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1 <?xml version='1.0' encoding='UTF-8'?>
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2 <tool id="RNPxl" name="RNPxl" version="2.0.0">
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3 <description>Tool for RNP cross linking experiment analysis.</description>
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4 <macros>
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5 <token name="@EXECUTABLE@">RNPxl</token>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="stdio"/>
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9 <expand macro="requirements"/>
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10 <command>RNPxl
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11
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12 #if $param_in_mzML:
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13 -in_mzML $param_in_mzML
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14 #end if
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15 #if $param_length:
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16 -length $param_length
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17 #end if
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18 #if $param_sequence:
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19 -sequence "$param_sequence"
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20 #end if
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21
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22 #if $rep_param_target_nucleotides:
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23 -target_nucleotides
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24 #for token in $rep_param_target_nucleotides:
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25 #if " " in str(token):
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26 "$token.param_target_nucleotides"
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27 #else
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28 $token.param_target_nucleotides
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29 #end if
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30 #end for
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31 #end if
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32
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33 #if $rep_param_mapping:
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34 -mapping
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35 #for token in $rep_param_mapping:
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36 #if " " in str(token):
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37 "$token.param_mapping"
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38 #else
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39 $token.param_mapping
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40 #end if
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41 #end for
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42 #end if
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43
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44 #if $rep_param_restrictions:
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45 -restrictions
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46 #for token in $rep_param_restrictions:
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47 #if " " in str(token):
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48 "$token.param_restrictions"
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49 #else
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50 $token.param_restrictions
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51 #end if
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52 #end for
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53 #end if
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54
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55 #if $rep_param_modifications:
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56 -modifications
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57 #for token in $rep_param_modifications:
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58 #if " " in str(token):
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59 "$token.param_modifications"
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60 #else
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61 $token.param_modifications
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62 #end if
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63 #end for
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64 #end if
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65 #if $param_peptide_mass_threshold:
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66 -peptide_mass_threshold $param_peptide_mass_threshold
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67 #end if
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68 #if $param_precursor_variant_mz_threshold:
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69 -precursor_variant_mz_threshold $param_precursor_variant_mz_threshold
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70 #end if
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71 #if $param_CysteineAdduct:
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72 -CysteineAdduct
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73 #end if
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74 #if $param_in_OMSSA_ini:
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75 -in_OMSSA_ini $param_in_OMSSA_ini
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76 #end if
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77 #if $param_in_fasta:
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78 -in_fasta $param_in_fasta
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79 #end if
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80 #if $param_marker_ions_tolerance:
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81 -marker_ions_tolerance $param_marker_ions_tolerance
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82 #end if
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83 #if $param_out_idXML:
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84 -out_idXML $param_out_idXML
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85 #end if
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86 #if $param_out_csv:
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87 -out_csv $param_out_csv
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88 #end if
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89 -threads \${GALAXY_SLOTS:-24}
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90 #if $adv_opts.adv_opts_selector=='advanced':
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91 #if $adv_opts.param_continue:
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92 -continue
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93 #end if
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94 #if $adv_opts.param_force:
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95 -force
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96 #end if
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97 #end if
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98 </command>
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99 <inputs>
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100 <param name="param_in_mzML" type="data" format="mzml" optional="False" label="Input file" help="(-in_mzML) "/>
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101 <param name="param_length" type="integer" value="4" label="Oligonucleotide maximum length" help="(-length) "/>
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102 <param name="param_sequence" type="text" size="30" label="Sequence to restrict the generation of oligonucleotide chains" help="(-sequence) (disabled for empty sequence)">
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103 <sanitizer>
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104 <valid initial="string.printable">
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105 <remove value="'"/>
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106 <remove value="""/>
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107 </valid>
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108 </sanitizer>
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109 </param>
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110 <repeat name="rep_param_target_nucleotides" min="0" max="1" title="param_target_nucleotides">
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111 <param name="param_target_nucleotides" type="text" size="30" value="A=C10H14N5O7P C=C9H14N3O8P G=C10H14N5O8P U=C9H13N2O9P" label="format: target nucleotide=empirical formula of nucleoside monophosphate" help="(-target_nucleotides) e.g. A=C10H14N5O7P, ..., U=C10H14N5O7P, X=C9H13N2O8PS where X represents e.g. tU <br> or e.g. Y=C10H14N5O7PS where Y represents tG">
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112 <sanitizer>
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113 <valid initial="string.printable">
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114 <remove value="'"/>
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115 <remove value="""/>
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116 </valid>
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117 </sanitizer>
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118 </param>
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119 </repeat>
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120 <repeat name="rep_param_mapping" min="0" max="1" title="param_mapping">
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121 <param name="param_mapping" type="text" size="30" value="A->A C->C G->G U->U" label="format: source->target e.g. A->A, ..., U->U, U->X" help="(-mapping) ">
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122 <sanitizer>
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123 <valid initial="string.printable">
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124 <remove value="'"/>
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125 <remove value="""/>
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126 </valid>
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127 </sanitizer>
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128 </param>
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129 </repeat>
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130 <repeat name="rep_param_restrictions" min="0" max="1" title="param_restrictions">
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131 <param name="param_restrictions" type="text" size="30" value="A=0 C=0 U=0 G=0" label="format: target nucleotide=min_count: e.g U=1 if at least one U must be in the generated sequence" help="(-restrictions) ">
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132 <sanitizer>
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133 <valid initial="string.printable">
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134 <remove value="'"/>
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135 <remove value="""/>
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136 </valid>
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137 </sanitizer>
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138 </param>
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139 </repeat>
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140 <repeat name="rep_param_modifications" min="0" max="1" title="param_modifications">
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141 <param name="param_modifications" type="text" size="30" value="-H2O -H2O-HPO3 -HPO3 -H2O+HPO3 +HPO3" label="format: empirical formula e.g -H2O, ..., H2O+PO3" help="(-modifications) ">
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142 <sanitizer>
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143 <valid initial="string.printable">
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144 <remove value="'"/>
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145 <remove value="""/>
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146 </valid>
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147 </sanitizer>
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148 </param>
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149 </repeat>
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150 <param name="param_peptide_mass_threshold" type="float" value="600.0" label="Lower peptide mass (Da) threshold" help="(-peptide_mass_threshold) "/>
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151 <param name="param_precursor_variant_mz_threshold" type="float" value="260.0" label="Lower m/z (Th) threshold for precursor variant" help="(-precursor_variant_mz_threshold) "/>
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152 <param name="param_CysteineAdduct" type="boolean" truevalue="-CysteineAdduct" falsevalue="" checked="false" optional="True" label="Use this flag if the +152 adduct is expected" help="(-CysteineAdduct) "/>
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153 <param name="param_in_OMSSA_ini" type="data" format="txt" optional="False" label="Ini file for the OMSSA search engine" help="(-in_OMSSA_ini) "/>
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154 <param name="param_in_fasta" type="data" format="fasta" optional="False" label="Fasta file for search result annotation" help="(-in_fasta) "/>
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155 <param name="param_marker_ions_tolerance" type="float" value="0.05" label="mz tolerance used to determine marker ions" help="(-marker_ions_tolerance) "/>
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156 <expand macro="advanced_options">
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157 <param name="param_continue" type="boolean" truevalue="-continue" falsevalue="" checked="false" optional="True" label="Do not recreate intermediate files to continue after unexpected crash" help="(-continue) "/>
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158 <param name="param_force" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/>
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159 </expand>
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160 </inputs>
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161 <outputs>
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162 <data name="param_out_idXML" format="idxml"/>
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163 <data name="param_out_csv" format="tabular"/>
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164 </outputs>
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165 <help>**What it does**
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166
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167 Tool for RNP cross linking experiment analysis.
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168
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169
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170 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/UTILS_RNPxl.html</help>
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171 <expand macro="references"/>
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172 </tool>
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