annotate MapAlignerIdentification.xml @ 9:77b66c1c5415 draft default tip

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author galaxyp
date Fri, 14 Jun 2024 21:29:16 +0000
parents 8434f070e939
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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: [Map Alignment]-->
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3 <tool id="MapAlignerIdentification" name="MapAlignerIdentification" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
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4 <description>Corrects retention time distortions between maps based on common peptide identifications</description>
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5 <macros>
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6 <token name="@EXECUTABLE@">MapAlignerIdentification</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_cond.in &&
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17 #if $in_cond.in_select == "no"
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18 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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19 ${' '.join(["cp '%s' 'in_cond.in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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20 #else
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21 cp '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
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22 #end if
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23 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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24 mkdir out &&
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25 mkdir ${' '.join(["'out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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26 #end if
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27 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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28 mkdir trafo_out &&
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29 mkdir ${' '.join(["'trafo_out/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
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30 #end if
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31 #if $design:
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32 mkdir design &&
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33 cp '$design' 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)' &&
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34 #end if
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35 #if $reference.file:
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36 mkdir reference.file &&
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37 cp '$reference.file' 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)' &&
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38 #end if
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39
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40 ## Main program call
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41
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42 set -o pipefail &&
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43 @EXECUTABLE@ -write_ctd ./ &&
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44 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
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45 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
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46 -in
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47 #if $in_cond.in_select == "no"
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48 ${' '.join(["'in_cond.in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_cond.in) if f])}
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49 #else
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50 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
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51 #end if
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52 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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53 -out
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54 ${' '.join(["'out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), f.ext) for i, f in enumerate($in_cond.in) if f])}
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55 #end if
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56 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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57 -trafo_out
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58 ${' '.join(["'trafo_out/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("trafoxml")) for i, f in enumerate($in_cond.in) if f])}
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59 #end if
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60 #if $design:
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61 -design
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62 'design/${re.sub("[^\w\-_]", "_", $design.element_identifier)}.$gxy2omsext($design.ext)'
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63 #end if
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64 #if $reference.file:
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65 -reference:file
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66 'reference.file/${re.sub("[^\w\-_]", "_", $reference.file.element_identifier)}.$gxy2omsext($reference.file.ext)'
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67 #end if
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68 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
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69 | tee '$stdout'
0
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70 #end if
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71
4
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72 ## Postprocessing
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73 #if "trafo_out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
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74 ${' '.join(["&& mv -n 'trafo_out/%(bn)s/%(id)s.%(gext)s' 'trafo_out/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("trafoxml")} for i, f in enumerate($in_cond.in) if f])}
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75 #end if
4
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76 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
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77 && mv '@EXECUTABLE@.ctd' '$ctd_out'
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78 #end if]]></command>
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79 <configfiles>
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80 <inputs name="args_json" data_style="paths"/>
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81 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
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82 </configfiles>
0
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83 <inputs>
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84 <conditional name="in_cond">
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85 <param name="in_select" type="select" label="Run tool in batch mode for -in">
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86 <option value="no">No: process all datasets jointly</option>
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87 <option value="yes">Yes: process each dataset in an independent job</option>
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88 </param>
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89 <when value="no">
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90 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" multiple="true" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
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91 </when>
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92 <when value="yes">
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93 <param argument="-in" type="data" format="consensusxml,featurexml,idxml,sqlite" label="Input files to align (all must have the same file type)" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
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94 </when>
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95 </conditional>
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96 <param argument="-design" type="data" format="tabular" optional="true" label="Input file containing the experimental design" help=" select tabular data sets(s)"/>
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97 <param argument="-store_original_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the original retention times (before transformation) as meta data in the output?" help=""/>
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98 <section name="reference" title="Options to define a reference file (use either 'file' or 'index', not both)" help="" expanded="false">
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99 <param name="file" argument="-reference:file" type="data" format="consensusxml,featurexml,idxml,sqlite" optional="true" label="File to use as reference" help=" select consensusxml,featurexml,idxml,sqlite data sets(s)"/>
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100 <param name="index" argument="-reference:index" type="integer" min="0" value="0" label="Use one of the input files as reference ('1' for the first file, etc.)" help="If '0', no explicit reference is set - the algorithm will select a reference"/>
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101 </section>
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102 <section name="algorithm" title="Algorithm parameters section" help="" expanded="false">
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103 <param name="score_type" argument="-algorithm:score_type" type="text" optional="true" value="" label="Name of the score type to use for ranking and filtering (.oms input only)" help="If left empty, a score type is picked automatically">
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104 <expand macro="list_string_san" name="score_type"/>
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105 </param>
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106 <param name="score_cutoff" argument="-algorithm:score_cutoff" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use only IDs above a score cut-off (parameter 'min_score') for alignment?" help=""/>
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107 <param name="min_score" argument="-algorithm:min_score" type="float" value="0.05" label="If 'score_cutoff' is 'true': Minimum score for an ID to be considered" help="Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
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108 <param name="min_run_occur" argument="-algorithm:min_run_occur" type="integer" min="2" value="2" label="Minimum number of runs (incl" help="reference, if any) in which a peptide must occur to be used for the alignment.. Unless you have very few runs or identifications, increase this value to focus on more informative peptides"/>
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109 <param name="max_rt_shift" argument="-algorithm:max_rt_shift" type="float" min="0.0" value="0.5" label="Maximum realistic RT difference for a peptide (median per run vs" help="reference). Peptides with higher shifts (outliers) are not used to compute the alignment.. If 0, no limit (disable filter); if &gt; 1, the final value in seconds; if &lt;= 1, taken as a fraction of the range of the reference RT scale"/>
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110 <param name="use_unassigned_peptides" argument="-algorithm:use_unassigned_peptides" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Should unassigned peptide identifications be used when computing an alignment of feature or consensus maps" help="If 'false', only peptide IDs assigned to features will be used"/>
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111 <param name="use_feature_rt" argument="-algorithm:use_feature_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="When aligning feature or consensus maps, don't use the retention time of a peptide identification directly; instead, use the retention time of the centroid of the feature (apex of the elution profile) that the peptide was matched to" help="If different identifications are matched to one feature, only the peptide closest to the centroid in RT is used.. Precludes 'use_unassigned_peptides'"/>
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112 <param name="use_adducts" argument="-algorithm:use_adducts" type="boolean" truevalue="true" falsevalue="false" checked="true" label="If IDs contain adducts, treat differently adducted variants of the same molecule as different" help=""/>
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113 </section>
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114 <section name="model" title="Options to control the modeling of retention time transformations from data" help="" expanded="false">
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115 <param name="type" argument="-model:type" type="select" label="Type of model" help="">
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116 <option value="linear">linear</option>
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117 <option value="b_spline" selected="true">b_spline</option>
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118 <option value="lowess">lowess</option>
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119 <option value="interpolated">interpolated</option>
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120 <expand macro="list_string_san" name="type"/>
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121 </param>
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122 <section name="linear" title="Parameters for 'linear' model" help="" expanded="false">
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123 <param name="symmetric_regression" argument="-model:linear:symmetric_regression" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Perform linear regression on 'y - x' vs" help="'y + x', instead of on 'y' vs. 'x'"/>
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124 <param name="x_weight" argument="-model:linear:x_weight" type="select" label="Weight x values" help="">
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125 <option value="1/x">1/x</option>
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126 <option value="1/x2">1/x2</option>
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127 <option value="ln(x)">ln(x)</option>
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128 <option value="x" selected="true">x</option>
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129 <expand macro="list_string_san" name="x_weight"/>
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130 </param>
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131 <param name="y_weight" argument="-model:linear:y_weight" type="select" label="Weight y values" help="">
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132 <option value="1/y">1/y</option>
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133 <option value="1/y2">1/y2</option>
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134 <option value="ln(y)">ln(y)</option>
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135 <option value="y" selected="true">y</option>
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136 <expand macro="list_string_san" name="y_weight"/>
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137 </param>
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138 <param name="x_datum_min" argument="-model:linear:x_datum_min" type="float" value="1e-15" label="Minimum x value" help=""/>
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139 <param name="x_datum_max" argument="-model:linear:x_datum_max" type="float" value="1000000000000000.0" label="Maximum x value" help=""/>
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140 <param name="y_datum_min" argument="-model:linear:y_datum_min" type="float" value="1e-15" label="Minimum y value" help=""/>
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141 <param name="y_datum_max" argument="-model:linear:y_datum_max" type="float" value="1000000000000000.0" label="Maximum y value" help=""/>
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142 </section>
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143 <section name="b_spline" title="Parameters for 'b_spline' model" help="" expanded="false">
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144 <param name="wavelength" argument="-model:b_spline:wavelength" type="float" min="0.0" value="0.0" label="Determines the amount of smoothing by setting the number of nodes for the B-spline" help="The number is chosen so that the spline approximates a low-pass filter with this cutoff wavelength. The wavelength is given in the same units as the data; a higher value means more smoothing. '0' sets the number of nodes to twice the number of input points"/>
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145 <param name="num_nodes" argument="-model:b_spline:num_nodes" type="integer" min="0" value="5" label="Number of nodes for B-spline fitting" help="Overrides 'wavelength' if set (to two or greater). A lower value means more smoothing"/>
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146 <param name="extrapolate" argument="-model:b_spline:extrapolate" type="select" label="Method to use for extrapolation beyond the original data range" help="'linear': Linear extrapolation using the slope of the B-spline at the corresponding endpoint. 'b_spline': Use the B-spline (as for interpolation). 'constant': Use the constant value of the B-spline at the corresponding endpoint. 'global_linear': Use a linear fit through the data (which will most probably introduce discontinuities at the ends of the data range)">
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147 <option value="linear" selected="true">linear</option>
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148 <option value="b_spline">b_spline</option>
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149 <option value="constant">constant</option>
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150 <option value="global_linear">global_linear</option>
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151 <expand macro="list_string_san" name="extrapolate"/>
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152 </param>
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153 <param name="boundary_condition" argument="-model:b_spline:boundary_condition" type="integer" min="0" max="2" value="2" label="Boundary condition at B-spline endpoints: 0 (value zero), 1 (first derivative zero) or 2 (second derivative zero)" help=""/>
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154 </section>
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155 <section name="lowess" title="Parameters for 'lowess' model" help="" expanded="false">
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156 <param name="span" argument="-model:lowess:span" type="float" min="0.0" max="1.0" value="0.666666666666667" label="Fraction of datapoints (f) to use for each local regression (determines the amount of smoothing)" help="Choosing this parameter in the range .2 to .8 usually results in a good fit"/>
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157 <param name="num_iterations" argument="-model:lowess:num_iterations" type="integer" min="0" value="3" label="Number of robustifying iterations for lowess fitting" help=""/>
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158 <param name="delta" argument="-model:lowess:delta" type="float" value="-1.0" label="Nonnegative parameter which may be used to save computations (recommended value is 0.01 of the range of the input" help="e.g. for data ranging from 1000 seconds to 2000 seconds, it could be set to 10). Setting a negative value will automatically do this"/>
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159 <param name="interpolation_type" argument="-model:lowess:interpolation_type" type="select" label="Method to use for interpolation between datapoints computed by lowess" help="'linear': Linear interpolation. 'cspline': Use the cubic spline for interpolation. 'akima': Use an akima spline for interpolation">
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160 <option value="linear">linear</option>
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161 <option value="cspline" selected="true">cspline</option>
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162 <option value="akima">akima</option>
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163 <expand macro="list_string_san" name="interpolation_type"/>
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164 </param>
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165 <param name="extrapolation_type" argument="-model:lowess:extrapolation_type" type="select" label="Method to use for extrapolation outside the data range" help="'two-point-linear': Uses a line through the first and last point to extrapolate. 'four-point-linear': Uses a line through the first and second point to extrapolate in front and and a line through the last and second-to-last point in the end. 'global-linear': Uses a linear regression to fit a line through all data points and use it for interpolation">
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166 <option value="two-point-linear">two-point-linear</option>
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167 <option value="four-point-linear" selected="true">four-point-linear</option>
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168 <option value="global-linear">global-linear</option>
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169 <expand macro="list_string_san" name="extrapolation_type"/>
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170 </param>
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171 </section>
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172 <section name="interpolated" title="Parameters for 'interpolated' model" help="" expanded="false">
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173 <param name="interpolation_type" argument="-model:interpolated:interpolation_type" type="select" label="Type of interpolation to apply" help="">
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174 <option value="linear">linear</option>
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175 <option value="cspline" selected="true">cspline</option>
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176 <option value="akima">akima</option>
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177 <expand macro="list_string_san" name="interpolation_type"/>
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178 </param>
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179 <param name="extrapolation_type" argument="-model:interpolated:extrapolation_type" type="select" label="Type of extrapolation to apply: two-point-linear: use the first and last data point to build a single linear model, four-point-linear: build two linear models on both ends using the first two / last two points, global-linear: use all points to build a single linear model" help="Note that global-linear may not be continuous at the border">
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180 <option value="two-point-linear" selected="true">two-point-linear</option>
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181 <option value="four-point-linear">four-point-linear</option>
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182 <option value="global-linear">global-linear</option>
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183 <expand macro="list_string_san" name="extrapolation_type"/>
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184 </param>
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185 </section>
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186 </section>
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187 <expand macro="adv_opts_macro">
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188 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
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189 <param argument="-test" type="hidden" value="False" label="Enables the test mode (needed for internal use only)" help="" optional="true">
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190 <expand macro="list_string_san" name="test"/>
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191 </param>
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192 </expand>
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193 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
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194 <option value="out_FLAG">out (Output files (same file type as 'in'))</option>
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195 <option value="trafo_out_FLAG">trafo_out (Transformation output files)</option>
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196 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
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197 </param>
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198 </inputs>
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199 <outputs>
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200 <collection type="list" name="out" label="${tool.name} on ${on_string}: out">
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201 <discover_datasets directory="out" recurse="true" pattern="__name_and_ext__"/>
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202 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
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203 </collection>
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204 <collection type="list" name="trafo_out" label="${tool.name} on ${on_string}: trafo_out">
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205 <discover_datasets directory="trafo_out" recurse="true" format="trafoxml" pattern="__name__"/>
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206 <filter>OPTIONAL_OUTPUTS is not None and "trafo_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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207 </collection>
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208 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
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209 <filter>OPTIONAL_OUTPUTS is None</filter>
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210 </data>
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211 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
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212 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
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213 </data>
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214 </outputs>
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215 <tests>
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216 <!-- TOPP_MapAlignerIdentification_1 -->
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217 <test expect_num_outputs="2">
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218 <section name="adv_opts">
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219 <param name="force" value="false"/>
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220 <param name="test" value="true"/>
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221 </section>
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222 <conditional name="in_cond">
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223 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
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224 </conditional>
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225 <output_collection name="out" count="2"/>
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226 <param name="store_original_rt" value="false"/>
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227 <section name="reference">
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228 <param name="index" value="0"/>
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229 </section>
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230 <section name="algorithm">
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231 <param name="score_type" value=""/>
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232 <param name="score_cutoff" value="false"/>
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233 <param name="min_score" value="0.05"/>
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234 <param name="min_run_occur" value="2"/>
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235 <param name="max_rt_shift" value="0.0"/>
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236 <param name="use_unassigned_peptides" value="true"/>
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237 <param name="use_feature_rt" value="false"/>
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238 <param name="use_adducts" value="true"/>
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239 </section>
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240 <section name="model">
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241 <param name="type" value="b_spline"/>
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242 <section name="linear">
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243 <param name="symmetric_regression" value="false"/>
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244 <param name="x_weight" value="x"/>
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245 <param name="y_weight" value="y"/>
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246 <param name="x_datum_min" value="1e-15"/>
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247 <param name="x_datum_max" value="1000000000000000.0"/>
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248 <param name="y_datum_min" value="1e-15"/>
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249 <param name="y_datum_max" value="1000000000000000.0"/>
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250 </section>
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251 <section name="b_spline">
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252 <param name="wavelength" value="0.0"/>
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253 <param name="num_nodes" value="5"/>
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254 <param name="extrapolate" value="linear"/>
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255 <param name="boundary_condition" value="2"/>
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256 </section>
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257 <section name="lowess">
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258 <param name="span" value="0.666666666666667"/>
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259 <param name="num_iterations" value="3"/>
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260 <param name="delta" value="-1.0"/>
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261 <param name="interpolation_type" value="cspline"/>
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262 <param name="extrapolation_type" value="four-point-linear"/>
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263 </section>
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264 <section name="interpolated">
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265 <param name="interpolation_type" value="cspline"/>
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266 <param name="extrapolation_type" value="two-point-linear"/>
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267 </section>
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268 </section>
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269 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_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 <!-- TOPP_MapAlignerIdentification_2 -->
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280 <test expect_num_outputs="2">
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281 <section name="adv_opts">
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282 <param name="force" value="false"/>
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283 <param name="test" value="true"/>
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284 </section>
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285 <conditional name="in_cond">
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286 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
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287 </conditional>
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288 <output_collection name="out" count="1"/>
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289 <param name="store_original_rt" value="false"/>
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290 <section name="reference">
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291 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
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292 <param name="index" value="0"/>
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293 </section>
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294 <section name="algorithm">
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295 <param name="score_type" value=""/>
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296 <param name="score_cutoff" value="false"/>
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297 <param name="min_score" value="0.05"/>
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298 <param name="min_run_occur" value="2"/>
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299 <param name="max_rt_shift" value="0.0"/>
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300 <param name="use_unassigned_peptides" value="true"/>
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301 <param name="use_feature_rt" value="false"/>
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302 <param name="use_adducts" value="true"/>
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303 </section>
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304 <section name="model">
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305 <param name="type" value="b_spline"/>
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306 <section name="linear">
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307 <param name="symmetric_regression" value="false"/>
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308 <param name="x_weight" value="x"/>
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309 <param name="y_weight" value="y"/>
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310 <param name="x_datum_min" value="1e-15"/>
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311 <param name="x_datum_max" value="1000000000000000.0"/>
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312 <param name="y_datum_min" value="1e-15"/>
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313 <param name="y_datum_max" value="1000000000000000.0"/>
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314 </section>
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315 <section name="b_spline">
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316 <param name="wavelength" value="0.0"/>
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317 <param name="num_nodes" value="5"/>
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318 <param name="extrapolate" value="linear"/>
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319 <param name="boundary_condition" value="2"/>
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320 </section>
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321 <section name="lowess">
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322 <param name="span" value="0.666666666666667"/>
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323 <param name="num_iterations" value="3"/>
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324 <param name="delta" value="-1.0"/>
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325 <param name="interpolation_type" value="cspline"/>
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326 <param name="extrapolation_type" value="four-point-linear"/>
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327 </section>
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328 <section name="interpolated">
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329 <param name="interpolation_type" value="cspline"/>
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330 <param name="extrapolation_type" value="two-point-linear"/>
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331 </section>
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332 </section>
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333 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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334 <output name="ctd_out" ftype="xml">
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335 <assert_contents>
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336 <is_valid_xml/>
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337 </assert_contents>
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338 </output>
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339 <assert_stdout>
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340 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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341 </assert_stdout>
8
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342 </test>
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343 <!-- TOPP_MapAlignerIdentification_3 -->
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344 <test expect_num_outputs="2">
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345 <section name="adv_opts">
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346 <param name="force" value="false"/>
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347 <param name="test" value="true"/>
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348 </section>
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349 <conditional name="in_cond">
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350 <param name="in" value="MapAlignerIdentification_1_input2.featureXML,MapAlignerIdentification_1_input1.featureXML"/>
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351 </conditional>
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352 <output_collection name="out" count="2"/>
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353 <param name="store_original_rt" value="false"/>
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354 <section name="reference">
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355 <param name="index" value="1"/>
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356 </section>
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357 <section name="algorithm">
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358 <param name="score_type" value=""/>
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359 <param name="score_cutoff" value="false"/>
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360 <param name="min_score" value="0.05"/>
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361 <param name="min_run_occur" value="2"/>
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362 <param name="max_rt_shift" value="0.0"/>
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363 <param name="use_unassigned_peptides" value="true"/>
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364 <param name="use_feature_rt" value="false"/>
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365 <param name="use_adducts" value="true"/>
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366 </section>
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367 <section name="model">
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368 <param name="type" value="b_spline"/>
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369 <section name="linear">
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370 <param name="symmetric_regression" value="false"/>
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371 <param name="x_weight" value="x"/>
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372 <param name="y_weight" value="y"/>
8
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373 <param name="x_datum_min" value="1e-15"/>
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374 <param name="x_datum_max" value="1000000000000000.0"/>
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375 <param name="y_datum_min" value="1e-15"/>
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376 <param name="y_datum_max" value="1000000000000000.0"/>
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377 </section>
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378 <section name="b_spline">
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379 <param name="wavelength" value="0.0"/>
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380 <param name="num_nodes" value="5"/>
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381 <param name="extrapolate" value="linear"/>
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382 <param name="boundary_condition" value="2"/>
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383 </section>
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384 <section name="lowess">
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385 <param name="span" value="0.666666666666667"/>
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386 <param name="num_iterations" value="3"/>
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387 <param name="delta" value="-1.0"/>
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diff changeset
388 <param name="interpolation_type" value="cspline"/>
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389 <param name="extrapolation_type" value="four-point-linear"/>
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390 </section>
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391 <section name="interpolated">
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392 <param name="interpolation_type" value="cspline"/>
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393 <param name="extrapolation_type" value="two-point-linear"/>
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394 </section>
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395 </section>
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396 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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397 <output name="ctd_out" ftype="xml">
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398 <assert_contents>
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399 <is_valid_xml/>
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400 </assert_contents>
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401 </output>
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402 <assert_stdout>
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403 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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404 </assert_stdout>
8
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405 </test>
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406 <!-- TOPP_MapAlignerIdentification_4 -->
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407 <test expect_num_outputs="2">
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408 <section name="adv_opts">
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409 <param name="force" value="false"/>
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410 <param name="test" value="true"/>
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411 </section>
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412 <conditional name="in_cond">
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413 <param name="in" value="MapAlignerIdentification_1_input1.featureXML,MapAlignerIdentification_1_input2.featureXML"/>
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414 </conditional>
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415 <output_collection name="out" count="2"/>
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416 <param name="store_original_rt" value="false"/>
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417 <section name="reference">
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418 <param name="index" value="2"/>
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419 </section>
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420 <section name="algorithm">
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421 <param name="score_type" value=""/>
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422 <param name="score_cutoff" value="false"/>
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423 <param name="min_score" value="0.05"/>
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424 <param name="min_run_occur" value="2"/>
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425 <param name="max_rt_shift" value="0.0"/>
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426 <param name="use_unassigned_peptides" value="true"/>
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427 <param name="use_feature_rt" value="false"/>
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428 <param name="use_adducts" value="true"/>
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429 </section>
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430 <section name="model">
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431 <param name="type" value="b_spline"/>
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432 <section name="linear">
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433 <param name="symmetric_regression" value="false"/>
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434 <param name="x_weight" value="x"/>
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435 <param name="y_weight" value="y"/>
8
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436 <param name="x_datum_min" value="1e-15"/>
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437 <param name="x_datum_max" value="1000000000000000.0"/>
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438 <param name="y_datum_min" value="1e-15"/>
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439 <param name="y_datum_max" value="1000000000000000.0"/>
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440 </section>
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441 <section name="b_spline">
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442 <param name="wavelength" value="0.0"/>
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443 <param name="num_nodes" value="5"/>
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444 <param name="extrapolate" value="linear"/>
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445 <param name="boundary_condition" value="2"/>
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446 </section>
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447 <section name="lowess">
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448 <param name="span" value="0.666666666666667"/>
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449 <param name="num_iterations" value="3"/>
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450 <param name="delta" value="-1.0"/>
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451 <param name="interpolation_type" value="cspline"/>
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452 <param name="extrapolation_type" value="four-point-linear"/>
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453 </section>
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454 <section name="interpolated">
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455 <param name="interpolation_type" value="cspline"/>
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456 <param name="extrapolation_type" value="two-point-linear"/>
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457 </section>
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458 </section>
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459 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
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460 <output name="ctd_out" ftype="xml">
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461 <assert_contents>
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462 <is_valid_xml/>
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463 </assert_contents>
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464 </output>
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465 <assert_stdout>
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466 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
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467 </assert_stdout>
8
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468 </test>
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469 <!-- TOPP_MapAlignerIdentification_5 -->
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470 <test expect_num_outputs="2">
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471 <section name="adv_opts">
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472 <param name="force" value="false"/>
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473 <param name="test" value="true"/>
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474 </section>
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diff changeset
475 <conditional name="in_cond">
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476 <param name="in" value="MapAlignerIdentification_5_input1.consensusXML,MapAlignerIdentification_5_input2.consensusXML"/>
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477 </conditional>
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diff changeset
478 <output_collection name="out" count="2"/>
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479 <param name="store_original_rt" value="false"/>
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diff changeset
480 <section name="reference">
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diff changeset
481 <param name="index" value="0"/>
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galaxyp
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diff changeset
482 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
483 <section name="algorithm">
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galaxyp
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diff changeset
484 <param name="score_type" value=""/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
485 <param name="score_cutoff" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
486 <param name="min_score" value="0.05"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
487 <param name="min_run_occur" value="2"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
488 <param name="max_rt_shift" value="0.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
489 <param name="use_unassigned_peptides" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
490 <param name="use_feature_rt" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
491 <param name="use_adducts" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
492 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
493 <section name="model">
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galaxyp
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diff changeset
494 <param name="type" value="b_spline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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495 <section name="linear">
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galaxyp
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496 <param name="symmetric_regression" value="false"/>
9
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galaxyp
parents: 8
diff changeset
497 <param name="x_weight" value="x"/>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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498 <param name="y_weight" value="y"/>
8
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galaxyp
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diff changeset
499 <param name="x_datum_min" value="1e-15"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
500 <param name="x_datum_max" value="1000000000000000.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
501 <param name="y_datum_min" value="1e-15"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
502 <param name="y_datum_max" value="1000000000000000.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
503 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
504 <section name="b_spline">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
505 <param name="wavelength" value="0.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
506 <param name="num_nodes" value="5"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
507 <param name="extrapolate" value="linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
508 <param name="boundary_condition" value="2"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
509 </section>
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galaxyp
parents: 6
diff changeset
510 <section name="lowess">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
511 <param name="span" value="0.666666666666667"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
512 <param name="num_iterations" value="3"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
513 <param name="delta" value="-1.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
514 <param name="interpolation_type" value="cspline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
515 <param name="extrapolation_type" value="four-point-linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
516 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
517 <section name="interpolated">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
518 <param name="interpolation_type" value="cspline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
519 <param name="extrapolation_type" value="two-point-linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
520 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
521 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
522 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
523 <output name="ctd_out" ftype="xml">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
524 <assert_contents>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
525 <is_valid_xml/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
526 </assert_contents>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
527 </output>
9
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 8
diff changeset
528 <assert_stdout>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
529 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 8
diff changeset
530 </assert_stdout>
8
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
531 </test>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
532 <!-- TOPP_MapAlignerIdentification_6 -->
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
533 <test expect_num_outputs="2">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
534 <section name="adv_opts">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
535 <param name="force" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
536 <param name="test" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
537 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
538 <conditional name="in_cond">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
539 <param name="in" value="MapAlignerIdentification_1_input1.featureXML"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
540 </conditional>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
541 <output_collection name="trafo_out" count="1"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
542 <param name="store_original_rt" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
543 <section name="reference">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
544 <param name="file" value="MapAlignerIdentification_1_input2.featureXML"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
545 <param name="index" value="0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
546 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
547 <section name="algorithm">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
548 <param name="score_type" value=""/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
549 <param name="score_cutoff" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
550 <param name="min_score" value="0.05"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
551 <param name="min_run_occur" value="2"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
552 <param name="max_rt_shift" value="0.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
553 <param name="use_unassigned_peptides" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
554 <param name="use_feature_rt" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
555 <param name="use_adducts" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
556 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
557 <section name="model">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
558 <param name="type" value="b_spline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
559 <section name="linear">
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galaxyp
parents: 6
diff changeset
560 <param name="symmetric_regression" value="false"/>
9
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
galaxyp
parents: 8
diff changeset
561 <param name="x_weight" value="x"/>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 8
diff changeset
562 <param name="y_weight" value="y"/>
8
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
563 <param name="x_datum_min" value="1e-15"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
564 <param name="x_datum_max" value="1000000000000000.0"/>
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galaxyp
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diff changeset
565 <param name="y_datum_min" value="1e-15"/>
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parents: 6
diff changeset
566 <param name="y_datum_max" value="1000000000000000.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
567 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
568 <section name="b_spline">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
569 <param name="wavelength" value="0.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
570 <param name="num_nodes" value="5"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
571 <param name="extrapolate" value="linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
572 <param name="boundary_condition" value="2"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
573 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
574 <section name="lowess">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
575 <param name="span" value="0.666666666666667"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
576 <param name="num_iterations" value="3"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
577 <param name="delta" value="-1.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
578 <param name="interpolation_type" value="cspline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
579 <param name="extrapolation_type" value="four-point-linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
580 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
581 <section name="interpolated">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
582 <param name="interpolation_type" value="cspline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
583 <param name="extrapolation_type" value="two-point-linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
584 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
585 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
586 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,trafo_out_FLAG"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
587 <output name="ctd_out" ftype="xml">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
588 <assert_contents>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
589 <is_valid_xml/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
590 </assert_contents>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
591 </output>
9
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 8
diff changeset
592 <assert_stdout>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 8
diff changeset
593 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 8
diff changeset
594 </assert_stdout>
8
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
595 </test>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
596 <!-- TOPP_MapAlignerIdentification_7 -->
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
597 <test expect_num_outputs="3">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
598 <section name="adv_opts">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
599 <param name="force" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
600 <param name="test" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
601 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
602 <conditional name="in_cond">
9
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 8
diff changeset
603 <param name="in" value="MapAlignerIdentification_7_input1_0.idXML"/>
8
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
604 </conditional>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
605 <output_collection name="out" count="1"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
606 <output_collection name="trafo_out" count="1"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
607 <param name="store_original_rt" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
608 <section name="reference">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
609 <param name="file" value="MapAlignerIdentification_7_input2.idXML"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
610 <param name="index" value="0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
611 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
612 <section name="algorithm">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
613 <param name="score_type" value=""/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
614 <param name="score_cutoff" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
615 <param name="min_score" value="0.05"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
616 <param name="min_run_occur" value="2"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
617 <param name="max_rt_shift" value="0.5"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
618 <param name="use_unassigned_peptides" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
619 <param name="use_feature_rt" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
620 <param name="use_adducts" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
621 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
622 <section name="model">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
623 <param name="type" value="b_spline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
624 <section name="linear">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
625 <param name="symmetric_regression" value="false"/>
9
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parents: 8
diff changeset
626 <param name="x_weight" value="x"/>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
627 <param name="y_weight" value="y"/>
8
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diff changeset
628 <param name="x_datum_min" value="1e-15"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
629 <param name="x_datum_max" value="1000000000000000.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
630 <param name="y_datum_min" value="1e-15"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
631 <param name="y_datum_max" value="1000000000000000.0"/>
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diff changeset
632 </section>
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diff changeset
633 <section name="b_spline">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
634 <param name="wavelength" value="0.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
635 <param name="num_nodes" value="5"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
636 <param name="extrapolate" value="linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
637 <param name="boundary_condition" value="2"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
638 </section>
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diff changeset
639 <section name="lowess">
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parents: 6
diff changeset
640 <param name="span" value="0.666666666666667"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
641 <param name="num_iterations" value="3"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 6
diff changeset
642 <param name="delta" value="-1.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
643 <param name="interpolation_type" value="cspline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
644 <param name="extrapolation_type" value="four-point-linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
645 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
646 <section name="interpolated">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
647 <param name="interpolation_type" value="cspline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
648 <param name="extrapolation_type" value="two-point-linear"/>
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diff changeset
649 </section>
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diff changeset
650 </section>
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diff changeset
651 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
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diff changeset
652 <output name="ctd_out" ftype="xml">
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653 <assert_contents>
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diff changeset
654 <is_valid_xml/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
655 </assert_contents>
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diff changeset
656 </output>
9
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657 <assert_stdout>
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parents: 8
diff changeset
658 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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659 </assert_stdout>
8
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diff changeset
660 </test>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
661 <!-- TOPP_MapAlignerIdentification_8 -->
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parents: 6
diff changeset
662 <test expect_num_outputs="3">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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663 <section name="adv_opts">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 6
diff changeset
664 <param name="force" value="false"/>
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665 <param name="test" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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666 </section>
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diff changeset
667 <conditional name="in_cond">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
668 <param name="in" value="MapAlignerIdentification_8_input1.oms"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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669 </conditional>
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670 <output_collection name="out" count="1"/>
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galaxyp
parents: 6
diff changeset
671 <output_collection name="trafo_out" count="1"/>
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diff changeset
672 <param name="store_original_rt" value="true"/>
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673 <section name="reference">
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674 <param name="file" value="MapAlignerIdentification_8_input2.oms"/>
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diff changeset
675 <param name="index" value="0"/>
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diff changeset
676 </section>
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diff changeset
677 <section name="algorithm">
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678 <param name="score_type" value=""/>
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parents: 6
diff changeset
679 <param name="score_cutoff" value="false"/>
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diff changeset
680 <param name="min_score" value="0.05"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 6
diff changeset
681 <param name="min_run_occur" value="2"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
682 <param name="max_rt_shift" value="0.5"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
683 <param name="use_unassigned_peptides" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
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diff changeset
684 <param name="use_feature_rt" value="false"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
galaxyp
parents: 6
diff changeset
685 <param name="use_adducts" value="true"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
686 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
687 <section name="model">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
688 <param name="type" value="b_spline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
689 <section name="linear">
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690 <param name="symmetric_regression" value="false"/>
9
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diff changeset
691 <param name="x_weight" value="x"/>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
692 <param name="y_weight" value="y"/>
8
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diff changeset
693 <param name="x_datum_min" value="1e-15"/>
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diff changeset
694 <param name="x_datum_max" value="1000000000000000.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
695 <param name="y_datum_min" value="1e-15"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
696 <param name="y_datum_max" value="1000000000000000.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
697 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
698 <section name="b_spline">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
699 <param name="wavelength" value="0.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
700 <param name="num_nodes" value="5"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 6
diff changeset
701 <param name="extrapolate" value="linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
702 <param name="boundary_condition" value="2"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
703 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
704 <section name="lowess">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
705 <param name="span" value="0.666666666666667"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
706 <param name="num_iterations" value="3"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
707 <param name="delta" value="-1.0"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
708 <param name="interpolation_type" value="cspline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
709 <param name="extrapolation_type" value="four-point-linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
710 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 6
diff changeset
711 <section name="interpolated">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 6
diff changeset
712 <param name="interpolation_type" value="cspline"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
713 <param name="extrapolation_type" value="two-point-linear"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
714 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
715 </section>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
716 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,trafo_out_FLAG"/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 6
diff changeset
717 <output name="ctd_out" ftype="xml">
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
718 <assert_contents>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
719 <is_valid_xml/>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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parents: 6
diff changeset
720 </assert_contents>
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
721 </output>
9
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parents: 8
diff changeset
722 <assert_stdout>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
723 <has_text_matching expression="@EXECUTABLE@ took .* \(wall\), .* \(CPU\), .* \(system\), .* \(user\)(; Peak Memory Usage: 32 MB)?."/>
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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parents: 8
diff changeset
724 </assert_stdout>
8
8434f070e939 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
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diff changeset
725 </test>
4
bf50f9eb1dcb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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diff changeset
726 </tests>
bf50f9eb1dcb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
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diff changeset
727 <help><![CDATA[Corrects retention time distortions between maps based on common peptide identifications.
0
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parents:
diff changeset
728
83983906eb4b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
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parents:
diff changeset
729
9
77b66c1c5415 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
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diff changeset
730 For more information, visit https://openms.de/doxygen/release/3.1.0/html/TOPP_MapAlignerIdentification.html]]></help>
4
bf50f9eb1dcb "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
galaxyp
parents: 2
diff changeset
731 <expand macro="references"/>
0
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732 </tool>