Mercurial > repos > galaxyp > pyprophet
changeset 0:f795005c14b7 draft default tip
Uploaded
author | galaxyp |
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date | Mon, 11 May 2015 12:31:49 -0400 |
parents | |
children | |
files | .shed.yml pyprophet.xml tool_dependencies.xml |
diffstat | 3 files changed, 88 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Mon May 11 12:31:49 2015 -0400 @@ -0,0 +1,3 @@ +# repository published to https://toolshed.g2.bx.psu.edu/repos/galaxyp/pyprophet +owner: galaxyp +name: pyprophet
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pyprophet.xml Mon May 11 12:31:49 2015 -0400 @@ -0,0 +1,79 @@ +<tool id="gp_pyprophet" name="PyProphet" version="0.1.0"> + <description></description> + <requirements> + <requirement type="package" version="0.3.2">pyprophet</requirement> + </requirements> + <command> +<![CDATA[ + pyprophet + --apply_scorer $scorer + --apply_weights $weights + --num_processes "\${GALAXY_SLOTS:-24}" + $compute_prop + $use_all_groups + $ignore_nan + $random + --final_statistics.lambda $lambda + --semi_supervised_learner.initial_fdr $initial_fdr + --semi_supervised_learner.initial_lambda $iteration_lambda + --semi_supervised_learner.iteration_fdr $iteration_fdr + --semi_supervised_learner.iteration_lambda $iteration_lambda + --semi_supervised_learner.num_iter $num_iter + --xeval.fraction $xeval_fraction + --xeval.num_iter $xeval_num_iter + + ${input} + +]]> + </command> + <inputs> + <param name="input" format="txt" type="data" label="Input files" help="" /> + <param name="scorer" format="txt" type="data" optional="True" label="File of existing classifier" + help="(--apply_scorer)" /> + <param name="weights" format="txt" type="data" optional="True" label="File of existing LDA weights" + help="(--apply_weights)" /> + + <param name="lambda" type="float" value="0.4" label="Final statistics lambda" help="(--final_statistics.lambda)" /> + <param name="initial_fdr" type="float" value="0.15" label="Semi supervised learner initial fdr" + help="(--semi_supervised_learner.initial_fdr)" /> + <param name="initial_lambda" type="float" value="0.4" label="Semi supervised learner initial lambda" + help="(--semi_supervised_learner.initial_lambda)" /> + <param name="iteration_fdr" type="float" value="0.02" label="Semi supervised learner iteration fdr" + help="(--semi_supervised_learner.iteration_fdr)" /> + <param name="iteration_lambda" type="float" value="0.4" label="Semi supervised learner iteration lambda" + help="(--semi_supervised_learner.iteration_lambda)" /> + <param name="num_iter" type="integer" value="5" label="Semi supervised learner num iter" + help="(--semi_supervised_learner.num_iter)" /> + <param name="xeval_fraction" type="float" value="0.5" label="Xeval fraction" + help="(--xeval.fraction)" /> + <param name="xeval_num_iter" type="integer" value="5" label="Xeval num iter" + help="(--xeval.num_iter)" /> + <param name="random" type="boolean" truevalue="--is_test" falsevalue="" checked="False" + label="Do not use random seed" help="(--is_test)" /> + <param name="ignore_nan" type="boolean" truevalue="--ignore.invalid_score_columns" falsevalue="" checked="False" + label="Ignore score columns which only contain NaN or infinity values" help="(--ignore.invalid_score_columns)" /> + <param name="use_all_groups" type="boolean" truevalue="--final_statistics.fdr_all_pg" falsevalue="" checked="False" + label="Use all peak groups for score and q-value calculation" help="(--final_statistics.fdr_all_pg)" /> + <param name="compute_prop" type="boolean" truevalue="--compute.probabilities" falsevalue="" checked="False" + label="Compute approximate binned probability values" help="(--compute.probabilities)" /> + + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + <help> +<![CDATA[ +**What it does** + +The algorithm can take targeted proteomics data, learn a linear separation between true signal and the noise signal and then compute a q-value (false discovery rate) to achieve experiment-wide cutoffs. + +This program is a reimplementation of the original algorithm by `Uwe Schmitt`_. + +..`Uwe Schmitt`: https://github.com/uweschmitt/pyprophet + +]]> + </help> + <citations> + <citation type="doi">10.1038/nmeth.1584</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 11 12:31:49 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="pyprophet" version="0.13.2"> + <repository changeset_revision="30c076cbe970" name="package_pyprophet_0_13_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>