Mercurial > repos > bgruening > pileometh
changeset 7:15df15127c18 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c
| author | bgruening |
|---|---|
| date | Fri, 23 Mar 2018 17:52:57 -0400 |
| parents | 906db57d5d65 |
| children | 183cb55b1729 |
| files | MethylDackel.xml test-data/cg100.bed test-data/test7_output.tsv test-data/test8_output.tsv |
| diffstat | 4 files changed, 226 insertions(+), 16 deletions(-) [+] |
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--- a/MethylDackel.xml Tue Jun 13 01:01:31 2017 -0400 +++ b/MethylDackel.xml Fri Mar 23 17:52:57 2018 -0400 @@ -1,18 +1,10 @@ -<tool id="pileometh" name="MethylDackel" version="0.3.0"> +<tool id="pileometh" name="MethylDackel" version="0.3.0.1"> <description>A tool for processing bisulfite sequencing alignments</description> <requirements> <requirement type="package" version="0.3.0">methyldackel</requirement> </requirements> - <stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> - </stdio> <version_command><![CDATA[MethylDackel --version]]></version_command> - <command><![CDATA[ + <command detect_errors="aggressive"><![CDATA[ #if $reference_source.reference_source_selector == "cached": ln -s $reference_source.ref_file.fields.path reference.fasta && #else: @@ -44,6 +36,9 @@ #if $advanced_options.mbias_regionString: -r $advanced_options.mbias_regionString #end if + #if $advanced_options.regionBed: + -l '$advanced_options.regionBed' + #end if $advanced_options.keepDupes $advanced_options.keepSingleton $advanced_options.keepDiscordant @@ -75,6 +70,7 @@ #end if $advanced_options.CHG $advanced_options.CHH + $advanced_options.noCpG #end if reference.fasta @@ -82,7 +78,7 @@ $input_sortedAlignBAM #if $main_task.task == "mbias": - out_mbias && + out_mbias $main_task.tsv > out_mbias.tsv && touch out_mbias_OT.svg && touch out_mbias_OB.svg && touch out_mbias_CTOT.svg && @@ -131,7 +127,10 @@ <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" /> <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" /> </when> - <when value="mbias"/> + <when value="mbias"> + <param name="tsv" type="boolean" truevalue="--txt" falsevalue="" + label="output tab separated mbias metrics"/> + </when> </conditional> <conditional name="advanced_options"> <param name="options" type="select" label="Advanced options"> @@ -139,7 +138,8 @@ <option value="yes">Display advanced options</option> </param> <when value="yes"> - <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation"/> + <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation (e.g. chr1:1-100)"/> + <param name="regionBed" type="data" optional="true" format='bed' label="Bed file of regions for inclusion"/> <param name="keepDupes" type="boolean" checked="false" truevalue="--keepDupes" falsevalue="" label="By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated" /> <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" @@ -150,7 +150,7 @@ <param name="min_phred" type="integer" value="5" label="Minimum Phred threshold to include a base (default 5). This must be >0."/> <param name="max_pbdepth" type="integer" value="2000" label="Maximum per-base depth (default 2000)"/> <param name="min_pbdepth" type="integer" value="1" min="1" label="Minimum per-base depth" - help="Minimum per-base dpeth for reporting output. If you use --mergeContext (above), then this applies to the merged CpG/CHG (default 1). (-d)" /> + help="Minimum per-base depth for reporting output. If you use --mergeContext (above), then this applies to the merged CpG/CHG (default 1). (-d)" /> <param name="ignoreFlags" type="integer" value="3840" label="Ignore certain alignments" help="By deault, any alignment marked as secondary (bit 0x100), failing QC (bit 0x200), a PCR/optical duplicate (0x400) or supplemental (0x800) is ignored. This equates to a value of 0xF00 or 3840 in decimal. If you would like to change that, you can specify a new value here." /> @@ -170,10 +170,12 @@ <param name="methylKit" type="boolean" checked="false" truevalue="--methylKit" falsevalue="" label="Output in the format required by methylKit. This is mutually exclusive with --counts, --fraction, and --logit" /> + <param name="noCpG" type="boolean" checked="false" truevalue="--noCpG" falsevalue="" + label="Do not output CpG context methylation metrics" /> <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue="" - label="Additional output file with CHG methylation metrics" /> + label="Output CHG context methylation metrics" /> <param name="CHH" type="boolean" checked="false" truevalue="--CHH" falsevalue="" - label="Additional output file with CHH methylation metrics" /> + label="Output CHH context methylation metrics" /> <param name="nOT" type="text" value="" label="Original top strand absolute bounds (comma-separated, no spaces)" help="Like --OT, but always exclude INT bases from a given end @@ -196,6 +198,7 @@ <filter>not advanced_options['methylKit']</filter> <filter>not advanced_options['counts']</filter> <filter>not advanced_options['fraction']</filter> + <filter>not advanced_options['noCpG']</filter> </data> <data name="outFileExtractCpGLogit" format="bedgraph" from_work_dir="output_CpG.logit.bedGraph" label="${tool.name} on ${on_string} (logit)"> @@ -281,6 +284,11 @@ <filter>advanced_options['options'] == "yes"</filter> <filter>advanced_options['CHH']</filter> </data> + <data name="outFileMbiasTSV" format="tabular" from_work_dir="out_mbias.tsv" + label="${tool.name} on ${on_string} (methylation bias, tsv)"> + <filter>main_task['task'] == 'mbias'</filter> + <filter>main_task['tsv']</filter> + </data> <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg" label="${tool.name} on ${on_string} (methylation bias, original top strand)"> <filter>main_task['task'] == 'mbias'</filter> @@ -361,6 +369,27 @@ <param name="methylKit" value="true" /> <output name="outFileExtractCpGMethylKit" file="test_5.methylKit" ftype="text" compare="diff"/> </test> + <test> + <param name="task" value="mbias" /> + <param name="min_mapq" value="2" /> + <param name="options" value="yes"/> + <param name="tsv" value="--txt"/> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="cg100.fa" ftype="fasta" /> + <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/> + <output name="outFileMbiasTSV" file="test7_output.tsv" ftype="tabular" compare="diff"/> + </test> + <test> + <param name="task" value="mbias" /> + <param name="min_mapq" value="2" /> + <param name="options" value="yes"/> + <param name="regionBed" ftype="bed" value="cg100.bed"/> + <param name="tsv" value="--txt"/> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="cg100.fa" ftype="fasta" /> + <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/> + <output name="outFileMbiasTSV" file="test8_output.tsv" ftype="tabular" compare="diff"/> + </test> </tests> <help><![CDATA[
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cg100.bed Fri Mar 23 17:52:57 2018 -0400 @@ -0,0 +1,1 @@ +chrCG 10 90
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test7_output.tsv Fri Mar 23 17:52:57 2018 -0400 @@ -0,0 +1,99 @@ +Strand Read Position nMethylated nUnmethylated +OT 1 1 1 0 +OT 2 1 1 0 +OT 1 3 1 0 +OT 2 3 1 0 +OT 1 5 1 0 +OT 2 5 1 0 +OT 1 7 1 0 +OT 2 7 1 0 +OT 1 9 1 0 +OT 2 9 1 0 +OT 1 11 1 0 +OT 2 11 1 0 +OT 1 13 1 0 +OT 2 13 1 0 +OT 1 15 1 0 +OT 2 15 1 0 +OT 1 17 0 1 +OT 2 17 1 0 +OT 1 19 1 0 +OT 2 19 1 0 +OT 1 21 1 0 +OT 2 21 1 0 +OT 1 23 1 0 +OT 2 23 1 0 +OT 1 25 1 0 +OT 2 25 1 0 +OT 1 27 1 0 +OT 2 27 1 0 +OT 1 29 1 0 +OT 2 29 1 0 +OT 1 31 1 0 +OT 2 31 1 0 +OT 1 33 1 0 +OT 2 33 1 0 +OT 1 35 1 0 +OT 2 35 1 0 +OT 1 37 1 0 +OT 2 37 1 0 +OT 1 39 1 0 +OT 2 39 1 0 +OT 1 41 1 0 +OT 2 41 1 0 +OT 1 43 1 0 +OT 2 43 1 0 +OT 1 45 1 0 +OT 2 45 1 0 +OT 1 47 1 0 +OT 2 47 1 0 +OT 1 49 1 0 +OT 2 49 1 0 +OT 1 51 1 0 +OT 2 51 1 0 +OT 1 53 1 0 +OT 2 53 1 0 +OT 1 55 1 0 +OT 2 55 1 0 +OT 1 57 1 0 +OT 2 57 1 0 +OT 1 59 1 0 +OT 2 59 1 0 +OT 1 61 1 0 +OT 2 61 1 0 +OT 1 63 1 0 +OT 2 63 1 0 +OT 1 65 1 0 +OT 2 65 1 0 +OT 1 67 1 0 +OT 2 67 1 0 +OT 1 69 1 0 +OT 2 69 1 0 +OT 1 71 1 0 +OT 2 71 1 0 +OT 1 73 1 0 +OT 2 73 1 0 +OT 1 75 1 0 +OT 2 75 1 0 +OT 1 77 1 0 +OT 2 77 1 0 +OT 1 79 1 0 +OT 2 79 1 0 +OT 1 81 1 0 +OT 2 81 1 0 +OT 1 83 1 0 +OT 2 83 1 0 +OT 1 85 1 0 +OT 2 85 1 0 +OT 1 87 1 0 +OT 2 87 1 0 +OT 1 89 1 0 +OT 2 89 1 0 +OT 1 91 1 0 +OT 2 91 1 0 +OT 1 93 1 0 +OT 2 93 1 0 +OT 1 95 1 0 +OT 2 95 1 0 +OT 1 97 1 0 +OT 2 97 1 0
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test8_output.tsv Fri Mar 23 17:52:57 2018 -0400 @@ -0,0 +1,81 @@ +Strand Read Position nMethylated nUnmethylated +OT 1 11 1 0 +OT 2 11 1 0 +OT 1 13 1 0 +OT 2 13 1 0 +OT 1 15 1 0 +OT 2 15 1 0 +OT 1 17 0 1 +OT 2 17 1 0 +OT 1 19 1 0 +OT 2 19 1 0 +OT 1 21 1 0 +OT 2 21 1 0 +OT 1 23 1 0 +OT 2 23 1 0 +OT 1 25 1 0 +OT 2 25 1 0 +OT 1 27 1 0 +OT 2 27 1 0 +OT 1 29 1 0 +OT 2 29 1 0 +OT 1 31 1 0 +OT 2 31 1 0 +OT 1 33 1 0 +OT 2 33 1 0 +OT 1 35 1 0 +OT 2 35 1 0 +OT 1 37 1 0 +OT 2 37 1 0 +OT 1 39 1 0 +OT 2 39 1 0 +OT 1 41 1 0 +OT 2 41 1 0 +OT 1 43 1 0 +OT 2 43 1 0 +OT 1 45 1 0 +OT 2 45 1 0 +OT 1 47 1 0 +OT 2 47 1 0 +OT 1 49 1 0 +OT 2 49 1 0 +OT 1 51 1 0 +OT 2 51 1 0 +OT 1 53 1 0 +OT 2 53 1 0 +OT 1 55 1 0 +OT 2 55 1 0 +OT 1 57 1 0 +OT 2 57 1 0 +OT 1 59 1 0 +OT 2 59 1 0 +OT 1 61 1 0 +OT 2 61 1 0 +OT 1 63 1 0 +OT 2 63 1 0 +OT 1 65 1 0 +OT 2 65 1 0 +OT 1 67 1 0 +OT 2 67 1 0 +OT 1 69 1 0 +OT 2 69 1 0 +OT 1 71 1 0 +OT 2 71 1 0 +OT 1 73 1 0 +OT 2 73 1 0 +OT 1 75 1 0 +OT 2 75 1 0 +OT 1 77 1 0 +OT 2 77 1 0 +OT 1 79 1 0 +OT 2 79 1 0 +OT 1 81 1 0 +OT 2 81 1 0 +OT 1 83 1 0 +OT 2 83 1 0 +OT 1 85 1 0 +OT 2 85 1 0 +OT 1 87 1 0 +OT 2 87 1 0 +OT 1 89 1 0 +OT 2 89 1 0