Mercurial > repos > yhoogstrate > crossmap
changeset 4:131c32c22de9 draft
Uploaded
| author | yhoogstrate |
|---|---|
| date | Wed, 22 Jul 2015 08:31:24 -0400 |
| parents | 21a161d9ea4b |
| children | 39d95e2675f5 |
| files | crossmap.xml crossmap/crossmap.xml crossmap/tool_dependencies.xml tool_dependencies.xml |
| diffstat | 4 files changed, 77 insertions(+), 77 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crossmap.xml Wed Jul 22 08:31:24 2015 -0400 @@ -0,0 +1,71 @@ +<tool id="crossmap" name="crossmap" version="0.1.8"> + <description>Convert genome coordinates or annotation files between genome assemblies</description> + + <requirements> + <requirement type="package" version="0.1.8">crossmap</requirement> + </requirements> + + <stdio></stdio> + + <command> + CrossMap.py --help > $output + </command> + + <inputs> + <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of" /> + <!-- + <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of"> + <validator type="unspecified_build" /> + <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." /> + </param> + <param name="to_dbkey" type="select" label="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> + <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" help="Recommended values: same species = 0.95, different species = 0.10" /> + <conditional name="multiple"> + <param name="choice" type="select" label="Allow multiple output regions?" help="Recommended values: same species = No, different species = Yes"> + <option value="0" selected="true">No</option> + <option value="1">Yes</option> + </param> + <when value="0"> + <param name="minSizeQ" type="hidden" value="0" /> + <param name="minChainQ" type="hidden" value="0" /> + <param name="minChainT" type="hidden" value="0" /> + </when> + <when value="1"> + <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/> + <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/> + <param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/> + </when> + </conditional> + --> + </inputs> + + <outputs> + <data format="text" name="output" label="Output file"> + </data> + </outputs> + + <tests> + <test> + <param name="input" value="test1.hg19.txt"/> + <output name="output" file="test1.hg18.txt"/> + </test> + </tests> + + <help> + CrossMap is versatile tool to convert genome coordinates or annotation files between genome +assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF, +GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF +and VCF, reading from remote servers and file compression are supported. + </help> + + <citations> + <citation type="doi">10.1093/bioinformatics/btt730</citation> + </citations> +</tool>
--- a/crossmap/crossmap.xml Wed Jul 22 08:30:46 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,71 +0,0 @@ -<tool id="crossmap" name="crossmap" version="0.1.8"> - <description>Convert genome coordinates or annotation files between genome assemblies</description> - - <requirements> - <requirement type="package" version="0.1.8">crossmap</requirement> - </requirements> - - <stdio></stdio> - - <command> - CrossMap.py --help > $output - </command> - - <inputs> - <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of" /> - <!-- - <param format="interval,gff,gtf,vcf" name="input" type="data" label="Convert coordinates of"> - <validator type="unspecified_build" /> - <validator type="dataset_metadata_in_file" filename="liftOver.loc" metadata_name="dbkey" metadata_column="0" message="Liftover mappings are currently not available for the specified build." /> - </param> - <param name="to_dbkey" type="select" label="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> - <param name="minMatch" size="10" type="float" value="0.95" label="Minimum ratio of bases that must remap" help="Recommended values: same species = 0.95, different species = 0.10" /> - <conditional name="multiple"> - <param name="choice" type="select" label="Allow multiple output regions?" help="Recommended values: same species = No, different species = Yes"> - <option value="0" selected="true">No</option> - <option value="1">Yes</option> - </param> - <when value="0"> - <param name="minSizeQ" type="hidden" value="0" /> - <param name="minChainQ" type="hidden" value="0" /> - <param name="minChainT" type="hidden" value="0" /> - </when> - <when value="1"> - <param name="minSizeQ" size="10" type="integer" value="0" label="Minimum matching region size in dataset" help="Recommended value: set to >= 300 bases for complete transcripts"/> - <param name="minChainQ" size="10" type="integer" value="500" label="Minimum chain size in dataset"/> - <param name="minChainT" size="10" type="integer" value="500" label="Minimum chain size in target"/> - </when> - </conditional> - --> - </inputs> - - <outputs> - <data format="text" name="output" label="Output file"> - </data> - </outputs> - - <tests> - <test> - <param name="input" value="test1.hg19.txt"/> - <output name="output" file="test1.hg18.txt"/> - </test> - </tests> - - <help> - CrossMap is versatile tool to convert genome coordinates or annotation files between genome -assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF, -GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF -and VCF, reading from remote servers and file compression are supported. - </help> - - <citations> - <citation type="doi">10.1093/bioinformatics/btt730</citation> - </citations> -</tool>
--- a/crossmap/tool_dependencies.xml Wed Jul 22 08:30:46 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="crossmap" version="0.1.8"> - <repository changeset_revision="ebe9034b7450" name="package_crossmap_0_1_8" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jul 22 08:31:24 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="crossmap" version="0.1.8"> + <repository changeset_revision="ebe9034b7450" name="package_crossmap_0_1_8" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>