Mercurial > repos > iuc > crossmap_gff
changeset 7:1b57bf1bb4ec draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit e365f2835488e73b870c73502c24ff23d28b76a5
| author | iuc |
|---|---|
| date | Fri, 20 Oct 2017 02:48:09 -0400 |
| parents | 9ca13f08f2f7 |
| children | 45c57bf42470 |
| files | crossmap_gff.xml 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 | 8 files changed, 583 insertions(+), 53 deletions(-) [+] |
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--- a/crossmap_gff.xml Tue Sep 26 06:09:26 2017 -0400 +++ b/crossmap_gff.xml Fri Oct 20 02:48:09 2017 -0400 @@ -8,59 +8,49 @@ <expand macro="version_command"/> <command><![CDATA[ - CrossMap.py gff - '${chain_source.input_chain}' - '${seq_source.input}' +CrossMap.py gff +'${chain_source.input_chain}' +'${input}' - #if str($include_fails) == "True" - > - #end if +#if str($include_fails) == "True" + > +#end if - '${output}' +'${output}' ]]></command> <inputs> - <conditional name="seq_source"> - <expand macro="source" /> + <param name="input" type="data" format="gtf,gff,gff3" label="GTF/GFF file"/> - <when value="cached"> - <param format="gtf,gff,gff3" name="input" type="data" label="GTF/GFF 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> - </when> - <when value="history"> - <param type="data" format="gtf,gff,gff3" name="input" label="GTF/GFF file"/> - </when> - </conditional> <expand macro="chain" /> - <param name="include_fails" type="boolean" truevalue="True" checked="false" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/> + <param name="include_fails" type="boolean" truevalue="True" falsevalue="False" label="Include failed liftovers" help="If a coordinate can not be lift over, do you want to include it in the output (it is still being marked 'fail')"/> </inputs> <outputs> - <!-- GTF/GFF3? test... --> - <data format="gff" name="output" label="${tool.name} on ${on_string}" /> + <data name="output" format="gff" label="${tool.name} on ${on_string}" /> </outputs> <tests> - <!-- GFF --> <test> - <param name="input_format" value="gff"/> + <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> <param name="index_source" value="history"/> - <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> <param name="input_chain" value="aToB.over.chain" ftype="csv"/> <param name="include_fails" value="False"/> <output name="output" file="test_gff_01_output_a__only-matches.gtf"/> </test> <test> - <param name="input_format" value="gff"/> + <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> <param name="index_source" value="history"/> + <param name="input_chain" value="aToB.over.chain" ftype="csv"/> + <param name="include_fails" value="True"/> + + <output name="output" file="test_gff_01_output_a__all.gtf"/> + </test> + <test><!-- cached chain file --> <param name="input" value="test_gff_01_input_a.gtf" ftype="gtf"/> - <param name="input_chain" value="aToB.over.chain" ftype="csv"/> + <param name="index_source" value="cached"/> <param name="include_fails" value="True"/> <output name="output" file="test_gff_01_output_a__all.gtf"/> @@ -73,20 +63,19 @@ --------- Your input data should be either GTF/GFF2.5 or GFF3 format. - GFF (General Feature Format) is another plain text file used to describe - gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The - first eight fields are the same as GFF. Only chromosome and genome - coordinates are updated. The format of output is determined from the input. +GFF (General Feature Format) is another plain text file used to describe +gene structure. GTF (Gene Transfer Format) is a refined version of GTF. The +first eight fields are the same as GFF. Only chromosome and genome +coordinates are updated. The format of output is determined from the input. - NOTE: +Notes: - - Each feature (exon, intron, UTR, etc) is processed separately and - independently, and we do NOT check if features originally belonging to - the same gene were converted into the same gene. - - If user want to liftover gene annotation files, use BED12 format. +- Each feature (exon, intron, UTR, etc) is processed separately and + independently, and we do NOT check if features originally belonging to + the same gene were converted into the same gene. +- If user want to liftover gene annotation files, use BED12 format. -Please see `the manual <http://crossmap.sourceforge.net/#convert-gff-gtf-format-files>`__ for more details -]]></help> + ]]></help> <citations> <citation type="doi">10.1093/bioinformatics/btt730</citation>
--- a/macros.xml Tue Sep 26 06:09:26 2017 -0400 +++ b/macros.xml Fri Oct 20 02:48:09 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"> @@ -28,23 +29,16 @@ <param name="input_chain" type="select" label="Lift Over To"> <options from_data_table="liftOver"> <!-- - planemo can't update this ? - <filter type="data_meta" ref="input" key="dbkey"/> + <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 02:48:09 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 02:48:09 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 ${__HERE__}/aToB.over.chain
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_bed_02_output_a__only_fails.bed Fri Oct 20 02:48:09 2017 -0400 @@ -0,0 +1,5 @@ +chr1 100 10000 +chr2 100 10000 +chr3 100 10000 +chr4 8941700 8947200 +chr5 1 100000000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Fri Oct 20 02:48:09 2017 -0400 @@ -0,0 +1,12 @@ +<tables> + <!-- Locations of all fasta files under genome directory --> + <table name="all_fasta" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="${__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>