| Previous changeset 1:fa1aae53a2f3 (2016-06-28) |
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Commit message:
planemo upload for repository https://github.com/cdeanj/galaxytools/tree/master/tools/gene_fraction commit 9982b8cd32dc6ecef17cd8c3bf16f42d8eb30d75-dirty |
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modified:
coverage_sampler.xml tool_dependencies.xml |
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| diff -r fa1aae53a2f3 -r ec439b0e7512 coverage_sampler.xml --- a/coverage_sampler.xml Tue Jun 28 23:31:46 2016 -0400 +++ b/coverage_sampler.xml Thu Jun 30 02:15:50 2016 -0400 |
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| @@ -1,7 +1,7 @@ <tool id="gene_fraction" name="Coverage Sampler" version="0.1.0"> <description>A simple tool for calculating the amount of a gene that is covered by a sample of alignments</description> <requirements> - <requirement type="package" version="0.1">csa</requirement> + <requirement type="package" version="0.1">coverage_sampler</requirement> </requirements> <stdio> <exit_code range="1:" /> @@ -57,24 +57,48 @@ </test> </tests> <help><![CDATA[ -A simple tool for calculating the amount of a gene that is covered by a sample of alignments. + +**Coverage sampler** -Program: Coverage Sampler +Coverage sampler is a simple tool for calculating the amount of a gene that is covered by a sample of alignments. The tool takes +in as input a fasta and alignment file. The output of this program is a tab delimited text file describing the fraction of each gene +that was covered from a random sampling of alignments. + +------ -Contact: Chris Dean <cdean11@rams.colostate.edu> +**Options** + + -min INT Starting level to sample reads from (level is in percent) + + -max INT Ending level to sample reads from (level is in percent) -Usage: csa [options] + -skip INT Number of levels to skip + + -samples INT Number of iterations per sample level + + -t INT Gene fraction threshold (only genes with a gene fraction greater than this threshold are output) -Options: - -ref_fp STR/FILE ref file path - -sam_fp STR/FILE sam file path - -min INT starting sample level - -max INT ending sample level - -skip INT amount of sample levels to skip - -t INT gene fraction threshold - -samples INT iterations per sample level - -out_fp STR/FILE output file path - ]]></help> +------ + +**Output** + +A tab delimited text file with the following columns:: + + Level The sampling level alignments were taken at + Iteration The iteration number of the current sample level + Gene Id The reference name having a gene fraction greater than threshold + Gene Fraction The gene fraction for the current reference sequence (in percent) + Hits The number of alignments associated with the reference sequence + +------ + +**Development** + +Development is being done on github_ + +.. _github: https://github.com/cdeanj/coverage_sampler + + ]]></help> <citations> </citations> </tool> |
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| diff -r fa1aae53a2f3 -r ec439b0e7512 tool_dependencies.xml --- a/tool_dependencies.xml Tue Jun 28 23:31:46 2016 -0400 +++ b/tool_dependencies.xml Thu Jun 30 02:15:50 2016 -0400 |
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| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="csa" version="0.1"> + <package name="coverage_sampler" version="0.1"> <install version="1.0"> <actions> <action type="shell_command">git clone --recursive https://github.com/cdeanj/coverage_sampler.git</action> |