Mercurial > repos > galaxyp > openms_idmassaccuracy

comparison IDMassAccuracy.xml @ 15:585f8235da7e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author galaxyp
date Thu, 01 Dec 2022 18:58:59 +0000
parents 31bc4129f589
children 0819fd9da302
comparison
equal deleted inserted replaced
14:b889cb83a9e1 15:585f8235da7e
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: [Utilities]--> 3 <!--Proposed Tool Section: [Utilities]-->
4 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05"> 4 <tool id="IDMassAccuracy" name="IDMassAccuracy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
5 <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description> 5 <description>Calculates a distribution of the mass error from given mass spectra and IDs.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDMassAccuracy</token> 7 <token name="@EXECUTABLE@">IDMassAccuracy</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 && 17 mkdir in_cond.in &&
20 ${ ' '.join(["ln -s '%s' 'in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _]) } 18 #if $in_cond.in_select == "no"
21 mkdir id_in && 19 mkdir ${' '.join(["'in_cond.in/%s'" % (i) for i, f in enumerate($in_cond.in) if f])} &&
22 ${ ' '.join(["ln -s '%s' 'id_in/%s.%s' &&" % (_, re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _]) } 20 ${' '.join(["ln -s '%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])}
21 #else
22 ln -s '$in_cond.in' 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)' &&
23 #end if
24 mkdir id_in_cond.id_in &&
25 #if $id_in_cond.id_in_select == "no"
26 mkdir ${' '.join(["'id_in_cond.id_in/%s'" % (i) for i, f in enumerate($id_in_cond.id_in) if f])} &&
27 ${' '.join(["ln -s '%s' 'id_in_cond.id_in/%s/%s.%s' && " % (f, i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
28 #else
29 ln -s '$id_in_cond.id_in' 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)' &&
30 #end if
23 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 31 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
24 mkdir out_precursor && 32 mkdir out_precursor &&
25 #end if 33 #end if
26 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 34 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
27 mkdir out_fragment && 35 mkdir out_fragment &&
38 set -o pipefail && 46 set -o pipefail &&
39 @EXECUTABLE@ -write_ctd ./ && 47 @EXECUTABLE@ -write_ctd ./ &&
40 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' && 48 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
41 @EXECUTABLE@ -ini @EXECUTABLE@.ctd 49 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
42 -in 50 -in
43 ${' '.join(["'in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $in if _])} 51 #if $in_cond.in_select == "no"
52 ${' '.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])}
53 #else
54 'in_cond.in/${re.sub("[^\w\-_]", "_", $in_cond.in.element_identifier)}.$gxy2omsext($in_cond.in.ext)'
55 #end if
44 -id_in 56 -id_in
45 ${' '.join(["'id_in/%s.%s'"%(re.sub('[^\w\-_]', '_', _.element_identifier), $gxy2omsext(_.ext)) for _ in $id_in if _])} 57 #if $id_in_cond.id_in_select == "no"
58 ${' '.join(["'id_in_cond.id_in/%s/%s.%s'"%(i, re.sub('[^\w\-_]', '_', f.element_identifier), $gxy2omsext(f.ext)) for i, f in enumerate($id_in_cond.id_in) if f])}
59 #else
60 'id_in_cond.id_in/${re.sub("[^\w\-_]", "_", $id_in_cond.id_in.element_identifier)}.$gxy2omsext($id_in_cond.id_in.ext)'
61 #end if
46 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 62 #if "out_precursor_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
47 -out_precursor 63 -out_precursor
48 'out_precursor/output.${gxy2omsext("tabular")}' 64 'out_precursor/output.${gxy2omsext("tabular")}'
49 #end if 65 #end if
50 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',') 66 #if "out_fragment_FLAG" in str($OPTIONAL_OUTPUTS).split(',')
82 <configfiles> 98 <configfiles>
83 <inputs name="args_json" data_style="paths"/> 99 <inputs name="args_json" data_style="paths"/>
84 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile> 100 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
85 </configfiles> 101 </configfiles>
86 <inputs> 102 <inputs>
87 <param name="in" argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/> 103 <conditional name="in_cond">
88 <param name="id_in" argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/> 104 <param name="in_select" type="select" label="Run tool in batch mode for -in">
89 <param name="precursor_error_ppm" argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/> 105 <option value="no">No: process all datasets jointly</option>
90 <param name="fragment_error_ppm" argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/> 106 <option value="yes">Yes: process each dataset in an independent job</option>
91 <param name="fragment_mass_tolerance" argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/> 107 </param>
108 <when value="no">
109 <param argument="-in" type="data" format="mzml" multiple="true" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
110 </when>
111 <when value="yes">
112 <param argument="-in" type="data" format="mzml" multiple="false" optional="false" label="Input mzML file list, containing the spectra" help=" select mzml data sets(s)"/>
113 </when>
114 </conditional>
115 <conditional name="id_in_cond">
116 <param name="id_in_select" type="select" label="Run tool in batch mode for -id_in">
117 <option value="no">No: process all datasets jointly</option>
118 <option value="yes">Yes: process each dataset in an independent job</option>
119 </param>
120 <when value="no">
121 <param argument="-id_in" type="data" format="idxml" multiple="true" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
122 </when>
123 <when value="yes">
124 <param argument="-id_in" type="data" format="idxml" multiple="false" optional="false" label="Input idXML file list, containing the identifications" help=" select idxml data sets(s)"/>
125 </when>
126 </conditional>
127 <param argument="-precursor_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the precursor mass tolerances are estimated in ppm instead of Da" help=""/>
128 <param argument="-fragment_error_ppm" type="boolean" truevalue="true" falsevalue="false" checked="false" label="If this flag is used, the fragment mass tolerances are estimated in ppm instead of Da" help=""/>
129 <param argument="-fragment_mass_tolerance" type="float" optional="true" value="0.5" label="Maximal fragment mass tolerance which is allowed for MS/MS spectra, used for the calculation of matching ions" help=""/>
92 <expand macro="adv_opts_macro"> 130 <expand macro="adv_opts_macro">
93 <param name="number_of_bins" argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/> 131 <param argument="-number_of_bins" type="integer" optional="true" min="10" value="100" label="Number of bins that should be used to calculate the histograms for the fitting" help=""/>
94 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/> 132 <param argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overrides tool-specific checks" help=""/>
95 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help=""> 133 <param argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
96 <expand macro="list_string_san"/> 134 <expand macro="list_string_san" name="test"/>
97 </param> 135 </param>
98 </expand> 136 </expand>
99 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs"> 137 <param name="OPTIONAL_OUTPUTS" type="select" optional="true" multiple="true" label="Optional outputs">
100 <option value="out_precursor_FLAG">out_precursor (Output file which contains the deviations from the precursors)</option> 138 <option value="out_precursor_FLAG">out_precursor (Output file which contains the deviations from the precursors)</option>
101 <option value="out_fragment_FLAG">out_fragment (Output file which contains the fragment ion m/z deviations)</option> 139 <option value="out_fragment_FLAG">out_fragment (Output file which contains the fragment ion m/z deviations)</option>
122 </data> 160 </data>
123 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd"> 161 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
124 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter> 162 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
125 </data> 163 </data>
126 </outputs> 164 </outputs>
127 <tests> 165 <tests><!-- TOPP_IDMassAccuracy_1 -->
128 <expand macro="autotest_IDMassAccuracy"/> 166 <test expect_num_outputs="5">
129 <expand macro="manutest_IDMassAccuracy"/> 167 <section name="adv_opts">
168 <param name="number_of_bins" value="10"/>
169 <param name="force" value="false"/>
170 <param name="test" value="true"/>
171 </section>
172 <conditional name="in_cond">
173 <param name="in" value="spectra.mzML"/>
174 </conditional>
175 <conditional name="id_in_cond">
176 <param name="id_in" value="MSGFPlusAdapter_1_out.idXML"/>
177 </conditional>
178 <output name="out_precursor" file="IDMassAccuracy_1_out_precursor.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
179 <param name="precursor_error_ppm" value="false"/>
180 <output name="out_fragment" file="IDMassAccuracy_1_out_fragment.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
181 <param name="fragment_error_ppm" value="false"/>
182 <param name="fragment_mass_tolerance" value="0.5"/>
183 <output name="out_precursor_fit" file="IDMassAccuracy_1_out_precursor_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
184 <output name="out_fragment_fit" file="IDMassAccuracy_1_out_fragment_fit.tsv" compare="sim_size" delta_frac="0.7" ftype="tabular"/>
185 <param name="OPTIONAL_OUTPUTS" value="ctd_out_FLAG,out_precursor_FLAG,out_fragment_FLAG,out_precursor_fit_FLAG,out_fragment_fit_FLAG"/>
186 <output name="ctd_out" ftype="xml">
187 <assert_contents>
188 <is_valid_xml/>
189 </assert_contents>
190 </output>
191 </test>
130 </tests> 192 </tests>
131 <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs. 193 <help><![CDATA[Calculates a distribution of the mass error from given mass spectra and IDs.
132 194
133 195
134 For more information, visit http://www.openms.de/doxygen/release/2.6.0/html/UTILS_IDMassAccuracy.html]]></help> 196 For more information, visit http://www.openms.de/doxygen/release/2.8.0/html/UTILS_IDMassAccuracy.html]]></help>
135 <expand macro="references"/> 197 <expand macro="references"/>
136 </tool> 198 </tool>