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comparison feature_alignment.xml @ 9:9ad7babdbedd draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/feature_alignment commit ceaef1a06c8600f9a042fc8f80f5b3fae75d4445-dirty
author galaxyp
date Sat, 30 May 2015 05:27:37 -0400
parents 4fd8df131c3c
children 23ecd1ee4422
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8:4fd8df131c3c 9:9ad7babdbedd
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.7">python</requirement> 4 <requirement type="package" version="2.7">python</requirement>
5 <requirement type="package" version="0.3.2">msproteomicstools</requirement> 5 <requirement type="package" version="0.3.2">msproteomicstools</requirement>
6 </requirements> 6 </requirements>
7 <stdio> 7 <stdio>
8 <exit_code level="fatal" range="1:"/> 8 <!-- Anything other than zero is an error -->
9 <exit_code range="1:" />
10 <exit_code range=":-1" />
11 <!-- In case the return code has not been set propery check stderr too -->
12 <regex match="Error:" />
13 <regex match="Exception:" />
9 </stdio> 14 </stdio>
10 <version_command>feature_alignment.py --version</version_command> 15 <version_command>feature_alignment.py --version</version_command>
11 <command> 16 <command>
12 <![CDATA[ 17 <![CDATA[
13 feature_alignment.py 18 feature_alignment.py
14 --in #echo '" "'.join([ str($file) for $file in $inputs ]) # 19 --in #echo '" "'.join([ str($file) for $file in $inputs ]) #
15 --file_format $oformat 20 --file_format $iformat
16 #if str($oformat) == "openswath": 21 ##if str($iformat) == "openswath":
17 --out $out 22 --out $out
18 #end if 23 ##end if
19 --out_matrix out_matrix.tsv 24 --out_matrix out_matrix.tsv
20 --out_ids $out_ids 25 --out_ids $out_ids
21 --fdr_cutoff $fdr_cutoff 26 --fdr_cutoff $fdr_cutoff
22 #if $max_fdr_quality and $max_fdr_quality is not None: 27 #if $max_fdr_quality:
23 --max_fdr_quality "$max_fdr_quality" 28 --max_fdr_quality $max_fdr_quality
24 #end if 29 #end if
25 --max_rt_diff $max_rt_diff 30 #if $max_rt_diff:
26 --iso_max_rt_diff $iso_max_rt_diff 31 --max_rt_diff $max_rt_diff
27 --frac_selected $frac_selected 32 #end if
33 #if $iso_max_rt_diff:
34 --iso_max_rt_diff $iso_max_rt_diff
35 #end if
36 #if $frac_selected:
37 --frac_selected $frac_selected
38 #end if
28 --method $method 39 --method $method
29 --matrix_output_method $matrix_output_method 40 --matrix_output_method $matrix_output_method
30 --realign_method $realign_method 41 --realign_method $realign_method
31 && 42 &&
32 mv out_matrix.tsv $out_matrix 43 mv out_matrix.tsv $out_matrix
33 44
34 ]]></command> 45 ]]></command>
35 <inputs> 46 <inputs>
36 47
37 <param name="inputs" type="data" multiple="True" 48 <param name="inputs" type="data" multiple="True" format="txt"
38 label="A list of mProphet output files containing all peakgroups" help="(--in)"/> 49 label="A list of mProphet output files containing all peakgroups" help="(--in)"/>
39 <param name="oformat" type="select" label="Which input file format is used" help="(--file_format)"> 50 <param name="iformat" type="select" label="Which input file format is used" help="(--file_format)">
40 <option value="openswath">OpenSwath</option> 51 <option value="openswath" selected="True">OpenSwath</option>
41 <option value="peakview" selected="True">Peakview</option> 52 <option value="peakview">Peakview</option>
42 </param> 53 </param>
43 54
44 <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="(--fdr_cutoff)" /> 55 <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="(--fdr_cutoff)" />
45 <param name="max_fdr_quality" type="text" default="-1.0" 56 <param name="max_fdr_quality" type="float" value="-1.0" default="-1.0" optional="True"
46 label="Extension score cutoff" 57 label="Extension score cutoff"
47 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)"/> 58 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)"/>
48 <param name="max_rt_diff" type="integer" value="30" default="30" 59 <param name="max_rt_diff" type="integer" value="30" default="30" optional="True"
49 label="Maximal difference in RT for two aligned features" help="(--max_rt_diff)"/> 60 label="Maximal difference in RT for two aligned features" help="(--max_rt_diff)"/>
50 <param name="iso_max_rt_diff" type="text" value="10" default="10" 61 <param name="iso_max_rt_diff" type="integer" value="10" default="10" optional="True"
51 label="Maximal difference in RT for two isotopic channels in the same run" help="(--iso_max_rt_diff)" /> 62 label="Maximal difference in RT for two isotopic channels in the same run" help="(--iso_max_rt_diff)" />
52 <param name="frac_selected" type="float" value="0.0" min="0" max="1" 63 <param name="frac_selected" type="float" value="0.0" min="0" max="1" optional="True"
53 label="Do not write peakgroup if selected in less than this fraction of runs" help="(--frac_selected)"/> 64 label="Do not write peakgroup if selected in less than this fraction of runs" help="(--frac_selected)"/>
54 <param name="method" type="select" 65 <param name="method" type="select"
55 label="Which method to use for the clustering" 66 label="Which method to use for the clustering"
56 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)" > 67 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)" >
57 <option value='best_overall' selected="True">best_overall</option> 68 <option value='best_overall' selected="True">best_overall</option>
86 <!-- Matrix containing one peak group per row --> 97 <!-- Matrix containing one peak group per row -->
87 <data format="tabular" name="out_matrix"/> 98 <data format="tabular" name="out_matrix"/>
88 <!-- Id file only containing the ids --> 99 <!-- Id file only containing the ids -->
89 <data format="tabular" name="out_ids"/> 100 <data format="tabular" name="out_ids"/>
90 <!-- Output file with filtered peakgroups for quantification (only works for OpenSWATH) --> 101 <!-- Output file with filtered peakgroups for quantification (only works for OpenSWATH) -->
91 <data format="text" name="out"> 102 <data format="tabular" name="out">
92 <filter>oformat == 'openswath'</filter> 103 <!-- according to the documentation this output only works for SWATH,
104 but it is a requirement argument in python argparse.
105 So we need to output it. -->
106 <!--filter>iformat == 'openswath'</filter-->
93 </data> 107 </data>
94 </outputs> 108 </outputs>
109 <tests>
110 <test>
111 <param name="inputs" value="feature_alignment_openswath_input_1.csv" ftype="txt" />
112 <param name="iformat" value="openswath" />
113 <param name="method" value="best_cluster_score" />
114 <param name="max_fdr_quality" value="0.4" />
115 <param name="matrix_output_method" value="RT" />
116 <output name="out_matrix" file="feature_alignment_1_openswath_output_matrix.csv" ftype="tabular" />
117 <output name="out_ids" file="feature_alignment_1_openswath_output_cluster_ids.csv" ftype="tabular" />
118 </test>
119 <test>
120 <param name="inputs" value="feature_alignment_openswath_input_1.csv" ftype="txt" />
121 <param name="iformat" value="openswath" />
122 <param name="method" value="best_overall" />
123 <param name="max_fdr_quality" value="0.4" />
124 <param name="matrix_output_method" value="RT" />
125 <output name="out_matrix" file="feature_alignment_2_output_2_matrix.csv" ftype="tabular" />
126 <output name="out_ids" file="feature_alignment_2_output_1_ids.csv" ftype="tabular" />
127 </test>
128 <!-- needs R dependency; The python equivalent should be enough I guess.
129 <test>
130 <param name="inputs" value="feature_alignment_3_openswath_input.csv" ftype="txt" />
131 <param name="iformat" value="openswath" />
132 <param name="realign_method" value="splineR" />
133 <param name="method" value="best_cluster_score" />
134 <param name="max_fdr_quality" value="0.4" />
135 <param name="maxtrix_output_method" value="RT" />
136 <output name="out_ids" file="feature_alignment_3_openswath_output_cluster_ids.csv" ftype="tabular" />
137 </test>
138 -->
139 <test>
140 <param name="inputs" value="feature_alignment_3_openswath_input.csv" ftype="txt" />
141 <param name="iformat" value="openswath" />
142 <param name="realign_method" value="splinePy" />
143 <param name="method" value="best_cluster_score" />
144 <param name="max_fdr_quality" value="0.4" />
145 <param name="matrix_output_method" value="RT" />
146 <output name="out_ids" file="feature_alignment_3_openswath_output_cluster_ids.csv" ftype="tabular" />
147 </test>
148 <test>
149 <param name="inputs" value="feature_alignment_peakview_input_2.csv" ftype="txt" />
150 <param name="iformat" value="peakview" />
151 <param name="method" value="best_cluster_score" />
152 <param name="max_fdr_quality" value="0.0001" />
153 <param name="fdr_cutoff" value="0.000000001" />
154 <param name="matrix_output_method" value="RT" />
155 <output name="out_matrix" file="feature_alignment_5_peakview_output_matrix.csv" ftype="tabular" />
156 </test>
157
158 </tests>
95 <help> 159 <help>
96 <![CDATA[ 160 <![CDATA[
97 161
98 **What it does** 162 **What it does**
99 163