Mercurial > repos > bgruening > pileometh
changeset 2:cda51d96a9bc draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit bff5ba839e2cb63792b0d25018460d76eb398002
| author | bgruening |
|---|---|
| date | Mon, 13 Feb 2017 07:09:59 -0500 |
| parents | d1b66015effd |
| children | f112bf3dd5ff |
| files | PileOMeth.xml test-data/test_2.bedGraph |
| diffstat | 2 files changed, 29 insertions(+), 3 deletions(-) [+] |
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--- a/PileOMeth.xml Wed Sep 21 13:37:19 2016 -0400 +++ b/PileOMeth.xml Mon Feb 13 07:09:59 2017 -0500 @@ -37,6 +37,9 @@ #if str($main_task.CTOB).strip() != "": --CTOB $main_task.CTOB #end if + $main_task.keepSingleton + $main_task.keepDiscordant + $main_task.fraction #end if #if $advanced_options.options=="yes": @@ -60,6 +63,8 @@ $input_sortedAlignBAM #if $main_task.task == "mbias": + $main_task.keepSingleton_mbias + $main_task.keepDiscordant_mbias out_mbias && touch out_mbias_OT.svg && touch out_mbias_OB.svg && @@ -108,8 +113,15 @@ <param name="OB" type="text" value="" label="Original bottom strand bounds (comma-separated, no spaces)" /> <param name="CTOT" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" /> <param name="CTOB" type="text" value="" label="Complementary to the original bottom strand bounds (comma-separated, no spaces)" /> + <param name="keepSingleton" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" /> + <param name="keepDiscordant" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" /> + <param name="fraction" type="boolean" checked="false" truevalue="--fraction" falsevalue="" /> + </when> - <when value="mbias"/> + <when value="mbias"> + <param name="keepSingleton_mbias" type="boolean" checked="false" truevalue="--keepSingleton" falsevalue="" /> + <param name="keepDiscordant_mbias" type="boolean" checked="false" truevalue="--keepDiscordant" falsevalue="" /> + </when> </conditional> <conditional name="advanced_options"> <param name="options" type="select" label="Advanced options"> @@ -145,13 +157,13 @@ label="${tool.name} on ${on_string} (CHG)"> <filter>main_task['task'] == 'extract'</filter> <filter>advanced_options['options'] == "yes"</filter> - <filter>advanced_options['CHG'] == "--CHG"</filter> + <filter>advanced_options['CHG']</filter> </data> <data name="outFileExtractCHH" format="bedgraph" from_work_dir="output_CHH.bedGraph" label="${tool.name} on ${on_string} (CHH)"> <filter>main_task['task'] == 'extract'</filter> <filter>advanced_options['options'] == "yes"</filter> - <filter>advanced_options['CHH'] == "--CHH" </filter> + <filter>advanced_options['CHH']</filter> </data> <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg" label="${tool.name} on ${on_string} (methylation bias, original top strand)"> @@ -190,6 +202,19 @@ <param name="input_sortedAlignBAM" value="cg_aln.bam" ftype="bam"/> <output name="outFileMbiasCpG" file="test_2_output.svg" ftype="svg" compare="diff"/> </test> + <test> + <param name="task" value="extract" /> + <param name="min_mapq" value="2" /> + <param name="options" value="yes"/> + <param name="CHH" value="True"/> + <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"/> + <param name="mergeContext" value="false"/> + <param name="options" value="yes"/> + <output name="outFileExtractCpG" file="test_1.bedGraph" ftype="bedgraph" compare="diff"/> + <output name="outFileExtractCHH" file="test_2.bedGraph" ftype="bedgraph" compare="diff"/> + </test> </tests> <help><![CDATA[ **What it does**