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comparison QualityControl.xml @ 4:bd210b86fb5d draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 19:18:12 +0000
parents 2f08fa7ab72c
children ea02cc72f0b9
comparison
equal deleted inserted replaced
3:4d950ff26e35 4:bd210b86fb5d
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTDConverter.-->
3 <!--Proposed Tool Section: [Quality Control]--> 3 <!--Proposed Tool Section: [Quality Control]-->
4 <tool id="QualityControl" name="QualityControl" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="QualityControl" name="QualityControl" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.</description> 5 <description>Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">QualityControl</token> 7 <token name="@EXECUTABLE@">QualityControl</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros> 9 </macros>
12 <expand macro="requirements"/> 10 <expand macro="requirements"/>
13 <expand macro="stdio"/> 11 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@ 12 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@ 13 @EXT_FOO@
16 #import re 14 #import re
17 15
18 ## Preprocessing 16 ## Preprocessing
19 mkdir in_cm && 17 mkdir in_cm &&
20 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' && 18 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
21 #if $in_raw: 19 #if $in_raw_cond.in_raw:
22 mkdir in_raw && 20 mkdir in_raw_cond.in_raw &&
23 ${ ' '.join(["ln -s '%s' 'in_raw/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _]) } 21 #if $in_raw_cond.in_raw_select == "no"
24 #end if 22 mkdir ${' '.join(["'in_raw_cond.in_raw/%s'" % (i) for i, f in enumerate($in_raw_cond.in_raw) if f])} &&
25 #if $in_postFDR: 23 ${' '.join(["ln -s '%s' 'in_raw_cond.in_raw/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
26 mkdir in_postFDR && 24 #else
27 ${ ' '.join(["ln -s '%s' 'in_postFDR/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _]) } 25 ln -s '$in_raw_cond.in_raw' 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)' &&
26 #end if
27 #end if
28 #if $in_postFDR_cond.in_postFDR:
29 mkdir in_postFDR_cond.in_postFDR &&
30 #if $in_postFDR_cond.in_postFDR_select == "no"
31 mkdir ${' '.join(["'in_postFDR_cond.in_postFDR/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} &&
32 ${' '.join(["ln -s '%s' 'in_postFDR_cond.in_postFDR/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
33 #else
34 ln -s '$in_postFDR_cond.in_postFDR' 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)' &&
35 #end if
28 #end if 36 #end if
29 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 37 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
30 mkdir out && 38 mkdir out &&
31 #end if 39 #end if
32 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 40 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
33 mkdir out_cm && 41 mkdir out_cm &&
34 #end if 42 #end if
35 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 43 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
36 mkdir out_feat && 44 mkdir out_feat &&
45 mkdir ${' '.join(["'out_feat/%s'" % (i) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])} &&
37 #end if 46 #end if
38 #if $in_contaminants: 47 #if $in_contaminants:
39 mkdir in_contaminants && 48 mkdir in_contaminants &&
40 ln -s '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' && 49 ln -s '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
41 #end if 50 #end if
42 #if $in_trafo: 51 #if $in_trafo_cond.in_trafo:
43 mkdir in_trafo && 52 mkdir in_trafo_cond.in_trafo &&
44 ${ ' '.join(["ln -s '%s' 'in_trafo/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _]) } 53 #if $in_trafo_cond.in_trafo_select == "no"
54 mkdir ${' '.join(["'in_trafo_cond.in_trafo/%s'" % (i) for i, f in enumerate($in_trafo_cond.in_trafo) if f])} &&
55 ${' '.join(["ln -s '%s' 'in_trafo_cond.in_trafo/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
56 #else
57 ln -s '$in_trafo_cond.in_trafo' 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)' &&
58 #end if
45 #end if 59 #end if
46 60
47 ## Main program call 61 ## Main program call
48 62
49 set -o pipefail && 63 set -o pipefail &&
50 @EXECUTABLE@ -write_ctd ./ && 64 @EXECUTABLE@ -write_ctd ./ &&
51 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 65 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
52 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 66 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
53 -in_cm 67 -in_cm
54 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' 68 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
55 #if $in_raw: 69 #if $in_raw_cond.in_raw:
56 -in_raw 70 -in_raw
57 ${' '.join(["'in_raw/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _])} 71 #if $in_raw_cond.in_raw_select == "no"
58 #end if 72 ${' '.join(["'in_raw_cond.in_raw/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_raw_cond.in_raw) if f])}
59 #if $in_postFDR: 73 #else
74 'in_raw_cond.in_raw/${re.sub("[^\w\-_]", "_", $in_raw_cond.in_raw.element_identifier)}.$gxy2omsext($in_raw_cond.in_raw.ext)'
75 #end if
76 #end if
77 #if $in_postFDR_cond.in_postFDR:
60 -in_postFDR 78 -in_postFDR
61 ${' '.join(["'in_postFDR/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])} 79 #if $in_postFDR_cond.in_postFDR_select == "no"
80 ${' '.join(["'in_postFDR_cond.in_postFDR/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
81 #else
82 'in_postFDR_cond.in_postFDR/${re.sub("[^\w\-_]", "_", $in_postFDR_cond.in_postFDR.element_identifier)}.$gxy2omsext($in_postFDR_cond.in_postFDR.ext)'
83 #end if
62 #end if 84 #end if
63 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 85 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
64 -out 86 -out
65 'out/output.${gxy2omsext("mztab")}' 87 'out/output.${gxy2omsext("mztab")}'
66 #end if 88 #end if
68 -out_cm 90 -out_cm
69 'out_cm/output.${gxy2omsext("consensusxml")}' 91 'out_cm/output.${gxy2omsext("consensusxml")}'
70 #end if 92 #end if
71 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 93 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
72 -out_feat 94 -out_feat
73 ${' '.join(["'out_feat/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in_postFDR if _])} 95 ${' '.join(["'out_feat/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext("featurexml")) for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
74 #end if 96 #end if
75 #if $in_contaminants: 97 #if $in_contaminants:
76 -in_contaminants 98 -in_contaminants
77 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' 99 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)'
78 #end if 100 #end if
79 #if $in_trafo: 101 #if $in_trafo_cond.in_trafo:
80 -in_trafo 102 -in_trafo
81 ${' '.join(["'in_trafo/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _])} 103 #if $in_trafo_cond.in_trafo_select == "no"
104 ${' '.join(["'in_trafo_cond.in_trafo/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($in_trafo_cond.in_trafo) if f])}
105 #else
106 'in_trafo_cond.in_trafo/${re.sub("[^\w\-_]", "_", $in_trafo_cond.in_trafo.element_identifier)}.$gxy2omsext($in_trafo_cond.in_trafo.ext)'
107 #end if
82 #end if 108 #end if
83 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 109 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
84 | tee '$stdout' 110 | tee '$stdout'
85 #end if 111 #end if
86 112
90 #end if 116 #end if
91 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 117 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
92 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm' 118 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
93 #end if 119 #end if
94 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 120 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
95 ${' '.join(["&& mv -n 'in_postFDR/%(id)s.%(gext)s' 'out_feat/%(id)s'"%{"id": re.sub('[^\w\-_]', '_', _.element_identifier), "gext": $gxy2omsext("featurexml")} for _ in $out_feat if _])} 121 ${' '.join(["&& mv -n 'out_feat/%(bn)s/%(id)s.%(gext)s' 'out_feat/%(bn)s/%(id)s'"%{"bn": i, "id": re.sub('[^\w\-_]', '_', f.element_identifier), "gext": $gxy2omsext("featurexml")} for i, f in enumerate($in_postFDR_cond.in_postFDR) if f])}
96 #end if 122 #end if
97 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS 123 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
98 && mv '@EXECUTABLE@.ctd' '$ctd_out' 124 && mv '@EXECUTABLE@.ctd' '$ctd_out'
99 #end if]]></command> 125 #end if]]></command>
100 <configfiles> 126 <configfiles>
101 <inputs name="args_json" data_style="paths"/> 127 <inputs name="args_json" data_style="paths"/>
102 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 128 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
103 </configfiles> 129 </configfiles>
104 <inputs> 130 <inputs>
105 <param name="in_cm" argument="-in_cm" type="data" format="consensusxml" optional="false" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/> 131 <param argument="-in_cm" type="data" format="consensusxml" optional="false" label="ConsensusXML input, generated by FeatureLinke" help=" select consensusxml data sets(s)"/>
106 <param name="in_raw" argument="-in_raw" type="data" format="mzml" multiple="true" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/> 132 <conditional name="in_raw_cond">
107 <param name="in_postFDR" argument="-in_postFDR" type="data" format="featurexml" multiple="true" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/> 133 <param name="in_raw_select" type="select" label="Run tool in batch mode for -in_raw">
108 <param name="in_contaminants" argument="-in_contaminants" type="data" format="fasta" optional="true" label="Proteins considered contaminants" help=" select fasta data sets(s)"/> 134 <option value="no">No: process all datasets jointly</option>
109 <param name="in_trafo" argument="-in_trafo" type="data" format="trafoxml" multiple="true" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/> 135 <option value="yes">Yes: process each dataset in an independent job</option>
136 </param>
137 <when value="no">
138 <param argument="-in_raw" type="data" format="mzml" multiple="true" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
139 </when>
140 <when value="yes">
141 <param argument="-in_raw" type="data" format="mzml" multiple="false" optional="true" label="MzML input (after InternalCalibration, if available)" help=" select mzml data sets(s)"/>
142 </when>
143 </conditional>
144 <conditional name="in_postFDR_cond">
145 <param name="in_postFDR_select" type="select" label="Run tool in batch mode for -in_postFDR">
146 <option value="no">No: process all datasets jointly</option>
147 <option value="yes">Yes: process each dataset in an independent job</option>
148 </param>
149 <when value="no">
150 <param argument="-in_postFDR" type="data" format="featurexml" multiple="true" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
151 </when>
152 <when value="yes">
153 <param argument="-in_postFDR" type="data" format="featurexml" multiple="false" optional="true" label="FeatureXMLs after FDR filtering" help=" select featurexml data sets(s)"/>
154 </when>
155 </conditional>
156 <param argument="-in_contaminants" type="data" format="fasta" optional="true" label="Proteins considered contaminants" help=" select fasta data sets(s)"/>
157 <conditional name="in_trafo_cond">
158 <param name="in_trafo_select" type="select" label="Run tool in batch mode for -in_trafo">
159 <option value="no">No: process all datasets jointly</option>
160 <option value="yes">Yes: process each dataset in an independent job</option>
161 </param>
162 <when value="no">
163 <param argument="-in_trafo" type="data" format="trafoxml" multiple="true" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
164 </when>
165 <when value="yes">
166 <param argument="-in_trafo" type="data" format="trafoxml" multiple="false" optional="true" label="trafoXMLs from MapAligners" help=" select trafoxml data sets(s)"/>
167 </when>
168 </conditional>
169 <param argument="-out_evd" type="text" optional="true" value="" label="If a Path is given, a MQEvidence txt-file will be created in this directory" help="If the directory does not exist, it will be created as well">
170 <expand macro="list_string_san" name="out_evd"/>
171 </param>
110 <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false"> 172 <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false">
111 <param name="unit" argument="-FragmentMassError:unit" display="radio" type="select" optional="false" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML"> 173 <param name="unit" argument="-FragmentMassError:unit" type="select" optional="true" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
112 <option value="auto" selected="true">auto</option> 174 <option value="auto" selected="true">auto</option>
113 <option value="ppm">ppm</option> 175 <option value="ppm">ppm</option>
114 <option value="da">da</option> 176 <option value="da">da</option>
115 <expand macro="list_string_san"/> 177 <expand macro="list_string_san" name="unit"/>
116 </param> 178 </param>
117 <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" optional="true" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/> 179 <param name="tolerance" argument="-FragmentMassError:tolerance" type="float" optional="true" value="20.0" label="m/z search window for matching peaks in two spectra" help=""/>
118 </section> 180 </section>
119 <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false"> 181 <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false">
120 <param name="assume_all_target" argument="-MS2_id_rate:assume_all_target" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits)" help=""/> 182 <param name="assume_all_target" argument="-MS2_id_rate:assume_all_target" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run even if target/decoy annotation is missing (accepts all pep_ids as target hits)" help=""/>
121 </section> 183 </section>
122 <expand macro="adv_opts_macro"> 184 <expand macro="adv_opts_macro">
123 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 185 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
124 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 186 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
125 <expand macro="list_string_san"/> 187 <expand macro="list_string_san" name="test"/>
126 </param> 188 </param>
127 </expand> 189 </expand>
128 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 190 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
129 <option value="out_FLAG">out (Output mzTab with QC information)</option> 191 <option value="out_FLAG">out (Output mzTab with QC information)</option>
130 <option value="out_cm_FLAG">out_cm (ConsensusXML with QC information (as metavalues))</option> 192 <option value="out_cm_FLAG">out_cm (ConsensusXML with QC information (as metavalues))</option>
138 </data> 200 </data>
139 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml"> 201 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
140 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter> 202 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
141 </data> 203 </data>
142 <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat"> 204 <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat">
143 <discover_datasets directory="out_feat" format="featurexml" pattern="__name__"/> 205 <discover_datasets directory="out_feat" recurse="true" format="featurexml" pattern="__name__"/>
144 <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter> 206 <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
145 </collection> 207 </collection>
146 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout"> 208 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
147 <filter>OPTIONAL_OUTPUTS is None</filter> 209 <filter>OPTIONAL_OUTPUTS is None</filter>
148 </data> 210 </data>
149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 211 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 212 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
151 </data> 213 </data>
152 </outputs> 214 </outputs>
153 <tests> 215 <tests><!-- TOPP_QualityControl_1 -->
154 <expand macro="autotest_QualityControl"/> 216 <test expect_num_outputs="3">
155 <expand macro="manutest_QualityControl"/> 217 <section name="adv_opts">
218 <param name="force" value="false"/>
219 <param name="test" value="true"/>
220 </section>
221 <param name="in_cm" value="QualityControl_1_in.consensusXML"/>
222 <conditional name="in_raw_cond">
223 <param name="in_raw" value="QualityControl_1_in1.mzML.gz,QualityControl_1_in2.mzML.gz,QualityControl_1_in3.mzML.gz"/>
224 </conditional>
225 <conditional name="in_postFDR_cond">
226 <param name="in_postFDR" value="QualityControl_1_in1.featureXML,QualityControl_1_in2.featureXML,QualityControl_1_in3.featureXML"/>
227 </conditional>
228 <output name="out" file="QualityControl_1_out.mzTab" compare="sim_size" delta_frac="0.7" ftype="mztab"/>
229 <output name="out_cm" file="QualityControl_1_out.consensusXML" compare="sim_size" delta_frac="0.7" ftype="consensusxml"/>
230 <param name="in_contaminants" value="QualityControl_1.fasta"/>
231 <conditional name="in_trafo_cond">
232 <param name="in_trafo" value="QualityControl_1_in1.trafoXML,QualityControl_1_in2.trafoXML,QualityControl_1_in3.trafoXML"/>
233 </conditional>
234 <param name="out_evd" value=""/>
235 <section name="FragmentMassError">
236 <param name="unit" value="auto"/>
237 <param name="tolerance" value="20.0"/>
238 </section>
239 <section name="MS2_id_rate">
240 <param name="assume_all_target" value="false"/>
241 </section>
242 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_FLAG,out_cm_FLAG"/>
243 <output name="ctd_out" ftype="xml">
244 <assert_contents>
245 <is_valid_xml/>
246 </assert_contents>
247 </output>
248 </test>
156 </tests> 249 </tests>
157 <help><![CDATA[Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get. 250 <help><![CDATA[Computes various QC metrics from many possible input files (only the consensusXML is required). The more optional files you provide, the more metrics you get.
158 251
159 252
160 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_QualityControl.html]]></help> 253 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/TOPP_QualityControl.html]]></help>
161 <expand macro="references"/> 254 <expand macro="references"/>
162 </tool> 255 </tool>