| Next changeset 1:d1b66015effd (2016-09-21) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit 033c712216994524fdd120b771052ac4ca9e51c0-dirty |
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added:
PileOMeth.xml all_fasta.loc.sample static/images/example.svg test-data/cg100.fa test-data/cg_aln.bam test-data/test_1.bedGraph test-data/test_2_output.svg tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r 65575e70af7e PileOMeth.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/PileOMeth.xml Fri Sep 18 11:39:55 2015 -0400 |
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| b'@@ -0,0 +1,212 @@\n+<tool id="pileometh" name="PileOMeth" version="0.1.5">\n+ <description>A tool for processing bisulfite sequencing alignments</description>\n+ <requirements>\n+ <requirement type="package" version="0.1.5">pileometh</requirement>\n+ </requirements>\n+ <stdio>\n+ <!-- Anything other than zero is an error -->\n+ <exit_code range="1:" />\n+ <exit_code range=":-1" />\n+ <!-- In case the return code has not been set propery check stderr too -->\n+ <regex match="Error:" />\n+ <regex match="Exception:" />\n+ </stdio>\n+ <version_command><![CDATA[PileOMeth 2>&1 | head -n 2 | tail -n 1]]></version_command>\n+ <command><![CDATA[\n+ ln -s $reference_source.ref_file reference.fasta &&\n+\n+ PileOMeth\n+ $main_task.task\n+\n+ #if $main_task.task == "extract":\n+ -o output\n+ $main_task.mergeContext\n+ #end if\n+\n+ #if $advanced_options.options=="yes":\n+ #if $advanced_options.mbias_regionString:\n+ -r $advanced_options.mbias_regionString\n+ #end if\n+ $advanced_options.keepDupes\n+ $advanced_options.keepSingleton\n+ -q $advanced_options.min_mapq\n+ -p $advanced_options.min_phred\n+ -D $advanced_options.max_pbdepth\n+ $advanced_options.CHG\n+ $advanced_options.CHH\n+ #end if\n+\n+ reference.fasta\n+\n+ $input_sortedAlignBAM\n+\n+ #if $main_task.task == "mbias":\n+ out_mbias\n+ #end if\n+ ]]></command>\n+ <inputs>\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Load reference genome from">\n+ <option value="cached">Local cache</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Using reference genome" help="Reference sequence">\n+ <options from_data_table="all_fasta"/>\n+ <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>\n+ </param>\n+ </when>\n+ <when value="history">\n+ <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />\n+ </when>\n+ </conditional>\n+\n+ <param name="input_sortedAlignBAM" multiple="False" type="data" format="bam" label="sorted_alignments.bam"/>\n+ <conditional name="main_task">\n+ <param name="task" type="select" label="What do you want to do?" >\n+ <option value="extract">Extract methylation metrics from an alignment file in BAM/CRAM format</option>\n+ <option value="mbias">Determine the position-dependent methylation bias in a dataset, producing diagnostic SVG images</option>\n+ </param>\n+ <when value="extract">\n+ <param name="mergeContext" type="boolean" checked="false" truevalue="--mergeContext" falsevalue=""\n+ label="Merge per-Cytosine metrics from CpG and CHG contexts into per-CPG or per-CHG metrics" help="(--mergeContext)" />\n+ </when>\n+ <when value="mbias"/>\n+ </conditional>\n+ <conditional name="advanced_options">\n+ <param name="options" type="select" label="Advanced options">\n+ <option value="">Hide advanced options</option>\n+ <option value="yes">Display advanced options</option>\n+ </param>\n+ <when value="yes">\n+ <param name="mbias_regionString" type="text" value="" label="Region string in'..b'ate\n+3. The end coordinate\n+4. The methylation percentage rounded to an integer\n+5. The number of alignments/pairs reporting methylated bases\n+6. The number of alignments/pairs reporting unmethylated bases\n+\n+All coordinates are 0-based half open, which conforms to the bedGraph definition. When paired-end reads are aligned, it can often occur that their alignments overlap. In such cases, PileOMeth will not count both reads of the pair in its output, as doing so would lead to incorrect downstream statistical results.\n+\n+An example of the output is below::\n+\n+#track type="bedGraph" description="SRR1182519.sorted CpG methylation levels"\n+#1 25115 25116 100 3 0\n+#1 29336 29337 50 1 1\n+\n+Note the header line, which starts with "track". The "description" field is used as a label in programs such as IGV. Each of the subsequent lines describe single Cytosines, the 25116th and 29337th base on chromosome 1, respectively. The first position has 3 alignments (or pairs of alignments) indicating methylation and 0 indicating unmethylation (100% methylation) and the second position has 1 alignment each supporting methylation and unmethylation (50% methylation).\n+\n+**Per-CpG/CHG metrics**\n+\n+In many circumstances, it\'s desireable for metrics from individual Cytosines in a CpG to be merged, producing per-CpG metrics rather than per-Cytosine metrics. This can be accomplished with the **Merge per-Cytosine** parameter. If this is used, then this output::\n+\n+#track type="bedGraph" description="SRR1182519.sorted CpG methylation levels"\n+#1 25114 25115 100 2 1\n+#1 25115 25116 100 3 0\n+\n+is changed to this::\n+\n+#track type="bedGraph" description="SRR1182519.sorted merged CpG methylation levels"\n+#1 25114 25116 100 5 1\n+\n+This also works for CHG-level metrics. If bedGraph files containing per-Cytosine metrics already exist, they can be converted to instead contain per-CpG/CHG metrics with PileOMeth mergeContext.\n+\n+**Methylation bias plotting and correction**\n+\n+In an ideal experiment, we expect that the probability of observing a methylated C is constant across the length of any given read. In practice, however, there are often increases/decreases in observed methylation rate at the ends of reads and/or more global changes. These are termed methylation bias and including such regions in the extracted methylation metrics will result in noisier and less accurate data. For this reason, users are strongly encouraged to make a methylation bias plot.\n+\n+That command will create a methylation bias (mbias for short) plot for each of the strands for which there are valid alignments.\n+The resulting mbias graphs are in SVG format and can be viewed in most modern web browsers:\n+\n+.. image:: example.svg\n+\n+\n+If you have paired-end data, both reads in the pair will be shown separately, as is the case above. The program will suggest regions for inclusion ("--OT 2,0,0,98" above) and mark them on the plot, if applicable. The format of this output is described in PileOMeth extract -h. These suggestions should not be accepted blindly; users are strongly encouraged to have a look for themselves and tweak the actual bounds as appropriate. The lines indicate the average methylation percentage at a given position and the shaded regions the 99.9% confidence interval around it. This is useful in gauging how many methylation calls a given position has relative to its neighbors. Note the spike in methylation at the end of read #2 and the corresponding dip at the beginning of read #1. This is common and these regions can be ignored with the suggested trimming bounds. Note also that the numbers refer to the first and last base that should be included during methylation extraction, not the last and first base to ignore!.\n+\n+-----\n+\n+**PileOMeth** is a Free and Open Source Software, see more details on the PileOMeth_ Website.\n+\n+.. _PileOMeth: https://github.com/dpryan79/PileOMeth\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 65575e70af7e all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/all_fasta.loc.sample Fri Sep 18 11:39:55 2015 -0400 |
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| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
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| diff -r 000000000000 -r 65575e70af7e static/images/example.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/example.svg Fri Sep 18 11:39:55 2015 -0400 |
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x="615" y="340" text-anchor="start" dominant-baseline="middle">#2</text>\n+</svg>\n' |
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| diff -r 000000000000 -r 65575e70af7e test-data/cg100.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cg100.fa Fri Sep 18 11:39:55 2015 -0400 |
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| @@ -0,0 +1,2 @@ +>chrCG +cgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcgcA |
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| diff -r 000000000000 -r 65575e70af7e test-data/cg_aln.bam |
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| Binary file test-data/cg_aln.bam has changed |
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| diff -r 000000000000 -r 65575e70af7e test-data/test_1.bedGraph --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_1.bedGraph Fri Sep 18 11:39:55 2015 -0400 |
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| @@ -0,0 +1,49 @@ +track type="bedGraph" description="output CpG methylation levels" +chrCG 0 1 100 1 0 +chrCG 2 3 100 1 0 +chrCG 4 5 100 1 0 +chrCG 6 7 100 1 0 +chrCG 8 9 100 1 0 +chrCG 10 11 100 1 0 +chrCG 12 13 100 1 0 +chrCG 14 15 100 1 0 +chrCG 18 19 100 1 0 +chrCG 20 21 100 1 0 +chrCG 22 23 100 1 0 +chrCG 24 25 100 1 0 +chrCG 26 27 100 1 0 +chrCG 28 29 100 1 0 +chrCG 30 31 100 1 0 +chrCG 32 33 100 1 0 +chrCG 34 35 100 1 0 +chrCG 36 37 100 1 0 +chrCG 38 39 100 1 0 +chrCG 40 41 100 1 0 +chrCG 42 43 100 1 0 +chrCG 44 45 100 1 0 +chrCG 46 47 100 1 0 +chrCG 48 49 100 1 0 +chrCG 50 51 100 1 0 +chrCG 52 53 100 1 0 +chrCG 54 55 100 1 0 +chrCG 56 57 100 1 0 +chrCG 58 59 100 1 0 +chrCG 60 61 100 1 0 +chrCG 62 63 100 1 0 +chrCG 64 65 100 1 0 +chrCG 66 67 100 1 0 +chrCG 68 69 100 1 0 +chrCG 70 71 100 1 0 +chrCG 72 73 100 1 0 +chrCG 74 75 100 1 0 +chrCG 76 77 100 1 0 +chrCG 78 79 100 1 0 +chrCG 80 81 100 1 0 +chrCG 82 83 100 1 0 +chrCG 84 85 100 1 0 +chrCG 86 87 100 1 0 +chrCG 88 89 100 1 0 +chrCG 90 91 100 1 0 +chrCG 92 93 100 1 0 +chrCG 94 95 100 1 0 +chrCG 96 97 100 1 0 |
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| diff -r 000000000000 -r 65575e70af7e test-data/test_2_output.svg --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_2_output.svg Fri Sep 18 11:39:55 2015 -0400 |
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| diff -r 000000000000 -r 65575e70af7e tool-data/all_fasta.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/all_fasta.loc.sample Fri Sep 18 11:39:55 2015 -0400 |
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| @@ -0,0 +1,18 @@ +#This file lists the locations and dbkeys of all the fasta files +#under the "genome" directory (a directory that contains a directory +#for each build). The script extract_fasta.py will generate the file +#all_fasta.loc. This file has the format (white space characters are +#TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, all_fasta.loc could look something like this: +# +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +# +#Your all_fasta.loc file should contain an entry for each individual +#fasta file. So there will be multiple fasta files for each build, +#such as with hg19 above. +# |
| b |
| diff -r 000000000000 -r 65575e70af7e tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Fri Sep 18 11:39:55 2015 -0400 |
| b |
| @@ -0,0 +1,7 @@ +<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> +</tables> |
| b |
| diff -r 000000000000 -r 65575e70af7e tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Sep 18 11:39:55 2015 -0400 |
| [ |
| @@ -0,0 +1,22 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="pileometh" version="0.1.5"> + <install version="1.0"> + <actions> + <action target_filename="PileOMeth-0.1.5.tar.gz" type="download_by_url">https://github.com/dpryan79/PileOMeth/archive/0.1.5.tar.gz</action> + <action type="shell_command">make</action> + <action type="shell_command">make install prefix=$INSTALL_DIR</action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + <environment_variable name="PILEOMETH_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> + <![CDATA[ + PileOMeth: A tool for processing bisulfite sequencing alignments. + See https://github.com/dpryan79/PileOMeth/ + ]]> + </readme> + </package> +</tool_dependency> |
