Mercurial > repos > galaxyp > openms_inspectadapter

annotate InspectAdapter.xml @ 0:f24ef0b2174b draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
author galaxyp
date Wed, 01 Mar 2017 09:56:24 -0500
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f24ef0b2174b 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 CTD2Galaxy.-->
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3 <!--Proposed Tool Section: [Identification]-->
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4 <tool id="InspectAdapter" name="InspectAdapter" version="2.1.0">
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5 <description>Annotates MS/MS spectra using Inspect.</description>
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6 <macros>
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7 <token name="@EXECUTABLE@">InspectAdapter</token>
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8 <import>macros.xml</import>
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9 </macros>
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10 <expand macro="references"/>
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11 <expand macro="stdio"/>
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12 <expand macro="requirements"/>
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13 <command>InspectAdapter
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14
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15 #if $param_in:
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16 -in $param_in
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17 #end if
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18 #if $param_out:
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19 -out $param_out
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20 #end if
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21 #if $param_inspect_in:
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22 -inspect_in
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23 #end if
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24 #if $param_inspect_out:
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25 -inspect_out
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26 #end if
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27 #if $param_inspect_directory:
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28 -inspect_directory "$param_inspect_directory"
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29 #end if
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30 #if $param_temp_data_directory:
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31 -temp_data_directory "$param_temp_data_directory"
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32 #end if
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33 #if $param_dbs:
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34 -dbs "$param_dbs"
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35 #end if
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36 #if $param_trie_dbs:
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37 -trie_dbs "$param_trie_dbs"
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38 #end if
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39 #if $param_new_db:
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40 -new_db "$param_new_db"
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41 #end if
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42 #if $param_instrument:
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43 -instrument
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44 #if " " in str($param_instrument):
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45 "$param_instrument"
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46 #else
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47 $param_instrument
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48 #end if
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49 #end if
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50 #if $param_precursor_mass_tolerance:
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51 -precursor_mass_tolerance $param_precursor_mass_tolerance
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52 #end if
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53 #if $param_peak_mass_tolerance:
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54 -peak_mass_tolerance $param_peak_mass_tolerance
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55 #end if
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56 #if $param_list_modifications:
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57 -list_modifications
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58 #end if
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59 #if $param_modifications:
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60 -modifications "$param_modifications"
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61 #end if
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62 #if $param_use_monoisotopic_mod_mass:
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63 -use_monoisotopic_mod_mass
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64 #end if
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65 #if $param_modifications_xml_file:
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66 -modifications_xml_file "$param_modifications_xml_file"
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67 #end if
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68 #if $param_cleavage:
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69 -cleavage "$param_cleavage"
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70 #end if
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71 #if $param_inspect_output:
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72 -inspect_output $param_inspect_output
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73 #end if
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74 #if $param_inspect_input:
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75 -inspect_input $param_inspect_input
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76 #end if
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77 #if $param_multicharge:
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78 -multicharge
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79 #end if
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80 #if $param_max_modifications_pp:
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81 -max_modifications_pp $param_max_modifications_pp
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82 #end if
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83 #if $param_tag_count:
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84 -tag_count $param_tag_count
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85 #end if
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86 #if $param_no_tmp_dbs:
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87 -no_tmp_dbs
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88 #end if
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89 #if $param_p_value:
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90 -p_value $param_p_value
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91 #end if
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92 #if $param_contact_name:
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93 -contact_name "$param_contact_name"
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94 #end if
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95 #if $param_contact_institution:
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96 -contact_institution "$param_contact_institution"
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97 #end if
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98 #if $param_contact_info:
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99 -contact_info "$param_contact_info"
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100 #end if
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101 #if $param_blind_blind:
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102 -blind:blind
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103 #end if
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104 #if $param_blind_blind_only:
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105 -blind:blind_only
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106 #end if
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107 #if $param_blind_p_value_blind:
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108 -blind:p_value_blind $param_blind_p_value_blind
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109 #end if
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110 #if $param_blind_snd_db:
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111 -blind:snd_db "$param_blind_snd_db"
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112 #end if
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113 #if $param_blind_max_ptm_size:
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114 -blind:max_ptm_size $param_blind_max_ptm_size
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115 #end if
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116 #if $adv_opts.adv_opts_selector=='advanced':
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117 #if $adv_opts.param_force:
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118 -force
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119 #end if
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120 #end if
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121 </command>
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122 <inputs>
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123 <param name="param_in" type="data" format="mzxml" optional="False" label="input file in mzXML or mzData format" help="(-in) &lt;br&gt;Note: In mode 'inspect_out' an Inspect results file is read"/>
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124 <param name="param_inspect_in" display="radio" type="boolean" truevalue="-inspect_in" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in mzXML, &lt;br&gt;write an Inspect input file and generate a trie database" help="(-inspect_in) "/>
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125 <param name="param_inspect_out" display="radio" type="boolean" truevalue="-inspect_out" falsevalue="" checked="false" optional="True" label="if this flag is set the InspectAdapter will read in a Inspect results file &lt;br&gt;and write idXML" help="(-inspect_out) "/>
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126 <param name="param_inspect_directory" type="text" size="30" label="the directory in which Inspect is located" help="(-inspect_directory) ">
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127 <sanitizer>
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128 <valid initial="string.printable">
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129 <remove value="'"/>
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130 <remove value="&quot;"/>
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131 </valid>
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132 </sanitizer>
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133 </param>
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134 <param name="param_temp_data_directory" type="text" size="30" label="a directory in which some temporary files can be stored" help="(-temp_data_directory) ">
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135 <sanitizer>
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136 <valid initial="string.printable">
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137 <remove value="'"/>
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138 <remove value="&quot;"/>
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139 </valid>
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140 </sanitizer>
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141 </param>
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142 <param name="param_dbs" type="text" size="30" label="name(s) of database(s) to search in (FASTA and SwissProt supported)" help="(-dbs) ">
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143 <sanitizer>
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144 <valid initial="string.printable">
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145 <remove value="'"/>
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146 <remove value="&quot;"/>
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147 </valid>
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148 </sanitizer>
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149 </param>
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150 <param name="param_trie_dbs" type="text" size="30" label="name(s) of databases(s) to search in (trie-format)" help="(-trie_dbs) ">
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151 <sanitizer>
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152 <valid initial="string.printable">
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153 <remove value="'"/>
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154 <remove value="&quot;"/>
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155 </valid>
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156 </sanitizer>
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157 </param>
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158 <param name="param_new_db" type="text" size="30" label="name of the merged trie database" help="(-new_db) ">
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159 <sanitizer>
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160 <valid initial="string.printable">
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161 <remove value="'"/>
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162 <remove value="&quot;"/>
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163 </valid>
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164 </sanitizer>
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165 </param>
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166 <param name="param_instrument" display="radio" type="select" optional="True" label="the instrument that was used to measure the spectra &lt;br&gt;(If set to QTOF, uses a QTOF-derived fragmentation model, &lt;br&gt;and does not attempt to correct the parent mass.)" help="(-instrument) ">
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167 <option value="ESI-ION-TRAP">ESI-ION-TRAP</option>
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168 <option value="QTOF">QTOF</option>
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169 <option value="FT-Hybrid">FT-Hybrid</option>
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170 </param>
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171 <param name="param_precursor_mass_tolerance" type="float" value="2.0" label="the precursor mass tolerance" help="(-precursor_mass_tolerance) "/>
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172 <param name="param_peak_mass_tolerance" type="float" value="1.0" label="the peak mass tolerance" help="(-peak_mass_tolerance) "/>
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173 <param name="param_list_modifications" display="radio" type="boolean" truevalue="-list_modifications" falsevalue="" checked="false" optional="True" label="show a list of the available modifications" help="(-list_modifications) "/>
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174 <param name="param_modifications" type="text" size="30" label="the colon-separated modifications; may be &lt;br&gt;&lt;name&gt;,&lt;type&gt;," help="(-modifications) e.g.: Deamidation,opt or &lt;br&gt;&lt;composition&gt;,&lt;residues&gt;,&lt;type&gt;,&lt;name&gt;, e.g.: H2C2O,KCS,opt,Acetyl or &lt;br&gt;&lt;mass&gt;,&lt;residues&gt;,&lt;type&gt;,&lt;name&gt;, e.g.: 42.0367,KCS,opt,Acetyl or &lt;br&gt;Valid values for type are &quot;fix&quot; and &quot;opt&quot; (default) &lt;br&gt;If you want terminal PTMs, write &quot;cterm&quot; or &quot;nterm&quot; instead of residues">
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175 <sanitizer>
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176 <valid initial="string.printable">
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177 <remove value="'"/>
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178 <remove value="&quot;"/>
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179 </valid>
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180 </sanitizer>
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181 </param>
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182 <param name="param_use_monoisotopic_mod_mass" display="radio" type="boolean" truevalue="-use_monoisotopic_mod_mass" falsevalue="" checked="false" optional="True" label="use monoisotopic masses for the modifications" help="(-use_monoisotopic_mod_mass) "/>
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183 <param name="param_modifications_xml_file" type="text" size="30" label="name of an XML file with the modifications" help="(-modifications_xml_file) ">
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184 <sanitizer>
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185 <valid initial="string.printable">
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186 <remove value="'"/>
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187 <remove value="&quot;"/>
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188 </valid>
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189 </sanitizer>
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190 </param>
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191 <param name="param_cleavage" type="text" size="30" value="Trypsin" label="the enzyme used for digestion" help="(-cleavage) ">
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192 <sanitizer>
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193 <valid initial="string.printable">
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194 <remove value="'"/>
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195 <remove value="&quot;"/>
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196 </valid>
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197 </sanitizer>
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198 </param>
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199 <param name="param_inspect_input" type="data" format="text" label="name for the input file of Inspect (may only be used in a full run)" help="(-inspect_input) "/>
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200 <param name="param_multicharge" display="radio" type="boolean" truevalue="-multicharge" falsevalue="" checked="false" optional="True" label="attempt to guess the precursor charge and mass, &lt;br&gt;and consider multiple charge states if feasible" help="(-multicharge) "/>
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201 <param name="param_max_modifications_pp" type="integer" value="-1" label="number of PTMs permitted in a single peptide" help="(-max_modifications_pp) "/>
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202 <param name="param_tag_count" type="integer" value="-1" label="number of tags to generate" help="(-tag_count) "/>
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203 <param name="param_no_tmp_dbs" display="radio" type="boolean" truevalue="-no_tmp_dbs" falsevalue="" checked="false" optional="True" label="no temporary databases are used" help="(-no_tmp_dbs) "/>
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204 <param name="param_p_value" type="float" value="1.0" label="annotations with inferior p-value are ignored" help="(-p_value) "/>
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205 <param name="param_contact_name" type="text" size="30" value="unknown" label="Name of the contact" help="(-contact_name) ">
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206 <sanitizer>
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207 <valid initial="string.printable">
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208 <remove value="'"/>
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209 <remove value="&quot;"/>
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210 </valid>
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211 </sanitizer>
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212 </param>
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213 <param name="param_contact_institution" type="text" size="30" value="unknown" label="Name of the contact institution" help="(-contact_institution) ">
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214 <sanitizer>
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215 <valid initial="string.printable">
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216 <remove value="'"/>
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217 <remove value="&quot;"/>
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218 </valid>
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219 </sanitizer>
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220 </param>
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221 <param name="param_contact_info" type="text" size="30" value="unknown" label="Some information about the contact" help="(-contact_info) ">
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222 <sanitizer>
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223 <valid initial="string.printable">
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224 <remove value="'"/>
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225 <remove value="&quot;"/>
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226 </valid>
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227 </sanitizer>
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228 </param>
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229 <param name="param_blind_blind" display="radio" type="boolean" truevalue="-blind:blind" falsevalue="" checked="false" optional="True" label="perform a blind search (allowing arbitrary modification masses), &lt;br&gt;is preceeded by a normal search to gain a smaller database" help="(-blind) &lt;br&gt;(in full mode only)"/>
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230 <param name="param_blind_blind_only" display="radio" type="boolean" truevalue="-blind:blind_only" falsevalue="" checked="false" optional="True" label="like blind but no prior search is performed to reduce the database size" help="(-blind_only) "/>
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231 <param name="param_blind_p_value_blind" type="float" value="1.0" label="used for generating the minimized database" help="(-p_value_blind) "/>
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232 <param name="param_blind_snd_db" type="text" size="30" label="name of the minimized trie database generated when using blind mode" help="(-snd_db) ">
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233 <sanitizer>
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234 <valid initial="string.printable">
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235 <remove value="'"/>
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236 <remove value="&quot;"/>
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237 </valid>
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238 </sanitizer>
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239 </param>
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240 <param name="param_blind_max_ptm_size" type="float" value="250.0" label="maximum modification size (in Da) to conside" help="(-max_ptm_size) "/>
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241 <expand macro="advanced_options">
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242 <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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243 </expand>
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244 </inputs>
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245 <outputs>
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246 <data name="param_out" format="idxml"/>
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247 <data name="param_inspect_output" format="data"/>
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248 </outputs>
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249 <help>Annotates MS/MS spectra using Inspect.
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250
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251
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252 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_InspectAdapter.html</help>
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253 </tool>