Mercurial > repos > bgruening > openms

comparison IDMapper.xml @ 4:6ead64a594bd draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/openms commit 7a5239910fda9ed90cca286a38855703b40b1b56-dirty
author bgruening
date Wed, 27 Jan 2016 10:06:49 -0500
parents 3d84209d3178
children
comparison
equal deleted inserted replaced
3:ec62782f6c68 4:6ead64a594bd
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version="1.0" encoding="UTF-8"?>
2 <tool id="IDMapper" name="IDMapper" version="1.12.0"> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <description>Assigns protein/peptide identifications to features or consensus features.</description> 3 <!--Proposed Tool Section: [ID Processing]-->
4 <macros> 4 <tool id="IDMapper" name="IDMapper" version="2.0.0">
5 <token name="@EXECUTABLE@">IDMapper</token> 5 <description>Assigns protein/peptide identifications to features or consensus features.</description>
6 <import>macros.xml</import> 6 <macros>
7 </macros> 7 <token name="@EXECUTABLE@">IDMapper</token>
8 <expand macro="stdio"/> 8 <import>macros.xml</import>
9 <expand macro="requirements"/> 9 </macros>
10 <command>IDMapper 10 <expand macro="references"/>
11 <expand macro="stdio"/>
12 <expand macro="requirements"/>
13 <command>IDMapper
11 14
12 -id ${param_id} 15 #if $param_id:
13 -in ${param_in} 16 -id $param_id
14 -out ${param_out} 17 #end if
15 -rt_tolerance ${param_rt_tolerance} 18 #if $param_in:
16 -mz_tolerance ${param_mz_tolerance} 19 -in $param_in
17 -mz_measure ${param_mz_measure} 20 #end if
18 -mz_reference ${param_mz_reference} 21 #if $param_out:
19 ${param_ignore_charge} 22 -out $param_out
20 -threads \${GALAXY_SLOTS:-24} 23 #end if
21 ${param_use_centroid_rt} 24 #if $param_rt_tolerance:
22 ${param_use_centroid_mz} 25 -rt_tolerance $param_rt_tolerance
23 ${param_use_subelements} 26 #end if
27 #if $param_mz_tolerance:
28 -mz_tolerance $param_mz_tolerance
29 #end if
30 #if $param_mz_measure:
31 -mz_measure
32 #if &quot; &quot; in str($param_mz_measure):
33 &quot;$param_mz_measure&quot;
34 #else
35 $param_mz_measure
36 #end if
37 #end if
38 #if $param_mz_reference:
39 -mz_reference
40 #if &quot; &quot; in str($param_mz_reference):
41 &quot;$param_mz_reference&quot;
42 #else
43 $param_mz_reference
44 #end if
45 #end if
46 #if $param_ignore_charge:
47 -ignore_charge
48 #end if
49 -threads \${GALAXY_SLOTS:-24}
50 #if $param_feature_use_centroid_rt:
51 -feature:use_centroid_rt
52 #end if
53 #if $param_feature_use_centroid_mz:
54 -feature:use_centroid_mz
55 #end if
56 #if $param_consensus_use_subelements:
57 -consensus:use_subelements
58 #end if
59 #if $adv_opts.adv_opts_selector=='advanced':
60 #if $adv_opts.param_force:
61 -force
62 #end if
63 #if $adv_opts.param_consensus_annotate_ids_with_subelements:
64 -consensus:annotate_ids_with_subelements
65 #end if
66 #end if
24 </command> 67 </command>
25 <inputs> 68 <inputs>
26 <param name="param_id" type="data" format="idXML" optional="False" label="Protein/peptide identifications file" help="(-id)"/> 69 <param format="xml,txt" help="(-id) " label="Protein/peptide identifications file" name="param_id" optional="False" type="data"/>
27 <param name="param_in" type="data" format="featureXML,consensusXML" optional="False" label="Feature map/consensus map file" help="(-in)"/> 70 <param format="xml,consensusxml,mzq" help="(-in) " label="Feature map/consensus map file" name="param_in" optional="False" type="data"/>
28 <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.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." help="(-rt_tolerance)"/> 71 <param help="(-rt_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value" label="RT tolerance (in seconds) for the matching of peptide identifications and (consensus) features" min="0.0" name="param_rt_tolerance" optional="True" type="float" value="5.0"/>
29 <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.#br#Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value." help="(-mz_tolerance)"/> 72 <param help="(-mz_tolerance) &lt;br&gt;Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value" label="m/z tolerance (in ppm or Da) for the matching of peptide identifications and (consensus) features" min="0.0" name="param_mz_tolerance" optional="True" type="float" value="20.0"/>
30 <param name="param_mz_measure" type="select" optional="True" value="ppm" label="Unit of 'mz_tolerance'." help="(-mz_measure)"> 73 <param help="(-mz_measure) " label="Unit of 'mz_tolerance'" name="param_mz_measure" optional="True" type="select" value="ppm">
31 <option value="ppm">ppm</option> 74 <option value="ppm">ppm</option>
32 <option value="Da">Da</option> 75 <option value="Da">Da</option>
33 </param> 76 </param>
34 <param name="param_mz_reference" type="select" optional="True" value="precursor" label="Source of m/z values for peptide identifications. If 'precursor', the precursor-m/z from the idXML is used. If 'peptide',#br#masses are computed from the sequences of peptide hits; in this case, an identification matches if any of its hits matches.#br#('peptide' should be used together with 'feature:use_centroid_mz' to avoid false-positive matches.)" help="(-mz_reference)"> 77 <param 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.)" label="Source of m/z values for peptide identifications" name="param_mz_reference" optional="True" type="select" value="precursor">
35 <option value="precursor">precursor</option> 78 <option value="precursor">precursor</option>
36 <option value="peptide">peptide</option> 79 <option value="peptide">peptide</option>
37 </param> 80 </param>
38 <param name="param_ignore_charge" type="boolean" truevalue="-ignore_charge true" falsevalue="-ignore_charge false" 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)"/> 81 <param checked="false" falsevalue="" help="(-ignore_charge) " label="For feature/consensus maps: Assign an ID independently of whether its charge state matches that of the (consensus) feature" name="param_ignore_charge" optional="True" truevalue="-ignore_charge" type="boolean"/>
39 <param name="param_use_centroid_rt" type="boolean" truevalue="-feature:use_centroid_rt true" falsevalue="-feature:use_centroid_rt false" 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)"/> 82 <param checked="false" falsevalue="" help="(-use_centroid_rt) " label="Use the RT coordinates of the feature centroids for matching, instead of the RT ranges of the features/mass traces" name="param_feature_use_centroid_rt" optional="True" truevalue="-feature:use_centroid_rt" type="boolean"/>
40 <param name="param_use_centroid_mz" type="boolean" truevalue="-feature:use_centroid_mz true" falsevalue="-feature:use_centroid_mz false" 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.#br#(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)" help="(-use_centroid_mz)"/> 83 <param checked="false" falsevalue="" 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.)" label="Use the m/z coordinates of the feature centroids for matching, instead of the m/z ranges of the features/mass traces" name="param_feature_use_centroid_mz" optional="True" truevalue="-feature:use_centroid_mz" type="boolean"/>
41 <param name="param_use_subelements" type="boolean" truevalue="-consensus:use_subelements true" falsevalue="-consensus:use_subelements false" checked="false" optional="True" label="Match using RT and m/z of sub-features instead of consensus RT and m/z. A consensus feature matches if any of its sub-features matches." help="(-use_subelements)"/> 84 <param checked="false" falsevalue="" help="(-use_subelements) A consensus feature matches if any of its sub-features matches" label="Match using RT and m/z of sub-features instead of consensus RT and m/z" name="param_consensus_use_subelements" optional="True" truevalue="-consensus:use_subelements" type="boolean"/>
42 </inputs> 85 <expand macro="advanced_options">
43 <outputs> 86 <param checked="false" falsevalue="" help="(-force) " label="Overwrite tool specific checks" name="param_force" optional="True" truevalue="-force" type="boolean"/>
44 <data name="param_out" label="Output file (the format depends on the input file format)." format="consensusXML"> 87 <param checked="false" falsevalue="" help="(-annotate_ids_with_subelements) " label="Store the map index of the sub-feature in the peptide ID" name="param_consensus_annotate_ids_with_subelements" optional="True" truevalue="-consensus:annotate_ids_with_subelements" type="boolean"/>
45 <change_format> 88 </expand>
46 <when input="param_out_type" value="featureXML" format="featureXML"/> 89 </inputs>
47 </change_format> 90 <outputs>
48 </data> 91 <data format="input" metadata_source="param_in" name="param_out"/>
49 </outputs> 92 </outputs>
50 <help>**What it does** 93 <help>Assigns protein/peptide identifications to features or consensus features.
51
52 Assigns protein/peptide identifications to features or consensus features.
53 94
54 95
55 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html 96 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html</help>
56 97 </tool>
57 @REFERENCES@
58 </help>
59 </tool>