_cut.bam" />\n+ <param name="format" value="SVG" />\n+ <output name="plot_output">\n+ <assert_contents>\n+ <has_size value="7805" delta="2000"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="reference">\n+ <param name="source" value="history" />\n+ <param name="hist_genome" ftype="fasta" value="reference.fasta" />\n+ </conditional>\n+ <param name="alignment_file" ftype="bam" value="sars_cov2_trimmed_cut.bam" />\n+ <section name="adv">\n+ <param name="max_depth" value="50" />\n+ </section>\n+ <output name="plot_output">\n+ <assert_contents>\n+ <has_size value="25410" delta="15000" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <conditional name="reference">\n+ <param name="source" value="cached" />\n+ <param name="cached_genome" value="sars-cov-2-fragment" />\n+ </conditional>\n+ <param name="alignment_file" ftype="bam" value="sars_cov2_trimmed_cut.bam" />\n+ <output name="plot_output">\n+ <assert_contents>\n+ <has_size value="26303" delta="15000" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+\n+ </tests>\n+ <help><![CDATA[\n+\n+ **WGSCoveragePlotter from the jvarkit toolkit** \n+\n+ WGSCoveragePlotter_ is a tool to plot the coverage of aligned reads across a genomic contig. It takes\n+ as input a BAM file and a genomic contig in FASTA format and produces an image in either PNG or SVG format\n+ showing the depth of read coverage across the contig. \n+\n+ .. _WGSCoveragePlotter: http://lindenb.github.io/jvarkit/WGSCoveragePlotter.html\n+ ]]>\n+ </help>\n+ <citations>\n+ <citation type="doi">10.6084/m9.figshare.1425030</citation>\n+ </citations>\n+</tool>\n' |
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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 |
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| @@ -0,0 +1,1 @@ +sars-cov-2-fragment SARS-CoV-2 SARS-CoV-2 ${__HERE__}/reference.fasta |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -0,0 +1,1 @@ +MN908947.3 2000 12 60 61 |
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| diff -r 000000000000 -r 859e0611960c test-data/sars_cov2_trimmed_cut.bam |
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| Binary file test-data/sars_cov2_trimmed_cut.bam has changed |
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| 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 |
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| @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/all_fasta.loc" /> + </table> + <!-- Locations of samtools indexed genomes --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/fasta_indexes.loc" /> + </table> +</tables> \ No newline at end of file |
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| 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 |
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| @@ -0,0 +1,7 @@ +<tables> + <!-- Locations of FASTA index ffiles for testing --> + <table name="fasta_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/fasta_indexes.loc" /> + </table> +</tables> |