annotate feature_alignment.xml @ 1:25f43048bff3 draft

Uploaded
author galaxyp
date Mon, 11 May 2015 14:20:47 -0400
parents 7b4d70c9a139
children 8559c361b8a1
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
1 <tool id="feature_alignment" name="Feature Alignment" version="0.1">
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
2 <description>of peakgroups below a FDR</description>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
3 <stdio>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
4 <exit_code level="fatal" range="1:"/>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
5 </stdio>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
6 <version_command>feature_alignment.py --version</version_command>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
7 <command interpreter="python">
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
8 <![CDATA[
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
9 feature_alignment.py
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
10 --in #'" "'.join([ $file for $file in $inputs ])#
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
11 --file_format $oformat
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
12 #if str($out) == "openswath":
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
13 --out $out
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
14 #end if
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
15 --out_matrix out_matrix.tsv
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
16 --out_ids $out_ids
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
17 --fdr_cutoff $fdr_cutoff
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
18 #if $max_fdr_quality and $max_fdr_quality is not None:
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
19 --max_fdr_quality "$max_fdr_quality"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
20 #end if
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
21 --max_rt_diff $max_rt_diff
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
22 --iso_max_rt_diff $iso_max_rt_diff
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
23 --frac_selected $frac_selected
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
24 --method $method
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
25 --matrix_output_method $matrix_output_method
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
26 --realign_method $realign_method
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
27
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
28 &&
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
29 mv out_matrix.tsv $out_matrix
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
30
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
31 ]]></command>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
32 <inputs>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
33
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
34 <param name="inputs" type="data" multiple="True"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
35 label="A list of mProphet output files containing all peakgroups" help="(--in)"/>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
36 <param name="oformat" type="select" label="Which input file format is used" help="(--file_format)">
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
37 <option value="openswath">OpenSwath</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
38 <option value="peakview" selected="True">Peakview</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
39 </param>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
40
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
41 <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="(--fdr_cutoff)" />
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
42 <param name="max_fdr_quality" type="text" default="-1.0"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
43 label="Extension score cutoff"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
44 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)"/>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
45 <param name="max_rt_diff" type="integer" default="30"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
46 label="Maximal difference in RT for two aligned features" help="(--max_rt_diff)"/>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
47 <param name="iso_max_rt_diff" type="text" default="10"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
48 label="Maximal difference in RT for two isotopic channels in the same run" help="(--iso_max_rt_diff)" />
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
49 <param name="frac_selected" type="float" value="0.0" min="0" max="1"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
50 label="Do not write peakgroup if selected in less than this fraction of runs" help="(--frac_selected)"/>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
51 <param name="method" type="select"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
52 label="Which method to use for the clustering"
1
25f43048bff3 Uploaded
galaxyp
parents: 0
diff changeset
53 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)" >
0
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
54 <option value='best_overall' selected="True">best_overall</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
55 <option value='best_cluster_score'>best_cluster_score</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
56 <option value='global_best_cluster_score'>global_best_cluster_score</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
57 <option value='global_best_overall'>global_best_overall</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
58 <option value='LocalMST'>LocalMST</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
59 <option value='LocalMSTAllCluster'>LocalMSTAllCluster</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
60 </param>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
61
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
62 <param name="matrix_output_method" type="select"
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
63 label="Which columns are written besides Intensity" help="(--matrix_output_method)">
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
64 <option value='none' selected="True">None</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
65 <option value='RT'>RT</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
66 <option value='score'>Score</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
67 <option value='source'>Source</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
68 <option value='full'>Full</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
69 </param>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
70 <param name="realign_method" type="select" label="How to re-align runs in retention time" help="(--realign_method)">
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
71 <option value='diRT' selected="True">Use only deltaiRT from the input file</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
72 <option value='linear'>Perform a linear regression using best peakgroups</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
73 <!--option value='splineR'>Perform a spline fit using R</option-->
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
74 <!--option value='splineR_external'>Perform a spline fit using R</option-->
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
75 <option value='splinePy'>Use Python native spline from scikits.datasmooth (slow!)</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
76 <option value='lowess'>Use Robust locally weighted regression (lowess smoother)</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
77 <option value='CVSpline'>Splines with cross-validation</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
78 <option value='nonCVSpline'>Splines without cross-validation</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
79 <option value='earth' >Use Multivariate Adaptive Regression Splines using py-earth</option>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
80 </param>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
81 </inputs>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
82 <outputs>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
83 <!-- Matrix containing one peak group per row -->
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
84 <data format="tabular" name="out_matrix"/>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
85 <!-- Id file only containing the ids -->
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
86 <data format="tabular" name="out_ids"/>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
87 <!-- Output file with filtered peakgroups for quantification (only works for OpenSWATH) -->
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
88 <data format="text" name="out">
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
89 <filter>oformat == 'openswath'</filter>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
90 </data>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
91 </outputs>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
92 <help>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
93 <![CDATA[
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
94
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
95 **What it does**
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
96
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
97 This program will select all peakgroups below the FDR cutoff in all files and try to align them to each other.
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
98 If only one file is given, it will act as peakgroup selector (best by m_score)
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
99 and will apply the provided FDR cutoff.
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
100 ]]>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
101 </help>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
102 <citations>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
103 <citation type="doi"></citation>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
104 </citations>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
105 </tool>
7b4d70c9a139 Uploaded
galaxyp
parents:
diff changeset
106