Mercurial > repos > bgruening > pileometh
changeset 1:d1b66015effd draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/pileometh commit fc3727b1b39cd5654a523d03e0df2b9ac87ddcda
| author | bgruening |
|---|---|
| date | Wed, 21 Sep 2016 13:37:19 -0400 |
| parents | 65575e70af7e |
| children | cda51d96a9bc |
| files | PileOMeth.xml all_fasta.loc.sample tool_dependencies.xml |
| diffstat | 3 files changed, 63 insertions(+), 29 deletions(-) [+] |
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--- a/PileOMeth.xml Fri Sep 18 11:39:55 2015 -0400 +++ b/PileOMeth.xml Wed Sep 21 13:37:19 2016 -0400 @@ -1,7 +1,7 @@ -<tool id="pileometh" name="PileOMeth" version="0.1.5"> +<tool id="pileometh" name="PileOMeth" version="0.1.13"> <description>A tool for processing bisulfite sequencing alignments</description> <requirements> - <requirement type="package" version="0.1.5">pileometh</requirement> + <requirement type="package" version="0.1.13">pileometh</requirement> </requirements> <stdio> <!-- Anything other than zero is an error --> @@ -11,9 +11,13 @@ <regex match="Error:" /> <regex match="Exception:" /> </stdio> - <version_command><![CDATA[PileOMeth 2>&1 | head -n 2 | tail -n 1]]></version_command> + <version_command><![CDATA[PileOMeth --version]]></version_command> <command><![CDATA[ - ln -s $reference_source.ref_file reference.fasta && + #if $reference_source.reference_source_selector == "cached": + ln -s $reference_source.ref_file.fields.path reference.fasta && + #else: + ln -s $reference_source.ref_file reference.fasta && + #end if PileOMeth $main_task.task @@ -21,6 +25,18 @@ #if $main_task.task == "extract": -o output $main_task.mergeContext + #if str($main_task.OT).strip() != "": + --OT $main_task.OT + #end if + #if str($main_task.OB).strip() != "": + --OB $main_task.OB + #end if + #if str($main_task.CTOT).strip() != "": + --CTOT $main_task.CTOT + #end if + #if str($main_task.CTOB).strip() != "": + --CTOB $main_task.CTOB + #end if #end if #if $advanced_options.options=="yes": @@ -32,6 +48,9 @@ -q $advanced_options.min_mapq -p $advanced_options.min_phred -D $advanced_options.max_pbdepth + #if $main_task.task == "extract": + -d $advanced_options.min_pbdepth + #end if $advanced_options.CHG $advanced_options.CHH #end if @@ -41,7 +60,11 @@ $input_sortedAlignBAM #if $main_task.task == "mbias": - out_mbias + out_mbias && + touch out_mbias_OT.svg && + touch out_mbias_OB.svg && + touch out_mbias_CTOT.svg && + touch out_mbias_CTOB.svg #end if ]]></command> <inputs> @@ -70,6 +93,21 @@ <when value="extract"> <param name="mergeContext" type="boolean" checked="false" truevalue="--mergeContext" falsevalue="" label="Merge per-Cytosine metrics from CpG and CHG contexts into per-CPG or per-CHG metrics" help="(--mergeContext)" /> + <param name="OT" type="text" value="" label="Original top strand bounds (comma-separated, no spaces)" + help="Inclusion bounds for methylation calls from reads/pairs + origination from the original top strand. Suggested values can + be obtained from the MBias program. Each integer represents a + 1-based position on a read. For example --OT A,B,C,D + translates to, 'Include calls at positions from A through B + on read #1 and C through D on read #2'. If a 0 is used a any + position then that is translated to mean start/end of the + alignment, as appropriate. For example, --OT 5,0,0,0 would + include all but the first 4 bases on read #1. Users are + strongly advised to consult a methylation bias plot, for + example by using the MBias program." /> + <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)" /> </when> <when value="mbias"/> </conditional> @@ -87,6 +125,8 @@ <param name="min_mapq" type="integer" value="10" label="Minimum MAPQ threshold to include an alignment (default 10)"/> <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)" /> <param name="CHG" type="boolean" checked="false" truevalue="--CHG" falsevalue="" label="Additional output file with CHG methylation metrics" /> @@ -113,8 +153,20 @@ <filter>advanced_options['options'] == "yes"</filter> <filter>advanced_options['CHH'] == "--CHH" </filter> </data> - <data name="outFileMbiasCpG" format="svg" from_work_dir="out_mbias_OT.svg" - label="${tool.name} on ${on_string} (methylation bias)"> + <data name="outFileMbiasCpGOT" format="svg" from_work_dir="out_mbias_OT.svg" + label="${tool.name} on ${on_string} (methylation bias, original top strand)"> + <filter>main_task['task'] == 'mbias'</filter> + </data> + <data name="outFileMbiasCpGOB" format="svg" from_work_dir="out_mbias_OB.svg" + label="${tool.name} on ${on_string} (methylation bias, original bottom strand)"> + <filter>main_task['task'] == 'mbias'</filter> + </data> + <data name="outFileMbiasCpGCTOT" format="svg" from_work_dir="out_mbias_CTOT.svg" + label="${tool.name} on ${on_string} (methylation bias, complementary to the original top strand)"> + <filter>main_task['task'] == 'mbias'</filter> + </data> + <data name="outFileMbiasCpGCTOB" format="svg" from_work_dir="out_mbias_CTOB.svg" + label="${tool.name} on ${on_string} (methylation bias, complementary to the original bottom strand)"> <filter>main_task['task'] == 'mbias'</filter> </data> </outputs>
--- a/all_fasta.loc.sample Fri Sep 18 11:39:55 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,18 +0,0 @@ -#This file lists the locations and dbkeys of all the fasta files -#under the "genome" directory (a directory that contains a directory -#for each build). The script extract_fasta.py will generate the file -#all_fasta.loc. This file has the format (white space characters are -#TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, all_fasta.loc could look something like this: -# -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa -# -#Your all_fasta.loc file should contain an entry for each individual -#fasta file. So there will be multiple fasta files for each build, -#such as with hg19 above. -#
--- a/tool_dependencies.xml Fri Sep 18 11:39:55 2015 -0400 +++ b/tool_dependencies.xml Wed Sep 21 13:37:19 2016 -0400 @@ -1,13 +1,13 @@ <?xml version="1.0"?> <tool_dependency> - <package name="pileometh" version="0.1.5"> + <package name="pileometh" version="0.1.13"> <install version="1.0"> <actions> - <action target_filename="PileOMeth-0.1.5.tar.gz" type="download_by_url">https://github.com/dpryan79/PileOMeth/archive/0.1.5.tar.gz</action> + <action target_filename="PileOMeth-0.1.13.tar.gz" type="download_by_url">https://github.com/dpryan79/PileOMeth/archive/0.1.13.tar.gz</action> <action type="shell_command">make</action> - <action type="shell_command">make install prefix=$INSTALL_DIR</action> + <action type="shell_command">make install prefix=$INSTALL_DIR/bin</action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> <environment_variable name="PILEOMETH_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable> </action> </actions>