Mercurial > repos > galaxyp > openms_metaprosip

annotate MetaProSIP.xml @ 13:3a2985428366 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit f608f41d45664d04d3124c6ebc791bf8a566b3c5
author galaxyp
date Wed, 15 May 2019 05:13:44 -0400
parents d06e5c4396d7
children 7a0f18ee26c9
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0283517872f8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
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3 <!--Proposed Tool Section: [Utilities]-->
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4 <tool id="MetaProSIP" name="MetaProSIP" version="2.3.2">
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5 <description>Performs proteinSIP on peptide features for elemental flux analysis.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">MetaProSIP</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="requirements">
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11 <requirement type="package" version="3.4.1">r-base</requirement>
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12 <requirement type="package" version="3.0.1">r-gplots</requirement>
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13 </expand>
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14 <expand macro="stdio"/>
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15 <command detect_errors="aggressive"><![CDATA[
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16 MetaProSIP
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18 #if $param_in_mzML:
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19 -in_mzML $param_in_mzML
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20 #end if
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21 #if $param_in_fasta:
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22 -in_fasta $param_in_fasta
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23 #end if
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24 #if $param_out_csv:
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25 -out_csv $param_out_csv
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26 #end if
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27 #if $param_out_peptide_centric_csv:
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28 -out_peptide_centric_csv param_out_peptide_centric_csv
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29 #end if
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30 #if $param_in_featureXML:
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31 -in_featureXML $param_in_featureXML
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32 #end if
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33 #if $param_mz_tolerance_ppm:
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34 -mz_tolerance_ppm $param_mz_tolerance_ppm
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35 #end if
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36 #if $param_rt_tolerance_s:
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37 -rt_tolerance_s $param_rt_tolerance_s
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38 #end if
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39 #if $param_intensity_threshold:
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40 -intensity_threshold $param_intensity_threshold
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41 #end if
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42 #if $param_correlation_threshold:
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43 -correlation_threshold $param_correlation_threshold
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44 #end if
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45 #if $param_xic_threshold:
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46 -xic_threshold $param_xic_threshold
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47 #end if
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48 #if $param_decomposition_threshold:
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49 -decomposition_threshold $param_decomposition_threshold
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50 #end if
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51 #if $param_weight_merge_window:
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52 -weight_merge_window $param_weight_merge_window
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53 #end if
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54 #if $param_plot_extension:
1
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55 -plot_extension
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56 #if " " in str($param_plot_extension):
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57 "$param_plot_extension"
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58 #else
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59 $param_plot_extension
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60 #end if
0
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61 #end if
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62 -qc_output_directory images
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63 #if $param_labeling_element:
1
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64 -labeling_element
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65 #if " " in str($param_labeling_element):
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66 "$param_labeling_element"
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67 #else
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68 $param_labeling_element
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69 #end if
0
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70 #end if
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71 #if $param_use_unassigned_ids:
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72 -use_unassigned_ids
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73 #end if
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74 #if $param_use_averagine_ids:
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75 -use_averagine_ids
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76 #end if
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77 #if $param_report_natural_peptides:
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78 -report_natural_peptides
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79 #end if
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80 #if $param_filter_monoisotopic:
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81 -filter_monoisotopic
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82 #end if
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83 #if $param_cluster:
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84 -cluster
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85 #end if
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86 #if $adv_opts.adv_opts_selector=='advanced':
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87 #if $adv_opts.param_min_correlation_distance_to_averagine:
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88 -min_correlation_distance_to_averagine $adv_opts.param_min_correlation_distance_to_averagine
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89 #end if
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90 #if $adv_opts.param_pattern_15N_TIC_threshold:
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91 -pattern_15N_TIC_threshold $adv_opts.param_pattern_15N_TIC_threshold
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92 #end if
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93 #if $adv_opts.param_pattern_13C_TIC_threshold:
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94 -pattern_13C_TIC_threshold $adv_opts.param_pattern_13C_TIC_threshold
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95 #end if
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96 #if $adv_opts.param_pattern_2H_TIC_threshold:
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97 -pattern_2H_TIC_threshold $adv_opts.param_pattern_2H_TIC_threshold
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98 #end if
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99 #if $adv_opts.param_pattern_18O_TIC_threshold:
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100 -pattern_18O_TIC_threshold $adv_opts.param_pattern_18O_TIC_threshold
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101 #end if
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102 #if $adv_opts.param_heatmap_bins:
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103 -heatmap_bins $adv_opts.param_heatmap_bins
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104 #end if
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105 #if $adv_opts.param_observed_peak_fraction:
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106 -observed_peak_fraction $adv_opts.param_observed_peak_fraction
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107 #end if
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108 #if $adv_opts.param_min_consecutive_isotopes:
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109 -min_consecutive_isotopes $adv_opts.param_min_consecutive_isotopes
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110 #end if
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111 #if $adv_opts.param_score_plot_yaxis_min:
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112 -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min
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113 #end if
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114 #if $adv_opts.param_collect_method:
1
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115 -collect_method
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116 #if " " in str($adv_opts.param_collect_method):
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117 "$adv_opts.param_collect_method"
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118 #else
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119 $adv_opts.param_collect_method
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120 #end if
0
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121 #end if
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122 #if $adv_opts.param_lowRIA_correlation_threshold:
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123 -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
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124 #end if
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125 #if $adv_opts.param_force:
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126 -force
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127 #end if
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128 #end if
13
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129 -threads "\${GALAXY_SLOTS:-1}"
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130
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131 ## - add comment char to first line,
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132 ## - remove leading/trailing spaces in fields
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133 ## - remove empty line(s)
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134 ## - remove 'file://' and get basename of filenames in the table
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135 ## - add empty fields as '0' (MetaproSIP output has varying number of output columns, ie it omits the last columns if there are no values)
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136 && cat param_out_peptide_centric_csv |
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137 sed '1 s/^/#/' |
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138 sed 's/\t /\t/g; s/ \t/\t/g; s/ /_/g' |
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139 grep -v "^$" |
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140 sed "s/\tfile:\/\//\t/g; s/\t\/[^\t]\+\//\t/g; s/\.$param_plot_extension//g" |
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141 awk -v FS='\t' 'BEGIN{line=0}{if(line==0){ncol=NF; print $0}else{printf("%s",$0); for(i=0; i<ncol-NF; i++){printf("\t0")}printf("\n")}line+=1}' > "$param_out_peptide_centric_csv"
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142
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143 ## get html file (should be only one [?])
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144
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145 #if $param_collection or $param_plot_extension == 'pdf'
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146 && rm -f images/*\.html
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147 #else
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148 && mv images/*\.html '${html_file}'
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149 && mv images/ '${html_file.files_path}'
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150 #end if
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151 ]]></command>
0
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152 <inputs>
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153 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Centroided MS1 data" help="(-in_mzML) "/>
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154 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Protein sequence database" help="(-in_fasta) "/>
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155 <param name="param_in_featureXML" type="data" format="featurexml" optional="False" label="Feature data annotated with identifications (IDMapper)" help="(-in_featureXML) "/>
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156 <param name="param_mz_tolerance_ppm" type="float" value="10.0" label="Tolerance in ppm" help="(-mz_tolerance_ppm) "/>
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157 <param name="param_rt_tolerance_s" type="float" value="30.0" label="Rolerance window around feature rt for XIC extraction" help="(-rt_tolerance_s) "/>
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158 <param name="param_intensity_threshold" type="float" value="10.0" label="Intensity threshold to collect peaks in the MS1 spectrum" help="(-intensity_threshold) "/>
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159 <param name="param_correlation_threshold" type="float" value="0.7" label="Correlation threshold for reporting a RIA" help="(-correlation_threshold) "/>
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160 <param name="param_xic_threshold" type="float" value="0.7" label="Minimum correlation to mono-isotopic peak for retaining a higher isotopic peak" help="(-xic_threshold) If featureXML from reference file is used it should be disabled (set to -1) as no mono-isotopic peak is expected to be present"/>
13
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161 <param name="param_decomposition_threshold" type="float" value="0.7" label="Minimum R² of decomposition that must be achieved for a peptide to be reported" help="(-decomposition_threshold) "/>
0
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162 <param name="param_weight_merge_window" type="float" value="5.0" label="Decomposition coefficients within +- this rate window will be combined" help="(-weight_merge_window) "/>
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163 <param name="param_plot_extension" display="radio" type="select" optional="False" value="png" label="Extension used for plots (png|svg|pdf)" help="(-plot_extension) ">
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164 <option value="png" selected="true">png</option>
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165 <option value="svg">svg</option>
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166 <option value="pdf">pdf</option>
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167 </param>
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168 <param name="param_labeling_element" display="radio" type="select" optional="False" value="C" label="Which element (single letter code) is labeled" help="(-labeling_element) ">
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169 <option value="C" selected="true">C</option>
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170 <option value="N">N</option>
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171 <option value="H">H</option>
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172 <option value="O">O</option>
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173 </param>
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174 <param name="param_use_unassigned_ids" display="radio" type="boolean" truevalue="-use_unassigned_ids" falsevalue="" checked="false" optional="True" label="Include identifications not assigned to a feature in pattern detection" help="(-use_unassigned_ids) "/>
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175 <param name="param_use_averagine_ids" display="radio" type="boolean" truevalue="-use_averagine_ids" falsevalue="" checked="false" optional="True" label="Use averagine peptides as model to perform pattern detection on unidentified peptides" help="(-use_averagine_ids) "/>
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176 <param name="param_report_natural_peptides" display="radio" type="boolean" truevalue="-report_natural_peptides" falsevalue="" checked="false" optional="True" label="Whether purely natural peptides are reported in the quality report" help="(-report_natural_peptides) "/>
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177 <param name="param_filter_monoisotopic" display="radio" type="boolean" truevalue="-filter_monoisotopic" falsevalue="" checked="false" optional="True" label="Try to filter out mono-isotopic patterns to improve detection of low RIA patterns" help="(-filter_monoisotopic) "/>
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178 <param name="param_cluster" display="radio" type="boolean" truevalue="-cluster" falsevalue="" checked="false" optional="True" label="Perform grouping" help="(-cluster) "/>
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179 <param name="param_collection" type="boolean" checked="true" label="output images as collection" help="if enabled images are written to a collection amd to a webpage otherwise (pdf is always written to a collection)"/>
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180 <expand macro="advanced_options">
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181 <param name="param_min_correlation_distance_to_averagine" type="float" value="-1.0" label="Minimum difference in correlation between incorporation pattern and averagine pattern" help="(-min_correlation_distance_to_averagine) Positive values filter all RIAs passing the correlation threshold but that also show a better correlation to an averagine peptide. Disabled for values &lt;= -1"/>
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182 <param name="param_pattern_15N_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_15N_TIC_threshold) "/>
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183 <param name="param_pattern_13C_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_13C_TIC_threshold) "/>
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184 <param name="param_pattern_2H_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_2H_TIC_threshold) "/>
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185 <param name="param_pattern_18O_TIC_threshold" type="float" value="0.95" label="The most intense peaks of the theoretical pattern contributing to at least this TIC fraction are taken into account" help="(-pattern_18O_TIC_threshold) "/>
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186 <param name="param_heatmap_bins" type="integer" value="20" label="Number of RIA bins for heat map generation" help="(-heatmap_bins) "/>
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187 <param name="param_observed_peak_fraction" type="float" value="0.5" label="Fraction of observed/expected peaks" help="(-observed_peak_fraction) "/>
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188 <param name="param_min_consecutive_isotopes" type="integer" value="2" label="Minimum number of consecutive isotopic intensities needed" help="(-min_consecutive_isotopes) "/>
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189 <param name="param_score_plot_yaxis_min" type="float" value="0.0" label="The minimum value of the score axis" help="(-score_plot_yaxis_min) Values smaller than zero usually only make sense if the observed peak fraction is set to 0"/>
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190 <param name="param_collect_method" display="radio" type="select" optional="False" value="correlation_maximum" label="How RIAs are collected" help="(-collect_method) ">
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191 <option value="correlation_maximum" selected="true">correlation_maximum</option>
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192 <option value="decomposition_maximum">decomposition_maximum</option>
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193 </param>
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194 <param name="param_lowRIA_correlation_threshold" type="float" value="-1.0" label="Correlation threshold for reporting low RIA patterns" help="(-lowRIA_correlation_threshold) Disable and take correlation_threshold value for negative values"/>
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195 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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196 </expand>
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197 </inputs>
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198 <outputs>
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199 <data name="param_out_csv" format="tabular" label="${tool.name} on ${on_string}: tabular"/>
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200 <data name="param_out_peptide_centric_csv" format="tabular" label="${tool.name} on ${on_string}: peptide centric tabular"/>
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201 <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage">
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202 <filter>not param_collection and (param_plot_extension == 'png' or param_plot_extension == 'svg')</filter>
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203 </data>
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204 <collection name="images" type="list" label="${tool.name} on ${on_string}: images">
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205 <filter>param_collection or param_plot_extension == 'pdf'</filter>
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206 <discover_datasets pattern="__name_and_ext__" directory="images" />
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207 </collection>
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208 </outputs>
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209 <tests>
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210 <test>
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211 <param name="param_in_mzML" value="MetaProSIP_1_input.mzML" ftype="mzml"/>
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212 <param name="param_in_fasta" value="MetaProSIP_1_input.fasta" ftype="fasta"/>
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213 <param name="param_in_featureXML" value="MetaProSIP_1_input.featureXML" ftype="featurexml"/>
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214 <output name="param_out_csv" file="MetaProSIP_1_output_1.csv"/>
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215 <output name="param_out_peptide_centric_csv" file="MetaProSIP_1_output_2.csv" compare="sim_size" lines_diff="2"/>
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216 </test>
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217 </tests>
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218 <help>Performs proteinSIP on peptide features for elemental flux analysis.
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219
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220 ** Galaxy specific notes **
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221
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222 The peptide centric tabular data set generated by the tool is not rendered properly by Galaxy, because it has more than 50 columns. You might extract columns of interst.
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223 </help>
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224 <expand macro="references"/>
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225 </tool>