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annotate 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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1 <tool id="feature_alignment" name="Feature Alignment" version="0.1">
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2 <description>of peakgroups below a FDR</description>
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3 <requirements>
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4 <requirement type="package" version="2.7">python</requirement>
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5 <requirement type="package" version="0.3.2">msproteomicstools</requirement>
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6 </requirements>
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7 <stdio>
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8 <!-- Anything other than zero is an error -->
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9 <exit_code range="1:" />
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10 <exit_code range=":-1" />
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11 <!-- In case the return code has not been set propery check stderr too -->
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12 <regex match="Error:" />
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13 <regex match="Exception:" />
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14 </stdio>
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15 <version_command>feature_alignment.py --version</version_command>
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16 <command>
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17 <![CDATA[
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18 feature_alignment.py
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19 --in #echo '" "'.join([ str($file) for $file in $inputs ]) #
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20 --file_format $iformat
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21 ##if str($iformat) == "openswath":
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22 --out $out
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23 ##end if
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24 --out_matrix out_matrix.tsv
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25 --out_ids $out_ids
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26 --fdr_cutoff $fdr_cutoff
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27 #if $max_fdr_quality:
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28 --max_fdr_quality $max_fdr_quality
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29 #end if
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30 #if $max_rt_diff:
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31 --max_rt_diff $max_rt_diff
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32 #end if
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33 #if $iso_max_rt_diff:
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34 --iso_max_rt_diff $iso_max_rt_diff
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35 #end if
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36 #if $frac_selected:
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37 --frac_selected $frac_selected
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38 #end if
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39 --method $method
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40 --matrix_output_method $matrix_output_method
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41 --realign_method $realign_method
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42 &&
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43 mv out_matrix.tsv $out_matrix
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44
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45 ]]></command>
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46 <inputs>
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47
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48 <param name="inputs" type="data" multiple="True" format="txt"
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49 label="A list of mProphet output files containing all peakgroups" help="(--in)"/>
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50 <param name="iformat" type="select" label="Which input file format is used" help="(--file_format)">
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51 <option value="openswath" selected="True">OpenSwath</option>
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52 <option value="peakview">Peakview</option>
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53 </param>
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54
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55 <param name="fdr_cutoff" type="float" value="0.01" label="Seeding score cutoff" help="(--fdr_cutoff)" />
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56 <param name="max_fdr_quality" type="float" value="-1.0" default="-1.0" optional="True"
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57 label="Extension score cutoff"
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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)"/>
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59 <param name="max_rt_diff" type="integer" value="30" default="30" optional="True"
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60 label="Maximal difference in RT for two aligned features" help="(--max_rt_diff)"/>
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61 <param name="iso_max_rt_diff" type="integer" value="10" default="10" optional="True"
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62 label="Maximal difference in RT for two isotopic channels in the same run" help="(--iso_max_rt_diff)" />
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63 <param name="frac_selected" type="float" value="0.0" min="0" max="1" optional="True"
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64 label="Do not write peakgroup if selected in less than this fraction of runs" help="(--frac_selected)"/>
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65 <param name="method" type="select"
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66 label="Which method to use for the clustering"
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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)" >
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68 <option value='best_overall' selected="True">best_overall</option>
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69 <option value='best_cluster_score'>best_cluster_score</option>
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70 <option value='global_best_cluster_score'>global_best_cluster_score</option>
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71 <option value='global_best_overall'>global_best_overall</option>
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72 <option value='LocalMST'>LocalMST</option>
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73 <option value='LocalMSTAllCluster'>LocalMSTAllCluster</option>
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74 </param>
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75
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76 <param name="matrix_output_method" type="select"
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77 label="Which columns are written besides Intensity" help="(--matrix_output_method)">
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78 <option value='none' selected="True">None</option>
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79 <option value='RT'>RT</option>
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80 <option value='score'>Score</option>
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81 <option value='source'>Source</option>
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82 <option value='full'>Full</option>
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83 </param>
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84 <param name="realign_method" type="select" label="How to re-align runs in retention time" help="(--realign_method)">
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85 <option value='diRT' selected="True">Use only deltaiRT from the input file</option>
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86 <option value='linear'>Perform a linear regression using best peakgroups</option>
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87 <!--option value='splineR'>Perform a spline fit using R</option-->
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88 <!--option value='splineR_external'>Perform a spline fit using R</option-->
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89 <option value='splinePy'>Use Python native spline from scikits.datasmooth (slow!)</option>
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90 <option value='lowess'>Use Robust locally weighted regression (lowess smoother)</option>
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91 <option value='CVSpline'>Splines with cross-validation</option>
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92 <option value='nonCVSpline'>Splines without cross-validation</option>
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93 <option value='earth' >Use Multivariate Adaptive Regression Splines using py-earth</option>
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94 </param>
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95 </inputs>
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96 <outputs>
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97 <!-- Matrix containing one peak group per row -->
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98 <data format="tabular" name="out_matrix"/>
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99 <!-- Id file only containing the ids -->
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100 <data format="tabular" name="out_ids"/>
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101 <!-- Output file with filtered peakgroups for quantification (only works for OpenSWATH) -->
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102 <data format="tabular" name="out">
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103 <!-- according to the documentation this output only works for SWATH,
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104 but it is a requirement argument in python argparse.
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105 So we need to output it. -->
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106 <!--filter>iformat == 'openswath'</filter-->
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107 </data>
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108 </outputs>
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109 <tests>
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110 <test>
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111 <param name="inputs" value="feature_alignment_openswath_input_1.csv" ftype="txt" />
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112 <param name="iformat" value="openswath" />
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113 <param name="method" value="best_cluster_score" />
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114 <param name="max_fdr_quality" value="0.4" />
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115 <param name="matrix_output_method" value="RT" />
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116 <output name="out_matrix" file="feature_alignment_1_openswath_output_matrix.csv" ftype="tabular" />
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117 <output name="out_ids" file="feature_alignment_1_openswath_output_cluster_ids.csv" ftype="tabular" />
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118 </test>
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119 <test>
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120 <param name="inputs" value="feature_alignment_openswath_input_1.csv" ftype="txt" />
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121 <param name="iformat" value="openswath" />
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122 <param name="method" value="best_overall" />
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123 <param name="max_fdr_quality" value="0.4" />
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124 <param name="matrix_output_method" value="RT" />
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125 <output name="out_matrix" file="feature_alignment_2_output_2_matrix.csv" ftype="tabular" />
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126 <output name="out_ids" file="feature_alignment_2_output_1_ids.csv" ftype="tabular" />
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127 </test>
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128 <!-- needs R dependency; The python equivalent should be enough I guess.
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129 <test>
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130 <param name="inputs" value="feature_alignment_3_openswath_input.csv" ftype="txt" />
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131 <param name="iformat" value="openswath" />
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132 <param name="realign_method" value="splineR" />
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133 <param name="method" value="best_cluster_score" />
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134 <param name="max_fdr_quality" value="0.4" />
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135 <param name="maxtrix_output_method" value="RT" />
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136 <output name="out_ids" file="feature_alignment_3_openswath_output_cluster_ids.csv" ftype="tabular" />
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137 </test>
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138 -->
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139 <test>
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140 <param name="inputs" value="feature_alignment_3_openswath_input.csv" ftype="txt" />
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141 <param name="iformat" value="openswath" />
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142 <param name="realign_method" value="splinePy" />
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143 <param name="method" value="best_cluster_score" />
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144 <param name="max_fdr_quality" value="0.4" />
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145 <param name="matrix_output_method" value="RT" />
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146 <output name="out_ids" file="feature_alignment_3_openswath_output_cluster_ids.csv" ftype="tabular" />
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147 </test>
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148 <test>
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149 <param name="inputs" value="feature_alignment_peakview_input_2.csv" ftype="txt" />
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150 <param name="iformat" value="peakview" />
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151 <param name="method" value="best_cluster_score" />
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152 <param name="max_fdr_quality" value="0.0001" />
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153 <param name="fdr_cutoff" value="0.000000001" />
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154 <param name="matrix_output_method" value="RT" />
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155 <output name="out_matrix" file="feature_alignment_5_peakview_output_matrix.csv" ftype="tabular" />
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156 </test>
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157
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158 </tests>
0
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159 <help>
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160 <![CDATA[
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161
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162 **What it does**
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163
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164 This program will select all peakgroups below the FDR cutoff in all files and try to align them to each other.
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165 If only one file is given, it will act as peakgroup selector (best by m_score)
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166 and will apply the provided FDR cutoff.
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167 ]]>
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168 </help>
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169 <citations>
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170 </citations>
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171 </tool>
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172