Mercurial > repos > galaxyp > openms_multiplexresolver

annotate MultiplexResolver.xml @ 14:53b202a738c3 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:32:24 +0000
parents 021fdb80f204
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1 <!--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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2 <!--Proposed Tool Section: [Quantitation]-->
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3 <tool id="MultiplexResolver" name="MultiplexResolver" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Completes peptide multiplets and resolves conflicts within them</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">MultiplexResolver</token>
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7 <import>macros.xml</import>
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8 </macros>
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9 <expand macro="requirements"/>
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10 <expand macro="stdio"/>
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11 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
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12 @EXT_FOO@
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13 #import re
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14
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15 ## Preprocessing
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16 mkdir in &&
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17 cp '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
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18 #if $in_blacklist:
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19 mkdir in_blacklist &&
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20 cp '$in_blacklist' 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)' &&
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21 #end if
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22 mkdir out &&
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23 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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24 mkdir out_conflicts &&
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25 #end if
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27 ## Main program call
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29 set -o pipefail &&
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30 @EXECUTABLE@ -write_ctd ./ &&
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31 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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32 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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33 -in
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34 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
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35 #if $in_blacklist:
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36 -in_blacklist
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37 'in_blacklist/${re.sub("[^\w\-_]", "_", $in_blacklist.element_identifier)}.$gxy2omsext($in_blacklist.ext)'
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38 #end if
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39 -out
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40 'out/output.${gxy2omsext("consensusxml")}'
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41 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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42 -out_conflicts
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43 'out_conflicts/output.${gxy2omsext("consensusxml")}'
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44 #end if
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45 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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46 | tee '$stdout'
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47 #end if
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49 ## Postprocessing
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50 && mv 'out/output.${gxy2omsext("consensusxml")}' '$out'
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51 #if "out_conflicts_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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52 && mv 'out_conflicts/output.${gxy2omsext("consensusxml")}' '$out_conflicts'
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53 #end if
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54 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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55 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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56 #end if]]></command>
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57 <configfiles>
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58 <inputs name="args_json" data_style="paths"/>
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59 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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60 </configfiles>
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61 <inputs>
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62 <param argument="-in" type="data" format="consensusxml" label="Peptide multiplets with assigned sequence information" help=" select consensusxml data sets(s)"/>
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63 <param argument="-in_blacklist" type="data" format="mzml" optional="true" label="Optional input containing spectral peaks blacklisted during feature detection" help="Needed for generation of dummy features select mzml data sets(s)"/>
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64 <section name="algorithm" title="Parameters for the algorithm" help="" expanded="false">
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65 <param name="labels" argument="-algorithm:labels" type="text" value="[][Lys8,Arg10]" label="Labels used for labelling the samples" help="[...] specifies the labels for a single sample. For example. [][Lys8,Arg10] ... SILAC. [][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC. [Dimethyl0][Dimethyl6] ... Dimethyl. [Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl. [ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL">
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66 <expand macro="list_string_san" name="labels"/>
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67 </param>
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68 <param name="missed_cleavages" argument="-algorithm:missed_cleavages" type="integer" min="0" value="0" label="Maximum number of missed cleavages due to incomplete digestion" help="(Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)"/>
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69 <param name="mass_tolerance" argument="-algorithm:mass_tolerance" type="float" value="0.1" label="Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern" help=""/>
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70 <param name="mz_tolerance" argument="-algorithm:mz_tolerance" type="integer" value="10" label="m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted" help=""/>
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71 <param name="rt_tolerance" argument="-algorithm:rt_tolerance" type="integer" value="5" label="Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted" help=""/>
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72 </section>
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73 <section name="labels" title="Isotopic labels that can be specified in section 'algorithm:labels'" help="" expanded="false">
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74 <param name="Arg6" argument="-labels:Arg6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
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75 <param name="Arg10" argument="-labels:Arg10" type="float" min="0.0" value="10.0082686" label="Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267" help=""/>
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76 <param name="Lys4" argument="-labels:Lys4" type="float" min="0.0" value="4.0251069836" label="Label:2H(4) | H(-4) 2H(4) | unimod #481" help=""/>
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77 <param name="Lys6" argument="-labels:Lys6" type="float" min="0.0" value="6.0201290268" label="Label:13C(6) | C(-6) 13C(6) | unimod #188" help=""/>
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78 <param name="Lys8" argument="-labels:Lys8" type="float" min="0.0" value="8.0141988132" label="Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259" help=""/>
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79 <param name="Leu3" argument="-labels:Leu3" type="float" min="0.0" value="3.01883" label="Label:2H(3) | H(-3) 2H(3) | unimod #262" help=""/>
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80 <param name="Dimethyl0" argument="-labels:Dimethyl0" type="float" min="0.0" value="28.0313" label="Dimethyl | H(4) C(2) | unimod #36" help=""/>
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81 <param name="Dimethyl4" argument="-labels:Dimethyl4" type="float" min="0.0" value="32.056407" label="Dimethyl:2H(4) | 2H(4) C(2) | unimod #199" help=""/>
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82 <param name="Dimethyl6" argument="-labels:Dimethyl6" type="float" min="0.0" value="34.063117" label="Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510" help=""/>
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83 <param name="Dimethyl8" argument="-labels:Dimethyl8" type="float" min="0.0" value="36.07567" label="Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330" help=""/>
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84 <param name="ICPL0" argument="-labels:ICPL0" type="float" min="0.0" value="105.021464" label="ICPL | H(3) C(6) N O | unimod #365" help=""/>
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85 <param name="ICPL4" argument="-labels:ICPL4" type="float" min="0.0" value="109.046571" label="ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687" help=""/>
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86 <param name="ICPL6" argument="-labels:ICPL6" type="float" min="0.0" value="111.041593" label="ICPL:13C(6) | H(3) 13C(6) N O | unimod #364" help=""/>
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87 <param name="ICPL10" argument="-labels:ICPL10" type="float" min="0.0" value="115.0667" label="ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866" help=""/>
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88 </section>
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89 <expand macro="adv_opts_macro">
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90 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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91 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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92 <expand macro="list_string_san" name="test"/>
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93 </param>
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94 </expand>
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95 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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96 <option value="out_conflicts_FLAG">out_conflicts (Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information)</option>
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97 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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98 </param>
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99 </inputs>
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100 <outputs>
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101 <data name="out" label="${tool.name} on ${on_string}: out" format="consensusxml"/>
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102 <data name="out_conflicts" label="${tool.name} on ${on_string}: out_conflicts" format="consensusxml">
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103 <filter>OPTIONAL_OUTPUTS is not None and "out_conflicts_FLAG" in OPTIONAL_OUTPUTS</filter>
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104 </data>
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105 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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106 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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107 </data>
0
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108 </outputs>
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109 <tests>
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110 <!-- TOPP_MultiplexResolver_1 -->
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111 <test expect_num_outputs="3">
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112 <section name="adv_opts">
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113 <param name="force" value="false"/>
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114 <param name="test" value="true"/>
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115 </section>
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116 <param name="in" value="MultiplexResolver_1_input.consensusXML"/>
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117 <output name="out" value="MultiplexResolver_1_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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118 <output name="out_conflicts" value="MultiplexResolver_1_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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119 <section name="algorithm">
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120 <param name="labels" value="[][Lys4,Arg6][Lys8,Arg10]"/>
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121 <param name="missed_cleavages" value="1"/>
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122 <param name="mass_tolerance" value="0.1"/>
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123 <param name="mz_tolerance" value="10"/>
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124 <param name="rt_tolerance" value="5"/>
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125 </section>
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126 <section name="labels">
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127 <param name="Arg6" value="6.0201290268"/>
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128 <param name="Arg10" value="10.0082686"/>
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129 <param name="Lys4" value="4.0251069836"/>
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130 <param name="Lys6" value="6.0201290268"/>
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131 <param name="Lys8" value="8.0141988132"/>
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132 <param name="Leu3" value="3.01883"/>
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133 <param name="Dimethyl0" value="28.0313"/>
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134 <param name="Dimethyl4" value="32.056407"/>
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135 <param name="Dimethyl6" value="34.063117"/>
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136 <param name="Dimethyl8" value="36.07567"/>
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137 <param name="ICPL0" value="105.021464"/>
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138 <param name="ICPL4" value="109.046571"/>
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139 <param name="ICPL6" value="111.041593"/>
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140 <param name="ICPL10" value="115.0667"/>
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141 </section>
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142 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
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143 <output name="ctd_out" ftype="xml">
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144 <assert_contents>
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145 <is_valid_xml/>
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146 </assert_contents>
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147 </output>
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148 <assert_stdout>
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149 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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150 </assert_stdout>
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151 </test>
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152 <!-- TOPP_MultiplexResolver_2 -->
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153 <test expect_num_outputs="3">
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154 <section name="adv_opts">
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155 <param name="force" value="false"/>
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156 <param name="test" value="true"/>
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157 </section>
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158 <param name="in" value="MultiplexResolver_2_input.consensusXML"/>
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159 <output name="out" value="MultiplexResolver_2_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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160 <output name="out_conflicts" value="MultiplexResolver_2_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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161 <section name="algorithm">
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162 <param name="labels" value="[Dimethyl0][Dimethyl4][Dimethyl8]"/>
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163 <param name="missed_cleavages" value="4"/>
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164 <param name="mass_tolerance" value="0.1"/>
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165 <param name="mz_tolerance" value="10"/>
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166 <param name="rt_tolerance" value="5"/>
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167 </section>
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168 <section name="labels">
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169 <param name="Arg6" value="6.0201290268"/>
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170 <param name="Arg10" value="10.0082686"/>
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171 <param name="Lys4" value="4.0251069836"/>
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172 <param name="Lys6" value="6.0201290268"/>
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173 <param name="Lys8" value="8.0141988132"/>
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174 <param name="Leu3" value="3.01883"/>
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175 <param name="Dimethyl0" value="28.0313"/>
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176 <param name="Dimethyl4" value="32.056407"/>
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177 <param name="Dimethyl6" value="34.063117"/>
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178 <param name="Dimethyl8" value="36.07567"/>
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179 <param name="ICPL0" value="105.021464"/>
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180 <param name="ICPL4" value="109.046571"/>
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181 <param name="ICPL6" value="111.041593"/>
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182 <param name="ICPL10" value="115.0667"/>
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183 </section>
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184 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
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185 <output name="ctd_out" ftype="xml">
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186 <assert_contents>
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187 <is_valid_xml/>
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188 </assert_contents>
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189 </output>
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190 <assert_stdout>
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191 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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192 </assert_stdout>
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193 </test>
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194 <!-- TOPP_MultiplexResolver_3 -->
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195 <test expect_num_outputs="3">
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196 <section name="adv_opts">
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197 <param name="force" value="false"/>
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198 <param name="test" value="true"/>
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199 </section>
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200 <param name="in" value="MultiplexResolver_3_input.consensusXML"/>
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201 <output name="out" value="MultiplexResolver_3_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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202 <output name="out_conflicts" value="MultiplexResolver_3_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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203 <section name="algorithm">
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204 <param name="labels" value="[][Leu3]"/>
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205 <param name="missed_cleavages" value="2"/>
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206 <param name="mass_tolerance" value="0.1"/>
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207 <param name="mz_tolerance" value="10"/>
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208 <param name="rt_tolerance" value="5"/>
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209 </section>
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210 <section name="labels">
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211 <param name="Arg6" value="6.0201290268"/>
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212 <param name="Arg10" value="10.0082686"/>
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213 <param name="Lys4" value="4.0251069836"/>
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214 <param name="Lys6" value="6.0201290268"/>
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215 <param name="Lys8" value="8.0141988132"/>
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216 <param name="Leu3" value="3.01883"/>
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217 <param name="Dimethyl0" value="28.0313"/>
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218 <param name="Dimethyl4" value="32.056407"/>
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219 <param name="Dimethyl6" value="34.063117"/>
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220 <param name="Dimethyl8" value="36.07567"/>
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221 <param name="ICPL0" value="105.021464"/>
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222 <param name="ICPL4" value="109.046571"/>
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223 <param name="ICPL6" value="111.041593"/>
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224 <param name="ICPL10" value="115.0667"/>
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225 </section>
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226 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
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227 <output name="ctd_out" ftype="xml">
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228 <assert_contents>
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229 <is_valid_xml/>
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230 </assert_contents>
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231 </output>
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232 <assert_stdout>
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233 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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234 </assert_stdout>
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235 </test>
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236 <!-- TOPP_MultiplexResolver_4 -->
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237 <test expect_num_outputs="3">
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238 <section name="adv_opts">
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239 <param name="force" value="false"/>
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240 <param name="test" value="true"/>
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241 </section>
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242 <param name="in" value="MultiplexResolver_4_input.consensusXML"/>
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243 <param name="in_blacklist" value="MultiplexResolver_4_input.mzML"/>
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244 <output name="out" value="MultiplexResolver_4_output.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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245 <output name="out_conflicts" value="MultiplexResolver_4_output_conflicts.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
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246 <section name="algorithm">
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247 <param name="labels" value="[Dimethyl0][Dimethyl6]"/>
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248 <param name="missed_cleavages" value="3"/>
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249 <param name="mass_tolerance" value="0.1"/>
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250 <param name="mz_tolerance" value="10"/>
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251 <param name="rt_tolerance" value="10"/>
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252 </section>
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253 <section name="labels">
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254 <param name="Arg6" value="6.0201290268"/>
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255 <param name="Arg10" value="10.0082686"/>
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256 <param name="Lys4" value="4.0251069836"/>
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257 <param name="Lys6" value="6.0201290268"/>
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258 <param name="Lys8" value="8.0141988132"/>
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259 <param name="Leu3" value="3.01883"/>
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260 <param name="Dimethyl0" value="28.0313"/>
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261 <param name="Dimethyl4" value="32.056407"/>
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262 <param name="Dimethyl6" value="34.063117"/>
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263 <param name="Dimethyl8" value="36.07567"/>
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264 <param name="ICPL0" value="105.021464"/>
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265 <param name="ICPL4" value="109.046571"/>
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266 <param name="ICPL6" value="111.041593"/>
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267 <param name="ICPL10" value="115.0667"/>
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268 </section>
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269 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_conflicts_FLAG"/>
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270 <output name="ctd_out" ftype="xml">
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271 <assert_contents>
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272 <is_valid_xml/>
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273 </assert_contents>
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274 </output>
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275 <assert_stdout>
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276 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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277 </assert_stdout>
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278 </test>
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279 </tests>
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280 <help><![CDATA[Completes peptide multiplets and resolves conflicts within them.
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281
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282
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283 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MultiplexResolver.html]]></help>
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284 <expand macro="references"/>
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285 </tool>