Mercurial > repos > iuc > crossmap_bam
changeset 1:8e5feca6a518 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
| author | iuc |
|---|---|
| date | Fri, 20 Oct 2017 02:48:57 -0400 |
| parents | d04d5afec2e0 |
| children | 083774cc8472 |
| files | crossmap_bam.xml dump2/.gitignore dump2/out.bam.bam dump2/out.bam.unmap.bam dump2/out2.bam dump2/out2.sorted.bam dump2/out2.sorted.bam.bai dump2/out2.sorted.bam.bam dump2/output2.bam dump2/output2.unmap.bam macros.xml test-data/cached_locally/aToB.over.chain test-data/cached_locally/liftOver.loc test-data/test_bam_01_output_a.bam test-data/test_bam_01_output_a.unmap.bam test-data/test_bed_01_output_a__only_fails.bed test-data/test_bed_02_output_a__only_fails.bed tool_data_table_conf.xml.test |
| diffstat | 13 files changed, 628 insertions(+), 100 deletions(-) [+] |
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--- a/crossmap_bam.xml Tue Sep 26 05:44:53 2017 -0400 +++ b/crossmap_bam.xml Fri Oct 20 02:48:57 2017 -0400 @@ -7,70 +7,38 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - #if $input_file.extension == "bam": - #set $input_file = "input.sam" - samtools view -h '${seq_source.input}' > '${input_file}' && - #else: - #set $input_file = "input.bam" - ln -s '${seq_source.input}' '${input_file}' - #end if - CrossMap.py - bam +CrossMap.py bam +'${chain_source.input_chain}' +$optional_tags - "$chain_source.input_chain" - $optional_tags - - -m $insert_size - -s $insert_size_stdev - -t $insert_size_fold +-m $insert_size +-s $insert_size_stdev +-t $insert_size_fold - '${input_file}' - '${output}' +'${input}' +'${output}' - && samtools sort "${output}.sam" > '${output}' - && samtools sort "${output}.unmap.sam" > '${output_unmapped}' +&& mv '${output}.sorted.bam' '${output}' ]]></command> - <inputs> - <conditional name="seq_source"> - <expand macro="source" /> - <when value="cached"> - <param type="data" format="bam" name="input" label="BAM file"> - <validator type="unspecified_build"/> - <!-- Gives error in tests - <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="LiftOver mapping (chain file) is not available for the specified build."/> - --> - </param> - <param name="input_chain" type="select" label="Lift Over To"> - <options from_file="liftOver.loc"> - <column name="name" index="1"/> - <column name="value" index="2"/> - <column name="dbkey" index="0"/> - <filter type="data_meta" ref="input" key="dbkey" column="0"/> - </options> - </param> - </when> - <when value="history"> - <param type="data" format="bam" name="input" label="BAM/SAM file"/> - <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/> - </when> - </conditional> + <param name="input" type="data" format="bam" label="BAM file"/> + <expand macro="chain" /> - <param name="optional_tags" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM/SAM Headers" argument="-a"/> + + <param name="optional_tags" argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Add optional BAM Headers"/> - <param name="insert_size" type="float" value="200.0" label="Insert size" argument="-m" help="Average insert size of pair-end sequencing (bp) [default=200.0]"/> - <param name="insert_size_stdev" type="float" value="30.0" label="Insert size std. dev" argument="-s" help="Stanadard deviation of insert size. [default=30.0]"/> - <param name="insert_size_fold" type="float" value="3.0" label="Insert size std. dev foldchange" argument="-t" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean. [default=3.0]"/> -</inputs> + <param name="insert_size" argument="-m" type="float" value="200.0" label="Insert size" help="Average insert size of pair-end sequencing (bp)"/> + <param name="insert_size_stdev" argument="-s" type="float" value="30.0" label="Insert size std. dev" help="Stanadard deviation of insert size"/> + <param name="insert_size_fold" argument="-t" type="float" value="3.0" label="Insert size std. dev foldchange" help="A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean"/> + </inputs> <outputs> - <data format="bam" name="output" label="${tool.name} on ${on_string}" /> - <data format="bam" name="output_unmapped" label="${tool.name} (unmapped) on ${on_string}" /> + <data name="output" format="bam" label="${tool.name} on ${on_string}" /> + <!-- CrossMap 0.2.5 does not produce output_unmapped --> </outputs> <tests> - <!-- BAM/SAM --> <test> <param name="index_source" value="history"/> <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/> @@ -78,57 +46,77 @@ <param name="include_fails" value="False"/> <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/> - <output name="output_unmapped" file="test_bam_01_output_a.unmap.bam" compare="diff" lines_diff="8"/> + </test> + <test> + <param name="index_source" value="cached"/> + + <param name="input" value="test_bam_01_input_a.bam" ftype="bam"/> + <param name="include_fails" value="False"/> + + <output name="output" file="test_bam_01_output_a.bam" compare="diff" lines_diff="8"/> </test> </tests> <help><![CDATA[ @HELP_GENERAL@ -SAM / BAM +BAM --------- - CrossMap updates chromosomes, genome coordinates, header sections, and all - SAM flags accordingly. The program version (of CrossMap) is inserted into the - header section, along with the names of the original BAM file and the chain - file. For pair-end sequencing, insert size is also recalculated. +CrossMap updates chromosomes, genome coordinates, header sections, and all +BAM flags accordingly. The program version (of CrossMap) is inserted into the +header section, along with the names of the original BAM file and the chain +file. For pair-end sequencing, insert size is also recalculated. - **Optional tags** +**Optional tags** - Q - QC. QC failed. +Q + QC. QC failed. - N - Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly. +N + Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly. - M - Multiple mapped. Alignment can be liftover to multiple places. +M + Multiple mapped. Alignment can be liftover to multiple places. - U - Unique mapped. Alignment can be liftover to only 1 place. +U + Unique mapped. Alignment can be liftover to only 1 place. - **Tags for pair-end sequencing include:** +**Tags for pair-end sequencing include:** - QF = QC failed - NN = both read1 and read2 unmapped - NU = read1 unmapped, read2 unique mapped - NM = read1 unmapped, multiple mapped - UN = read1 uniquely mapped, read2 unmap - UU = both read1 and read2 uniquely mapped - UM = read1 uniquely mapped, read2 multiple mapped - MN = read1 multiple mapped, read2 unmapped - MU = read1 multiple mapped, read2 unique mapped - MM = both read1 and read2 multiple mapped +QF + QC failed +NN + both read1 and read2 unmapped +NU + read1 unmapped, read2 unique mapped +NM + read1 unmapped, multiple mapped +UN + read1 uniquely mapped, read2 unmap +UU + both read1 and read2 uniquely mapped +UM + read1 uniquely mapped, read2 multiple mapped +MN + read1 multiple mapped, read2 unmapped +MU + read1 multiple mapped, read2 unique mapped +MM + both read1 and read2 multiple mapped - **Tags for single-end sequencing include** +**Tags for single-end sequencing include** - QF = QC failed - SN = unmaped - SM = multiple mapped - SU = uniquely mapped +QF + QC failed +SN + unmaped +SM + multiple mapped +SU + uniquely mapped -See `the manual <http://crossmap.sourceforge.net/#convert-bam-sam-format-files>`__ for more details -]]></help> + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btt730</citation>
--- a/dump2/.gitignore Tue Sep 26 05:44:53 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -*
--- a/macros.xml Tue Sep 26 05:44:53 2017 -0400 +++ b/macros.xml Fri Oct 20 02:48:57 2017 -0400 @@ -2,12 +2,11 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="324">ucsc-wigtobigwig</requirement> - <requirement type="package" version="0.2.2">crossmap</requirement> + <requirement type="package" version="0.2.5">crossmap</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">0.2.2</token> + <token name="@WRAPPER_VERSION@">0.2.5</token> <xml name="stdio"> <stdio> <regex match="Aborted (core dumped)" source="stdout" level="fatal"/> @@ -16,7 +15,9 @@ </stdio> </xml> <xml name="version_command"> - <version_command>CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*'</version_command> + <version_command><![CDATA[ +CrossMap.py 2>&1 | head -n 1 | grep -E --only-matching 'CrossMap.*' + ]]></version_command> </xml> <xml name="chain"> <conditional name="chain_source"> @@ -26,25 +27,18 @@ </param> <when value="cached"> <param name="input_chain" type="select" label="Lift Over To"> - <options from_file="liftOver.loc"> - <column name="dbkey" index="0"/><!-- species/build 'from' --> - <column name="name" index="1"/><!-- species/build 'to' --> - <column name="value" index="2"/><!-- path of chain file --> + <options from_data_table="liftOver"> + <!-- <filter type="data_meta" ref="input" key="dbkey" column="0"/> + --> </options> </param> </when> <when value="history"> - <param type="data" format="csv" name="input_chain" label="LiftOver chain file"/> + <param name="input_chain" type="data" format="csv" label="LiftOver chain file"/> </when> </conditional> </xml> - <xml name="source"> - <param name="index_source" type="select" label="Source for Input Data"> - <option value="cached">Local data (in galaxy)</option> - <option value="history">From History</option> - </param> - </xml> <token name="@HELP_GENERAL@"> CrossMap --------
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/aToB.over.chain Fri Oct 20 02:48:57 2017 -0400 @@ -0,0 +1,498 @@ +chain 21270171362 chr1 249250621 + 10000 249233096 chr1 247249719 + 0 247199719 2 +619 137 0 +166661 50000 50000 +40302 50000 50000 +153649 50000 50000 +1098479 1 1 +47 1 1 +73 117 114 +773 1 1 +43 1 1 +864369 2 2 +51 3 0 +104 13694 13694 +104 0 3 +51 2 2 +134936 50000 50000 +1161048 150000 60000 +1440092 27273 50000 +7590365 50000 50000 +116914 100000 50000 +237250 50000 50000 +3518496 50000 50000 +12702424 150000 50000 +16145012 0 1 +7772 1 0 +4705841 0 1 +52977198 50000 50000 +157344 21065 50000 +16604841 50000 50000 +189539 150000 50000 +398739 21050000 20290000 +195588 50000 50000 +186739 150000 50000 +175055 50000 50000 +201709 100000 50000 +126477 130183 50000 +381 0 3 +315 0 2 +62 1 1 +45 1 0 +19 0 1 +8 1 1 +1158 1 0 +314 12 13 +2849 3 0 +5615 1 1 +37 1 1 +3172 6 4 +190 1 1 +34 1 1 +380 0 1 +2099 3 0 +765 2 2 +366 0 4 +1186 1 0 +460 0 1 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cached_locally/liftOver.loc Fri Oct 20 02:48:57 2017 -0400 @@ -0,0 +1,32 @@ +#This is a sample file distributed with Galaxy that is used by the +#liftOver tools. The liftOver.loc file has this format (white space +#characters are TAB characters): +# +#<FromSpecies> <ToSpecies> <PathToChainFile> +# +#So, for example, if you had the chain file to convert from anoCar1 to galGal3 +#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, +#then the liftOver.loc entry would look like this: +# +#<FromSpecies> <ToSpecies> <PathToChainFile> +#<dbkey> <name> <value> +# +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +# +#and your /depot/data2/galaxy/anoCar1/liftOver directory would +#contain all of your "chain" files (e.g.): +# +#-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain +#-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain +#-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain +#...etc... +# +#Your liftOver.loc file should include an entry per line for each build you can +#convert. For example: +# +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +#anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain +#anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain +#...etc... + +A B ${__HERE__}/aToB.over.chain
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_02_output_a__only_fails.bed Fri Oct 20 02:48:57 2017 -0400 @@ -0,0 +1,5 @@ +chr1 100 10000 +chr2 100 10000 +chr3 100 10000 +chr4 8941700 8947200 +chr5 1 100000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Oct 20 02:48:57 2017 -0400 @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__HERE__}/test-data/cached_locally/all_fasta.loc" /> + </table> + <!-- Locations of all liftOver files --> + <table name="liftOver" comment_char="#"> + <columns>dbkey, name, value</columns> + <file path="${__HERE__}/test-data/cached_locally/liftOver.loc" /> + </table> +</tables>