| Previous changeset 6:906db57d5d65 (2017-06-13) Next changeset 8:183cb55b1729 (2018-08-24) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/methyldackel commit 6a688af07eb65f08922cf59dabcbc1b16277db8c |
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modified:
MethylDackel.xml |
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added:
test-data/cg100.bed test-data/test7_output.tsv test-data/test8_output.tsv |
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| diff -r 906db57d5d65 -r 15df15127c18 MethylDackel.xml --- a/MethylDackel.xml Tue Jun 13 01:01:31 2017 -0400 +++ b/MethylDackel.xml Fri Mar 23 17:52:57 2018 -0400 |
| [ |
| b'@@ -1,18 +1,10 @@\n-<tool id="pileometh" name="MethylDackel" version="0.3.0">\n+<tool id="pileometh" name="MethylDackel" version="0.3.0.1">\n <description>A tool for processing bisulfite sequencing alignments</description>\n <requirements>\n <requirement type="package" version="0.3.0">methyldackel</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[MethylDackel --version]]></version_command>\n- <command><![CDATA[\n+ <command detect_errors="aggressive"><![CDATA[\n #if $reference_source.reference_source_selector == "cached":\n ln -s $reference_source.ref_file.fields.path reference.fasta &&\n #else:\n@@ -44,6 +36,9 @@\n #if $advanced_options.mbias_regionString:\n -r $advanced_options.mbias_regionString\n #end if\n+ #if $advanced_options.regionBed:\n+ -l \'$advanced_options.regionBed\'\n+ #end if\n $advanced_options.keepDupes\n $advanced_options.keepSingleton\n $advanced_options.keepDiscordant\n@@ -75,6 +70,7 @@\n #end if\n $advanced_options.CHG\n $advanced_options.CHH\n+ $advanced_options.noCpG\n #end if\n \n reference.fasta\n@@ -82,7 +78,7 @@\n $input_sortedAlignBAM\n \n #if $main_task.task == "mbias":\n- out_mbias &&\n+ out_mbias $main_task.tsv > out_mbias.tsv &&\n touch out_mbias_OT.svg &&\n touch out_mbias_OB.svg &&\n touch out_mbias_CTOT.svg &&\n@@ -131,7 +127,10 @@\n <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />\n <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" />\n </when>\n- <when value="mbias"/>\n+ <when value="mbias">\n+ <param name="tsv" type="boolean" truevalue="--txt" falsevalue=""\n+ label="output tab separated mbias metrics"/>\n+ </when>\n </conditional>\n <conditional name="advanced_options">\n <param name="options" type="select" label="Advanced options">\n@@ -139,7 +138,8 @@\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 which to extract methylation"/>\n+ <param name="mbias_regionString" type="text" value="" label="Region string in which to extract methylation (e.g. chr1:1-100)"/>\n+ <param name="regionBed" type="data" optional="true" format=\'bed\' label="Bed file of regions for inclusion"/>\n <param name="keepDupes" type="boolean" checked="false" truevalue="--keepDupes" falsevalue=""\n label="By default, any alignment marked as a duplicate is ignored. This option causes them to be incorporated" />\n <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue=""\n@@ -150,7 +150,7 @@\n <param name="min_phred" type="integer" value="5" label="Minimum Phred threshold to include a base (default 5). This must be >0."/>\n <param name="max_pbdepth" type="integer" value="2000" label="Maximum per-base depth (default 2000)"/>\n <param name="min_pbdepth" type="integer" value="1" min="1" label="Minimum per-base depth"\n- help="Minimum pe'..b'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." />\n@@ -170,10 +170,12 @@\n <param name="methylKit" type="boolean" checked="false" truevalue="--methylKit" falsevalue=""\n label="Output in the format required by methylKit. This is mutually exclusive with --counts, --fraction, and --logit" />\n \n+ <param name="noCpG" type="boolean" checked="false" truevalue="--noCpG" falsevalue=""\n+ label="Do not output CpG context methylation metrics" />\n <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue=""\n- label="Additional output file with CHG methylation metrics" />\n+ label="Output CHG context methylation metrics" />\n <param name="CHH" type="boolean" checked="false" truevalue="--CHH" falsevalue=""\n- label="Additional output file with CHH methylation metrics" />\n+ label="Output CHH context methylation metrics" />\n \n <param name="nOT" type="text" value="" label="Original top strand absolute bounds (comma-separated, no spaces)"\n help="Like --OT, but always exclude INT bases from a given end\n@@ -196,6 +198,7 @@\n <filter>not advanced_options[\'methylKit\']</filter>\n <filter>not advanced_options[\'counts\']</filter>\n <filter>not advanced_options[\'fraction\']</filter>\n+ <filter>not advanced_options[\'noCpG\']</filter>\n </data>\n <data name="outFileExtractCpGLogit" format="bedgraph" from_work_dir="output_CpG.logit.bedGraph" \n label="${tool.name} on ${on_string} (logit)">\n@@ -281,6 +284,11 @@\n <filter>advanced_options[\'options\'] == "yes"</filter>\n <filter>advanced_options[\'CHH\']</filter>\n </data>\n+ <data name="outFileMbiasTSV" format="tabular" from_work_dir="out_mbias.tsv"\n+ label="${tool.name} on ${on_string} (methylation bias, tsv)">\n+ <filter>main_task[\'task\'] == \'mbias\'</filter>\n+ <filter>main_task[\'tsv\']</filter>\n+ </data>\n <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg"\n label="${tool.name} on ${on_string} (methylation bias, original top strand)">\n <filter>main_task[\'task\'] == \'mbias\'</filter>\n@@ -361,6 +369,27 @@\n <param name="methylKit" value="true" />\n <output name="outFileExtractCpGMethylKit" file="test_5.methylKit" ftype="text" compare="diff"/>\n </test>\n+ <test>\n+ <param name="task" value="mbias" />\n+ <param name="min_mapq" value="2" />\n+ <param name="options" value="yes"/>\n+ <param name="tsv" value="--txt"/>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" value="cg100.fa" ftype="fasta" />\n+ <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>\n+ <output name="outFileMbiasTSV" file="test7_output.tsv" ftype="tabular" compare="diff"/>\n+ </test>\n+ <test>\n+ <param name="task" value="mbias" />\n+ <param name="min_mapq" value="2" />\n+ <param name="options" value="yes"/>\n+ <param name="regionBed" ftype="bed" value="cg100.bed"/>\n+ <param name="tsv" value="--txt"/>\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" value="cg100.fa" ftype="fasta" />\n+ <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/>\n+ <output name="outFileMbiasTSV" file="test8_output.tsv" ftype="tabular" compare="diff"/>\n+ </test>\n </tests>\n <help><![CDATA[\n \n' |
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| diff -r 906db57d5d65 -r 15df15127c18 test-data/cg100.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cg100.bed Fri Mar 23 17:52:57 2018 -0400 |
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| @@ -0,0 +1,1 @@ +chrCG 10 90 |
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| diff -r 906db57d5d65 -r 15df15127c18 test-data/test7_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test7_output.tsv Fri Mar 23 17:52:57 2018 -0400 |
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| @@ -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 |
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| diff -r 906db57d5d65 -r 15df15127c18 test-data/test8_output.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test8_output.tsv Fri Mar 23 17:52:57 2018 -0400 |
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| @@ -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 |