Mercurial > repos > galaxyp > feature_alignment
changeset 0:7b4d70c9a139 draft
Uploaded
author | galaxyp |
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date | Mon, 11 May 2015 12:20:44 -0400 |
parents | |
children | 25f43048bff3 |
files | .shed.yml feature_alignment.xml tool_dependencies.xml |
diffstat | 3 files changed, 116 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Mon May 11 12:20:44 2015 -0400 @@ -0,0 +1,3 @@ +# repository published to https://toolshed.g2.bx.psu.edu/repos/galaxyp/feature_alignment +owner: galaxyp +name: feature_alignment
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/feature_alignment.xml Mon May 11 12:20:44 2015 -0400 @@ -0,0 +1,107 @@ +<tool id="feature_alignment" name="Feature Alignment" version="0.1"> + <description>of peakgroups below a FDR</description> + <stdio> + <exit_code level="fatal" range="1:"/> + </stdio> + <version_command>feature_alignment.py --version</version_command> + <command interpreter="python"> +<![CDATA[ + feature_alignment.py + --in #'" "'.join([ $file for $file in $inputs ])# + --file_format $oformat + #if str($out) == "openswath": + --out $out + #end if + --out_matrix out_matrix.tsv + --out_ids $out_ids + --fdr_cutoff $fdr_cutoff + #if $max_fdr_quality and $max_fdr_quality is not None: + --max_fdr_quality "$max_fdr_quality" + #end if + --max_rt_diff $max_rt_diff + --iso_max_rt_diff $iso_max_rt_diff + --frac_selected $frac_selected + --method $method + --matrix_output_method $matrix_output_method + --realign_method $realign_method + + && + mv out_matrix.tsv $out_matrix + +]]></command> + <inputs> + + <param name="inputs" type="data" multiple="True" + label="A list of mProphet output files containing all peakgroups" help="(--in)"/> + <param name="oformat" type="select" label="Which input file format is used" help="(--file_format)"> + <option value="openswath">OpenSwath</option> + <option value="peakview" selected="True">Peakview</option> + </param> + + <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="(--fdr_cutoff)" /> + <param name="max_fdr_quality" type="text" default="-1.0" + label="Extension score cutoff" + help="During the extension phase of the algorithm, peakgroups of this quality will still be considered for alignment (in FDR) - it is possible to give a range in the format lower,higher+stepsize,stepsize - e.g. 0,0.31,0.01 (-1 will set it to fdr_cutoff) (--max_fdr_quality)"/> + <param name="max_rt_diff" type="integer" default="30" + label="Maximal difference in RT for two aligned features" help="(--max_rt_diff)"/> + <param name="iso_max_rt_diff" type="text" default="10" + label="Maximal difference in RT for two isotopic channels in the same run" help="(--iso_max_rt_diff)" /> + <param name="frac_selected" type="float" value="0.0" min="0" max="1" + label="Do not write peakgroup if selected in less than this fraction of runs" help="(--frac_selected)"/> + + <param name="method" type="select" + label="Which method to use for the clustering" + help="Note that the MST options will perform a local, MST guided alignment while the other options will use a reference-guided alignment. The global option will also move peaks which are below the selected FDR threshold. (--method)" /> + <option value='best_overall' selected="True">best_overall</option> + <option value='best_cluster_score'>best_cluster_score</option> + <option value='global_best_cluster_score'>global_best_cluster_score</option> + <option value='global_best_overall'>global_best_overall</option> + <option value='LocalMST'>LocalMST</option> + <option value='LocalMSTAllCluster'>LocalMSTAllCluster</option> + </param> + + <param name="matrix_output_method" type="select" + label="Which columns are written besides Intensity" help="(--matrix_output_method)"> + <option value='none' selected="True">None</option> + <option value='RT'>RT</option> + <option value='score'>Score</option> + <option value='source'>Source</option> + <option value='full'>Full</option> + </param> + <param name="realign_method" type="select" label="How to re-align runs in retention time" help="(--realign_method)"> + <option value='diRT' selected="True">Use only deltaiRT from the input file</option> + <option value='linear'>Perform a linear regression using best peakgroups</option> + <!--option value='splineR'>Perform a spline fit using R</option--> + <!--option value='splineR_external'>Perform a spline fit using R</option--> + <option value='splinePy'>Use Python native spline from scikits.datasmooth (slow!)</option> + <option value='lowess'>Use Robust locally weighted regression (lowess smoother)</option> + <option value='CVSpline'>Splines with cross-validation</option> + <option value='nonCVSpline'>Splines without cross-validation</option> + <option value='earth' >Use Multivariate Adaptive Regression Splines using py-earth</option> + </param> + </inputs> + <outputs> + <!-- Matrix containing one peak group per row --> + <data format="tabular" name="out_matrix"/> + <!-- Id file only containing the ids --> + <data format="tabular" name="out_ids"/> + <!-- Output file with filtered peakgroups for quantification (only works for OpenSWATH) --> + <data format="text" name="out"> + <filter>oformat == 'openswath'</filter> + </data> + </outputs> + <help> +<![CDATA[ + +**What it does** + +This program will select all peakgroups below the FDR cutoff in all files and try to align them to each other. +If only one file is given, it will act as peakgroup selector (best by m_score) +and will apply the provided FDR cutoff. +]]> + </help> + <citations> + <citation type="doi"></citation> + </citations> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon May 11 12:20:44 2015 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="msproteomicstools" version="0.3.2"> + <repository changeset_revision="a523661475a2" name="package_msproteomicstools_0_3_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency>