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comparison QualityControl.xml @ 0:e2f683fcd6bd draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 020906fb54bde7fc143c356f41975c378a741315"
author galaxyp
date Wed, 09 Sep 2020 20:02:21 +0000
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children 2f08fa7ab72c
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-1:000000000000 0:e2f683fcd6bd
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.-->
3 <!--Proposed Tool Section: [Quality Control]-->
4 <tool id="QualityControl" name="QualityControl" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
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>
6 <macros>
7 <token name="@EXECUTABLE@">QualityControl</token>
8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
11 </macros>
12 <expand macro="requirements"/>
13 <expand macro="stdio"/>
14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
15 @EXT_FOO@
16 #import re
17
18 ## Preprocessing
19 mkdir in_cm &&
20 ln -s '$in_cm' 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)' &&
21 #if $in_raw:
22 mkdir in_raw &&
23 ${ ' '.join(["ln -s '%s' 'in_raw/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _]) }
24 #end if
25 #if $in_postFDR:
26 mkdir in_postFDR &&
27 ${ ' '.join(["ln -s '%s' 'in_postFDR/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _]) }
28 #end if
29 mkdir out &&
30 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
31 mkdir out_cm &&
32 #end if
33 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
34 mkdir out_feat &&
35 #end if
36 #if $in_contaminants:
37 mkdir in_contaminants &&
38 ln -s '$in_contaminants' 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)' &&
39 #end if
40 #if $in_trafo:
41 mkdir in_trafo &&
42 ${ ' '.join(["ln -s '%s' 'in_trafo/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _]) }
43 #end if
44
45 ## Main program call
46
47 set -o pipefail &&
48 @EXECUTABLE@ -write_ctd ./ &&
49 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
50 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
51 -in_cm
52 'in_cm/${re.sub("[^\w\-_]", "_", $in_cm.element_identifier)}.$gxy2omsext($in_cm.ext)'
53 #if $in_raw:
54 -in_raw
55 ${' '.join(["'in_raw/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_raw if _])}
56 #end if
57 #if $in_postFDR:
58 -in_postFDR
59 ${' '.join(["'in_postFDR/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_postFDR if _])}
60 #end if
61 -out
62 'out/output.${gxy2omsext("mztab")}'
63 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
64 -out_cm
65 'out_cm/output.${gxy2omsext("consensusxml")}'
66 #end if
67 #if "out_feat_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
68 -out_feat
69 ${' '.join(["'out_feat/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext("featurexml")) for _ in $in_postFDR if _])}
70 #end if
71 #if $in_contaminants:
72 -in_contaminants
73 'in_contaminants/${re.sub("[^\w\-_]", "_", $in_contaminants.element_identifier)}.$gxy2omsext($in_contaminants.ext)'
74 #end if
75 #if $in_trafo:
76 -in_trafo
77 ${' '.join(["'in_trafo/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in_trafo if _])}
78 #end if
79 #if len(str($OPTIONAL_OUTPUTS).split(',')) == 0
80 | tee '$stdout'
81 #end if
82
83 ## Postprocessing
84 && mv 'out/output.${gxy2omsext("mztab")}' '$out'
85 #if "out_cm_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
86 && mv 'out_cm/output.${gxy2omsext("consensusxml")}' '$out_cm'
87 #end if
88 #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 _])}
90 #end if
91 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
92 && mv '@EXECUTABLE@.ctd' '$ctd_out'
93 #end if]]></command>
94 <configfiles>
95 <inputs name="args_json" data_style="paths"/>
96 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
97 </configfiles>
98 <inputs>
99 <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)"/>
100 <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)"/>
101 <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)"/>
102 <param name="in_contaminants" argument="-in_contaminants" type="data" format="fasta" optional="true" label="Proteins considered contaminants" help=" select fasta data sets(s)"/>
103 <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)"/>
104 <section name="FragmentMassError" title="Fragment Mass Error settings" help="" expanded="false">
105 <param name="unit" argument="-FragmentMassError:unit" display="radio" type="select" optional="false" label="Unit for mass tolerance" help="'auto' uses information from FeatureXML">
106 <option value="auto" selected="true">auto</option>
107 <option value="ppm">ppm</option>
108 <option value="da">da</option>
109 <expand macro="list_string_san"/>
110 </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=""/>
112 </section>
113 <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=""/>
115 </section>
116 <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=""/>
118 <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"/>
120 </param>
121 </expand>
122 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
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>
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>
125 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
126 </param>
127 </inputs>
128 <outputs>
129 <data name="out" label="${tool.name} on ${on_string}: out" format="mztab"/>
130 <data name="out_cm" label="${tool.name} on ${on_string}: out_cm" format="consensusxml">
131 <filter>OPTIONAL_OUTPUTS is not None and "out_cm_FLAG" in OPTIONAL_OUTPUTS</filter>
132 </data>
133 <collection type="list" name="out_feat" label="${tool.name} on ${on_string}: out_feat">
134 <discover_datasets directory="out_feat" format="featurexml" pattern="__name__"/>
135 <filter>OPTIONAL_OUTPUTS is not None and "out_feat_FLAG" in OPTIONAL_OUTPUTS</filter>
136 </collection>
137 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
138 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
139 </data>
140 </outputs>
141 <tests>
142 <expand macro="autotest_QualityControl"/>
143 <expand macro="manutest_QualityControl"/>
144 </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.
146
147
148 For more information, visit http://www.openms.de/documentation/TOPP_QualityControl.html]]></help>
149 <expand macro="references"/>
150 </tool>