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planemo upload commit 54155cb43a07d563ee6861c2410a167b9c879ff4-dirty |
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LICENSE README.md bam_to_bigwig.xml tool_dependencies.xml |
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| diff -r 000000000000 -r dd444ce346ae LICENSE --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/LICENSE Thu Jul 14 18:55:27 2016 -0400 |
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| @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2016 Rémi Marenco + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in all +copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE +SOFTWARE. |
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| diff -r 000000000000 -r dd444ce346ae README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Thu Jul 14 18:55:27 2016 -0400 |
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| @@ -0,0 +1,2 @@ +# bamToBigwig +Galaxy wrapper for Bam to Bigwig conversion |
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| diff -r 000000000000 -r dd444ce346ae bam_to_bigwig.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam_to_bigwig.xml Thu Jul 14 18:55:27 2016 -0400 |
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| @@ -0,0 +1,30 @@ +<tool id="bam_to_bigwig" name="Convert Bam to BigWig" version="0.1.0"> + <requirements> + <requirement type="package" version="312">ucsc_tools</requirement> + <requirement type="package" version="2.24">bedtools</requirement> + </requirements> + <stdio> + <exit_code range="1:" /> + </stdio> + <command><![CDATA[ + faToTwoBit $input_reference_fasta two_bit.2bit; + twoBitInfo two_bit.2bit stdout | sort -k2nr > chrom.sizes; + bedtools genomecov -bg -split -ibam $input_bam -g chrom.sizes > temp.bg; + bedGraphToBigWig temp.bg chrom.sizes $output_bigwig; + ]]></command> + <inputs> + <param format="bam" name="input_bam" type="data" label="Choose BAM file" /> + <param format="fasta" name="input_reference_fasta" + type="data" label="Choose Reference Genome (Fasta)" /> + </inputs> + <outputs> + <data format="bigwig" name="output_bigwig" /> + </outputs> + <help> + This tool converts a Bam file to a BigWig file. + + It needs: + - A Bam file + - The reference genome as a Fasta file + </help> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r dd444ce346ae tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 14 18:55:27 2016 -0400 |
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| @@ -0,0 +1,11 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ucsc_tools" version="312"> + <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + + <package name="bedtools" version="2.24"> + <repository changeset_revision="39b86c1e267d" name="package_bedtools_2_24" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + +</tool_dependency> |