Mercurial > repos > galaxyp > openms_masstraceextractor
comparison MassTraceExtractor.xml @ 1:cd7f683a669a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
| author | galaxyp |
|---|---|
| date | Wed, 09 Aug 2017 09:57:00 -0400 |
| parents | 2fdd110666cb |
| children | 074f89bd9ec9 |
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| 0:2fdd110666cb | 1:cd7f683a669a |
|---|---|
| 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 CTD2Galaxy.--> | 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: [Signal processing and preprocessing]--> | 3 <!--Proposed Tool Section: [Signal processing and preprocessing]--> |
| 4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.1.0"> | 4 <tool id="MassTraceExtractor" name="MassTraceExtractor" version="2.2.0"> |
| 5 <description>Detects mass traces in centroided LC-MS data.</description> | 5 <description>Detects mass traces in centroided LC-MS data.</description> |
| 6 <macros> | 6 <macros> |
| 7 <token name="@EXECUTABLE@">MassTraceExtractor</token> | 7 <token name="@EXECUTABLE@">MassTraceExtractor</token> |
| 8 <import>macros.xml</import> | 8 <import>macros.xml</import> |
| 9 </macros> | 9 </macros> |
| 37 #end if | 37 #end if |
| 38 #if $param_algorithm_mtd_mass_error_ppm: | 38 #if $param_algorithm_mtd_mass_error_ppm: |
| 39 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm | 39 -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm |
| 40 #end if | 40 #end if |
| 41 #if $param_algorithm_mtd_reestimate_mt_sd: | 41 #if $param_algorithm_mtd_reestimate_mt_sd: |
| 42 -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd | 42 -algorithm:mtd:reestimate_mt_sd |
| 43 #if " " in str($param_algorithm_mtd_reestimate_mt_sd): | |
| 44 "$param_algorithm_mtd_reestimate_mt_sd" | |
| 45 #else | |
| 46 $param_algorithm_mtd_reestimate_mt_sd | |
| 47 #end if | |
| 43 #end if | 48 #end if |
| 44 #if $param_algorithm_mtd_quant_method: | 49 #if $param_algorithm_mtd_quant_method: |
| 45 -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method | 50 -algorithm:mtd:quant_method |
| 51 #if " " in str($param_algorithm_mtd_quant_method): | |
| 52 "$param_algorithm_mtd_quant_method" | |
| 53 #else | |
| 54 $param_algorithm_mtd_quant_method | |
| 55 #end if | |
| 46 #end if | 56 #end if |
| 47 #if $param_algorithm_epd_width_filtering: | 57 #if $param_algorithm_epd_width_filtering: |
| 48 -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering | 58 -algorithm:epd:width_filtering |
| 59 #if " " in str($param_algorithm_epd_width_filtering): | |
| 60 "$param_algorithm_epd_width_filtering" | |
| 61 #else | |
| 62 $param_algorithm_epd_width_filtering | |
| 63 #end if | |
| 49 #end if | 64 #end if |
| 50 #if $param_algorithm_epd_enabled: | 65 #if $param_algorithm_epd_enabled: |
| 51 -algorithm:epd:enabled $param_algorithm_epd_enabled | 66 -algorithm:epd:enabled |
| 67 #if " " in str($param_algorithm_epd_enabled): | |
| 68 "$param_algorithm_epd_enabled" | |
| 69 #else | |
| 70 $param_algorithm_epd_enabled | |
| 71 #end if | |
| 52 #end if | 72 #end if |
| 53 #if $adv_opts.adv_opts_selector=='advanced': | 73 #if $adv_opts.adv_opts_selector=='advanced': |
| 54 #if $adv_opts.param_force: | 74 #if $adv_opts.param_force: |
| 55 -force | 75 -force |
| 56 #end if | 76 #end if |
| 57 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: | 77 #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: |
| 58 -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion | 78 -algorithm:mtd:trace_termination_criterion |
| 79 #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion): | |
| 80 "$adv_opts.param_algorithm_mtd_trace_termination_criterion" | |
| 81 #else | |
| 82 $adv_opts.param_algorithm_mtd_trace_termination_criterion | |
| 83 #end if | |
| 59 #end if | 84 #end if |
| 60 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers: | 85 #if $adv_opts.param_algorithm_mtd_trace_termination_outliers: |
| 61 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers | 86 -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers |
| 62 #end if | 87 #end if |
| 63 #if $adv_opts.param_algorithm_mtd_min_sample_rate: | 88 #if $adv_opts.param_algorithm_mtd_min_sample_rate: |