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comparison IDMapper.xml @ 11:138a734e21a1 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 19:53:25 +0000
parents d29bb4c9831e
children 2517c03f5cd3
comparison
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10:8ddb7bab1138 11:138a734e21a1
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: [ID Processing]--> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <tool id="IDMapper" name="IDMapper" version="2.3.0"> 4 <tool id="IDMapper" name="IDMapper" version="@TOOL_VERSION@+galaxy@GALAXY_VERSION@" profile="20.05">
5 <description>Assigns protein/peptide identifications to features or consensus features.</description> 5 <description>Assigns protein/peptide identifications to features or consensus features.</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IDMapper</token> 7 <token name="@EXECUTABLE@">IDMapper</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 <import>macros_autotest.xml</import>
10 <import>macros_test.xml</import>
9 </macros> 11 </macros>
10 <expand macro="references"/> 12 <expand macro="requirements"/>
11 <expand macro="stdio"/> 13 <expand macro="stdio"/>
12 <expand macro="requirements"/> 14 <command detect_errors="exit_code"><![CDATA[@QUOTE_FOO@
13 <command detect_errors="aggressive"><![CDATA[IDMapper 15 @EXT_FOO@
16 #import re
14 17
15 #if $param_id: 18 ## Preprocessing
16 -id $param_id 19 mkdir id &&
20 ln -s '$id' 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)' &&
21 mkdir in &&
22 ln -s '$in' 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)' &&
23 mkdir out &&
24 #if $spectra._in:
25 mkdir spectra.in &&
26 ln -s '$spectra._in' 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)' &&
17 #end if 27 #end if
18 #if $param_in: 28
19 -in $param_in 29 ## Main program call
30
31 set -o pipefail &&
32 @EXECUTABLE@ -write_ctd ./ &&
33 python3 '$__tool_directory__/fill_ctd.py' '@EXECUTABLE@.ctd' '$args_json' '$hardcoded_json' &&
34 @EXECUTABLE@ -ini @EXECUTABLE@.ctd
35 -id
36 'id/${re.sub("[^\w\-_]", "_", $id.element_identifier)}.$gxy2omsext($id.ext)'
37 -in
38 'in/${re.sub("[^\w\-_]", "_", $in.element_identifier)}.$gxy2omsext($in.ext)'
39 -out
40 'out/output.${in.ext}'
41 #if $spectra._in:
42 -spectra:in
43 'spectra.in/${re.sub("[^\w\-_]", "_", $spectra._in.element_identifier)}.$gxy2omsext($spectra._in.ext)'
20 #end if 44 #end if
21 #if $param_out: 45
22 -out $param_out 46 ## Postprocessing
23 #end if 47 && mv 'out/output.${in.ext}' '$out'
24 #if $param_rt_tolerance: 48 #if "ctd_out_FLAG" in $OPTIONAL_OUTPUTS
25 -rt_tolerance $param_rt_tolerance 49 && mv '@EXECUTABLE@.ctd' '$ctd_out'
26 #end if 50 #end if]]></command>
27 #if $param_mz_tolerance: 51 <configfiles>
28 -mz_tolerance $param_mz_tolerance 52 <inputs name="args_json" data_style="paths"/>
29 #end if 53 <configfile name="hardcoded_json"><![CDATA[{"log": "log.txt", "threads": "\${GALAXY_SLOTS:-1}", "no_progress": true}]]></configfile>
30 #if $param_mz_measure: 54 </configfiles>
31 -mz_measure
32 #if " " in str($param_mz_measure):
33 "$param_mz_measure"
34 #else
35 $param_mz_measure
36 #end if
37 #end if
38 #if $param_mz_reference:
39 -mz_reference
40 #if " " in str($param_mz_reference):
41 "$param_mz_reference"
42 #else
43 $param_mz_reference
44 #end if
45 #end if
46 #if $param_ignore_charge:
47 -ignore_charge
48 #end if
49 #if $param_feature_use_centroid_rt:
50 -feature:use_centroid_rt
51 #end if
52 #if $param_feature_use_centroid_mz:
53 -feature:use_centroid_mz
54 #end if
55 #if $param_consensus_use_subelements:
56 -consensus:use_subelements
57 #end if
58 #if $param_spectra_in:
59 -spectra:in $param_spectra_in
60 #end if
61 #if $adv_opts.adv_opts_selector=='advanced':
62 #if $adv_opts.param_force:
63 -force
64 #end if
65 #if $adv_opts.param_consensus_annotate_ids_with_subelements:
66 -consensus:annotate_ids_with_subelements
67 #end if
68 #end if
69 ]]></command>
70 <inputs> 55 <inputs>
71 <param name="param_id" type="data" format="mzid,idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/> 56 <param name="id" argument="-id" type="data" format="idxml,mzid" optional="false" label="Protein/peptide identifications file" help=" select idxml,mzid data sets(s)"/>
72 <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/> 57 <param name="in" argument="-in" type="data" format="consensusxml,featurexml,mzq" optional="false" label="Feature map/consensus map file" help=" select consensusxml,featurexml,mzq data sets(s)"/>
73 <param name="param_rt_tolerance" type="float" min="0.0" optional="True" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="(-rt_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> 58 <param name="rt_tolerance" argument="-rt_tolerance" type="float" optional="true" min="0.0" value="5.0" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
74 <param name="param_mz_tolerance" type="float" min="0.0" optional="True" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="(-mz_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> 59 <param name="mz_tolerance" argument="-mz_tolerance" type="float" optional="true" min="0.0" value="20.0" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" help="Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/>
75 <param name="param_mz_measure" display="radio" type="select" optional="False" value="ppm" label="Unit of 'mz_tolerance'" help="(-mz_measure) "> 60 <param name="mz_measure" argument="-mz_measure" display="radio" type="select" optional="false" label="Unit of 'mz_tolerance'" help="">
76 <option value="ppm" selected="true">ppm</option> 61 <option value="ppm" selected="true">ppm</option>
77 <option value="Da">Da</option> 62 <option value="Da">Da</option>
63 <expand macro="list_string_san"/>
78 </param> 64 </param>
79 <param name="param_mz_reference" display="radio" type="select" optional="False" value="precursor" label="Source of m/z values for peptide identifications" help="(-mz_reference) If 'precursor', the precursor-m/z from the idXML is used. If 'peptide', &lt;br&gt;masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches. &lt;br&gt;('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)"> 65 <param name="mz_reference" argument="-mz_reference" display="radio" type="select" optional="false" label="Source of m/z values for peptide identifications" help="If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',. masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.. ('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)">
80 <option value="precursor" selected="true">precursor</option> 66 <option value="precursor">precursor</option>
81 <option value="peptide">peptide</option> 67 <option value="peptide" selected="true">peptide</option>
68 <expand macro="list_string_san"/>
82 </param> 69 </param>
83 <param name="param_ignore_charge" display="radio" type="boolean" truevalue="-ignore_charge" falsevalue="" checked="false" optional="True" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help="(-ignore_charge) "/> 70 <section name="feature" title="Additional options for featureXML input" help="" expanded="false">
84 <param name="param_feature_use_centroid_rt" display="radio" type="boolean" truevalue="-feature:use_centroid_rt" falsevalue="" checked="false" optional="True" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" help="(-use_centroid_rt) "/> 71 <param name="use_centroid_rt" argument="-feature:use_centroid_rt" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" help=""/>
85 <param name="param_feature_use_centroid_mz" display="radio" type="boolean" truevalue="-feature:use_centroid_mz" falsevalue="" checked="false" optional="True" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" help="(-use_centroid_mz) &lt;br&gt;(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/> 72 <param name="use_centroid_mz" argument="-feature:use_centroid_mz" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" help="(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/>
86 <param name="param_consensus_use_subelements" display="radio" type="boolean" truevalue="-consensus:use_subelements" falsevalue="" checked="false" optional="True" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" help="(-use_subelements) A consensus feature matches if any of its sub-features matches"/> 73 </section>
87 <param name="param_spectra_in" type="data" format="mzml" optional="True" label="MS run used to annotated unidentified spectra to features or consensus features" help="(-in) "/> 74 <section name="consensus" title="Additional options for consensusXML input" help="" expanded="false">
88 <expand macro="advanced_options"> 75 <param name="use_subelements" argument="-consensus:use_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" help="A consensus feature matches if any of its sub-features matches"/>
89 <param name="param_force" display="radio" type="boolean" truevalue="-force" falsevalue="" checked="false" optional="True" label="Overwrite tool specific checks" help="(-force) "/> 76 <param name="annotate_ids_with_subelements" argument="-consensus:annotate_ids_with_subelements" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Store the map index of the sub-feature in the peptide ID" help=""/>
90 <param name="param_consensus_annotate_ids_with_subelements" display="radio" type="boolean" truevalue="-consensus:annotate_ids_with_subelements" falsevalue="" checked="false" optional="True" label="Store the map index of the sub-feature in the peptide ID" help="(-annotate_ids_with_subelements) "/> 77 </section>
78 <section name="spectra" title="Additional options for mzML input" help="" expanded="false">
79 <param name="_in" argument="-spectra:_in" type="data" format="mzml" optional="true" label="MS run used to annotated unidentified spectra to features or consensus features" help=" select mzml data sets(s)"/>
80 </section>
81 <expand macro="adv_opts_macro">
82 <param name="ignore_charge" argument="-ignore_charge" type="boolean" truevalue="true" falsevalue="false" checked="false" label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" help=""/>
83 <param name="force" argument="-force" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Overwrite tool specific checks" help=""/>
84 <param name="test" argument="-test" type="hidden" optional="true" value="False" label="Enables the test mode (needed for internal use only)" help="">
85 <expand macro="list_string_san"/>
86 </param>
91 </expand> 87 </expand>
88 <param name="OPTIONAL_OUTPUTS" type="select" multiple="true" label="Optional outputs" optional="true">
89 <option value="ctd_out_FLAG">Output used ctd (ini) configuration file</option>
90 </param>
92 </inputs> 91 </inputs>
93 <outputs> 92 <outputs>
94 <data name="param_out" metadata_source="param_in" format_source="param_in" /> 93 <data name="out" label="${tool.name} on ${on_string}: out" format_source="in" metadata_source="in"/>
94 <data name="ctd_out" format="xml" label="${tool.name} on ${on_string}: ctd">
95 <filter>OPTIONAL_OUTPUTS is not None and "ctd_out_FLAG" in OPTIONAL_OUTPUTS</filter>
96 </data>
95 </outputs> 97 </outputs>
96 <help>Assigns protein/peptide identifications to features or consensus features. 98 <tests>
99 <expand macro="autotest_IDMapper"/>
100 <expand macro="manutest_IDMapper"/>
101 </tests>
102 <help><![CDATA[Assigns protein/peptide identifications to features or consensus features.
97 103
98 104
99 For more information, visit https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/2.3.0/html/TOPP_IDMapper.html</help> 105 For more information, visit http://www.openms.de/documentation/TOPP_IDMapper.html]]></help>
106 <expand macro="references"/>
100 </tool> 107 </tool>