Mercurial > repos > galaxyp > openms_qualitycontrol

comparison QualityControl.xml @ 2:2f08fa7ab72c draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 55a2aeba8bfd8a6910630721de9857dcdfe05d3c"
author galaxyp
date Tue, 13 Oct 2020 20:32:44 +0000
parents e2f683fcd6bd
children bd210b86fb5d
comparison
equal deleted inserted replaced
1:6d9cd32c941b 2:2f08fa7ab72c
24 #end if 24 #end if
25 #if $in_postFDR: 25 #if $in_postFDR:
26 mkdir in_postFDR && 26 mkdir in_postFDR &&
27 ${ ' '.join(["ln -s '%s' 'in_postFDR/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _]) } 27 ${ ' '.join(["ln -s '%s' 'in_postFDR/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _]) }
28 #end if 28 #end if
29 mkdir out && 29 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
30 mkdir out &&
31 #end if
30 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 32 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
31 mkdir out_cm && 33 mkdir out_cm &&
32 #end if 34 #end if
33 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 35 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 mkdir out_feat && 36 mkdir out_feat &&
56 #end if 58 #end if
57 #if $in_postFDR: 59 #if $in_postFDR:
58 -in_postFDR 60 -in_postFDR
59 ${' '.join(["'in_postFDR/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])} 61 ${' '.join(["'in_postFDR/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])}
60 #end if 62 #end if
61 -out 63 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
62 'out/output.${gxy2omsext("mztab")}' 64 -out
65 'out/output.${gxy2omsext("mztab")}'
66 #end if
63 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 67 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
64 -out_cm 68 -out_cm
65 'out_cm/output.${gxy2omsext("consensusxml")}' 69 'out_cm/output.${gxy2omsext("consensusxml")}'
66 #end if 70 #end if
67 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 71 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
79 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0 83 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
80 | tee '$stdout' 84 | tee '$stdout'
81 #end if 85 #end if
82 86
83 ## Postprocessing 87 ## Postprocessing
84 && mv 'out/output.${gxy2omsext("mztab")}' '$out' 88 #if "out_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
89 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
90 #end if
85 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 91 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
86 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm' 92 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
87 #end if 93 #end if
88 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 94 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
89 ${' '.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 _])} 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 _])}
109 <expand macro="list_string_san"/> 115 <expand macro="list_string_san"/>
110 </param> 116 </param>
111 <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=""/> 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=""/>
112 </section> 118 </section>
113 <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false"> 119 <section name="MS2_id_rate" title="MS2 ID Rate settings" help="" expanded="false">
114 <param name="force_no_fdr" argument="-MS2_id_rate:force_no_fdr" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Forces the metric to run if FDR is missing (accepts all pep_ids as target hits)" help=""/> 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=""/>
115 </section> 121 </section>
116 <expand macro="adv_opts_macro"> 122 <expand macro="adv_opts_macro">
117 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/> 123 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
118 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 124 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
119 <expand macro="list_string_san"/> 125 <expand macro="list_string_san"/>
120 </param> 126 </param>
121 </expand> 127 </expand>
122 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true"> 128 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
123 <option value="out_cm_FLAG">out_cm (Forces the metric to run if FDR is missing (accepts all pep_ids as target hits))</option> 129 <option value="out_FLAG">out (Output mzTab with QC information)</option>
124 <option value="out_feat_FLAG">out_feat (Forces the metric to run if FDR is missing (accepts all pep_ids as target hits))</option> 130 <option value="out_cm_FLAG">out_cm (ConsensusXML with QC information (as metavalues))</option>
131 <option value="out_feat_FLAG">out_feat (FeatureXMLs with QC information (as metavalues))</option>
125 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option> 132 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
126 </param> 133 </param>
127 </inputs> 134 </inputs>
128 <outputs> 135 <outputs>
129 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/> 136 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab">
137 <filter>OPTIONAL_OUTPUTS is not None and "out_FLAG" in OPTIONAL_OUTPUTS</filter>
138 </data>
130 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml"> 139 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
131 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter> 140 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
132 </data> 141 </data>
133 <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat"> 142 <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat">
134 <discover_datasets directory="out_feat" format="featurexml" pattern="__name__"/> 143 <discover_datasets directory="out_feat" format="featurexml" pattern="__name__"/>
135 <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter> 144 <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
136 </collection> 145 </collection>
146 <data name="stdout" format="txt" label="${tool.name} on ${on_string}: stdout">
147 <filter>OPTIONAL_OUTPUTS is None</filter>
148 </data>
137 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 149 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
138 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 150 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
139 </data> 151 </data>
140 </outputs> 152 </outputs>
141 <tests> 153 <tests>
143 <expand macro="manutest_QualityControl"/> 155 <expand macro="manutest_QualityControl"/>
144 </tests> 156 </tests>
145 <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. 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.
146 158
147 159
148 For more information, visit http://www.openms.de/documentation/TOPP_QualityControl.html]]></help> 160 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/TOPP_QualityControl.html]]></help>
149 <expand macro="references"/> 161 <expand macro="references"/>
150 </tool> 162 </tool>