Mercurial > repos > galaxyp > openms_idmapper
comparison IDMapper.xml @ 0:026dbe52de09 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit fb85d488133bb2b5f483b52b2db0ac66038fafb8
| author | galaxyp |
|---|---|
| date | Wed, 01 Mar 2017 12:31:09 -0500 |
| parents | |
| children | 79186fbde4ea |
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| -1:000000000000 | 0:026dbe52de09 |
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| 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 CTD2Galaxy.--> | |
| 3 <!--Proposed Tool Section: [ID Processing]--> | |
| 4 <tool id="IDMapper" name="IDMapper" version="2.1.0"> | |
| 5 <description>Assigns protein/peptide identifications to features or consensus features.</description> | |
| 6 <macros> | |
| 7 <token name="@EXECUTABLE@">IDMapper</token> | |
| 8 <import>macros.xml</import> | |
| 9 </macros> | |
| 10 <expand macro="references"/> | |
| 11 <expand macro="stdio"/> | |
| 12 <expand macro="requirements"/> | |
| 13 <command>IDMapper | |
| 14 | |
| 15 #if $param_id: | |
| 16 -id $param_id | |
| 17 #end if | |
| 18 #if $param_in: | |
| 19 -in $param_in | |
| 20 #end if | |
| 21 #if $param_out: | |
| 22 -out $param_out | |
| 23 #end if | |
| 24 #if $param_rt_tolerance: | |
| 25 -rt_tolerance $param_rt_tolerance | |
| 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 $param_mz_measure | |
| 32 #end if | |
| 33 #if $param_mz_reference: | |
| 34 -mz_reference $param_mz_reference | |
| 35 #end if | |
| 36 #if $param_ignore_charge: | |
| 37 -ignore_charge | |
| 38 #end if | |
| 39 #if $param_feature_use_centroid_rt: | |
| 40 -feature:use_centroid_rt | |
| 41 #end if | |
| 42 #if $param_feature_use_centroid_mz: | |
| 43 -feature:use_centroid_mz | |
| 44 #end if | |
| 45 #if $param_consensus_use_subelements: | |
| 46 -consensus:use_subelements | |
| 47 #end if | |
| 48 #if $adv_opts.adv_opts_selector=='advanced': | |
| 49 #if $adv_opts.param_force: | |
| 50 -force | |
| 51 #end if | |
| 52 #if $adv_opts.param_consensus_annotate_ids_with_subelements: | |
| 53 -consensus:annotate_ids_with_subelements | |
| 54 #end if | |
| 55 #end if | |
| 56 </command> | |
| 57 <inputs> | |
| 58 <param name="param_id" type="data" format="mzid,idxml" optional="False" label="Protein/peptide identifications file" help="(-id) "/> | |
| 59 <param name="param_in" type="data" format="featurexml,consensusxml,mzq" optional="False" label="Feature map/consensus map file" help="(-in) "/> | |
| 60 <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) <br>Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> | |
| 61 <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) <br>Tolerance is understood as 'plus or minus x', so the matching range increases by twice the given value"/> | |
| 62 <param name="param_mz_measure" display="radio" type="select" optional="False" value="ppm" label="Unit of 'mz_tolerance'" help="(-mz_measure) "> | |
| 63 <option value="ppm" selected="true">ppm</option> | |
| 64 <option value="Da">Da</option> | |
| 65 </param> | |
| 66 <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', <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.)"> | |
| 67 <option value="precursor" selected="true">precursor</option> | |
| 68 <option value="peptide">peptide</option> | |
| 69 </param> | |
| 70 <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) "/> | |
| 71 <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) "/> | |
| 72 <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) <br>(If you choose 'peptide' as 'mz_reference', you should usually set this flag to avoid false-positive matches.)"/> | |
| 73 <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"/> | |
| 74 <expand macro="advanced_options"> | |
| 75 <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="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 </expand> | |
| 78 </inputs> | |
| 79 <outputs> | |
| 80 <data name="param_out" metadata_source="param_in" format="input"/> | |
| 81 </outputs> | |
| 82 <help>Assigns protein/peptide identifications to features or consensus features. | |
| 83 | |
| 84 | |
| 85 For more information, visit http://ftp.mi.fu-berlin.de/OpenMS/release-documentation/html/TOPP_IDMapper.html</help> | |
| 86 </tool> |