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comparison pyprophet_score.xml @ 1:f4056f393ab6 draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pyprophet commit d1c34e31a93761cf7cfd4068bcdb70495d4d90bb"
author galaxyp
date Tue, 14 Apr 2020 12:01:27 +0000
parents e40681ad5b1b
children
comparison
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0:e40681ad5b1b 1:f4056f393ab6
1 <tool id="pyprophet_score" name="PyProphet score" version="@VERSION@.0"> 1 <tool id="pyprophet_score" name="PyProphet score" version="@VERSION@.2">
2 <description> 2 <description>
3 Error-rate estimation for MS1, MS2 and transition-level data 3 Error-rate estimation for MS1, MS2 and transition-level data
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
14 14
15 #if str($conditional_classifier.classifier)=='XGBoost': 15 #if str($conditional_classifier.classifier)=='XGBoost':
16 $conditional_classifier.xgb_autotune 16 $conditional_classifier.xgb_autotune
17 #end if 17 #end if
18 #if $apply_weights: 18 #if $apply_weights:
19 --apply_weights 19 --apply_weights='$apply_weights'
20 #end if 20 #end if
21 --xeval_fraction=$xeval_fraction 21 --xeval_fraction=$xeval_fraction
22 --xeval_num_iter=$xeval_num_iter 22 --xeval_num_iter=$xeval_num_iter
23 --level=$level 23 --level=$level
24 --ss_initial_fdr=$ss_initial_fdr 24 --ss_initial_fdr=$ss_initial_fdr
40 --lfdr_eps=$lfdr_eps 40 --lfdr_eps=$lfdr_eps
41 --ipf_max_peakgroup_rank=$ipf_max_peakgroup_rank 41 --ipf_max_peakgroup_rank=$ipf_max_peakgroup_rank
42 --ipf_max_peakgroup_pep=$ipf_max_peakgroup_pep 42 --ipf_max_peakgroup_pep=$ipf_max_peakgroup_pep
43 $tric_chromprob 43 $tric_chromprob
44 $test_mode 44 $test_mode
45 --threads "\${GALAXY_SLOTS:-4}"
45 --out='./output.osw' && mv *_report.pdf report.pdf 46 --out='./output.osw' && mv *_report.pdf report.pdf
46
47 47
48 ]]> 48 ]]>
49 </command> 49 </command>
50 <inputs> 50 <inputs>
51 <param name="input" type="data" format="osw" label="Input file" help="This file needs to be in OSW format (--in)" /> 51 <param name="input" type="data" format="osw" label="Input file" help="This file needs to be in OSW format (--in)" />
57 <when value="LDA"/> 57 <when value="LDA"/>
58 <when value="XGBoost"> 58 <when value="XGBoost">
59 <param name="xgb_autotune" type="boolean" truevalue="--xgb_autotune" falsevalue="--no-xgb_autotune" label="XGBoost: Autotune hyperparameters" help="(--xgb_autotune / --no-xgb_autotune)"/> 59 <param name="xgb_autotune" type="boolean" truevalue="--xgb_autotune" falsevalue="--no-xgb_autotune" label="XGBoost: Autotune hyperparameters" help="(--xgb_autotune / --no-xgb_autotune)"/>
60 </when> 60 </when>
61 </conditional> 61 </conditional>
62 <param argument="apply_weights" type="data" format="txt" optional="True" label="Apply PyProphet score weights file instead of semi-supervised learning." /> 62 <param argument="apply_weights" type="data" format="osw" optional="True" label="Apply PyProphet score weights file (osw format) instead of semi-supervised learning." />
63 <param argument="--level" type="select" display="radio" label="The data level selected for scoring. 'ms1ms2' integrates both MS1- and MS2-level scores and can be used instead of 'ms2'-level results" > 63 <param argument="--level" type="select" display="radio" label="The data level selected for scoring. 'ms1ms2' integrates both MS1- and MS2-level scores and can be used instead of 'ms2'-level results" >
64 <option value="ms1" >MS1</option> 64 <option value="ms1" >MS1</option>
65 <option value="ms2" >MS2</option> 65 <option value="ms2" >MS2</option>
66 <option value="ms1ms2" selected="True" >MS1MS2</option> 66 <option value="ms1ms2" selected="True" >MS1MS2</option>
67 <option value="transition">transition</option> 67 <option value="transition">transition</option>
83 <option value="smoother">smoother</option> 83 <option value="smoother">smoother</option>
84 </param> 84 </param>
85 <param argument="pi0_smooth_df" type="integer" value="3" label="Number of degrees-of-freedom to use when estimating pi_0 with a smoother" /> 85 <param argument="pi0_smooth_df" type="integer" value="3" label="Number of degrees-of-freedom to use when estimating pi_0 with a smoother" />
86 <param name="pi0_smooth_log" type="boolean" truevalue="--pi0_smooth_log_pi0" falsevalue="--no-pi0_smooth_log_pi0" label="If True and pi0_method = 'smoother', pi0 will be estimated by applying a smoother to a scatterplot of log(pi0) estimates against the tuning parameter lambda" help="(--pi0_smooth_log_pi0 / --no-pi0_smooth_log_pi0)"/> 86 <param name="pi0_smooth_log" type="boolean" truevalue="--pi0_smooth_log_pi0" falsevalue="--no-pi0_smooth_log_pi0" label="If True and pi0_method = 'smoother', pi0 will be estimated by applying a smoother to a scatterplot of log(pi0) estimates against the tuning parameter lambda" help="(--pi0_smooth_log_pi0 / --no-pi0_smooth_log_pi0)"/>
87 <param name="lfdr_truncate" type="boolean" checked="True" truevalue="--lfdr_truncate" falsevalue="--no-lfdr_truncate" label="If True, local FDR values >1 are set to 1" help="(--lfdr_truncate / --no-lfdr_truncate)"/> 87 <param name="lfdr_truncate" type="boolean" checked="True" truevalue="--lfdr_truncate" falsevalue="--no-lfdr_truncate" label="If True, local FDR values >1 are set to 1" help="(--lfdr_truncate / --no-lfdr_truncate)"/>
88 <param name="lfdr_monotone" type="boolean" checked="True" truevalue="--lfdr_monotone" falsevallUE="--no-lfdr_monotone" label="If True, local FDR values are non-decreasing with increasing p-values" help="(--lfdr_monotone / --no-lfdr_monotone)"/> 88 <param name="lfdr_monotone" type="boolean" checked="True" truevalue="--lfdr_monotone" falsevalue="--no-lfdr_monotone" label="If True, local FDR values are non-decreasing with increasing p-values" help="(--lfdr_monotone / --no-lfdr_monotone)"/>
89 <param argument="--lfdr_transformation" type="select" display="radio" label="Either a 'probit' or 'logit' transformation is applied to the p-values so that a local FDR estimate can be formed that does not involve edge effects of the [0,1] interval in which the p-values lie" > 89 <param argument="--lfdr_transformation" type="select" display="radio" label="Either a 'probit' or 'logit' transformation is applied to the p-values so that a local FDR estimate can be formed that does not involve edge effects of the [0,1] interval in which the p-values lie" >
90 <option value="probit" selected="True" >probit</option> 90 <option value="probit" selected="True" >probit</option>
91 <option value="logit">logit</option> 91 <option value="logit">logit</option>
92 </param> 92 </param>
93 <param argument="--lfdr_adj" type="float" value="1.5" label="Numeric value that is applied as a multiple of the smoothing bandwidth used in the density estimation" /> 93 <param argument="--lfdr_adj" type="float" value="1.5" label="Numeric value that is applied as a multiple of the smoothing bandwidth used in the density estimation" />
114 <param name="pi0_lambda_steps" value="0.01" /> 114 <param name="pi0_lambda_steps" value="0.01" />
115 <param name="test_mode" value="True" /> 115 <param name="test_mode" value="True" />
116 <output name="output" file="score.osw" compare="sim_size" /> 116 <output name="output" file="score.osw" compare="sim_size" />
117 <output name="score_report" file="score_report.pdf" compare="sim_size" /> 117 <output name="score_report" file="score_report.pdf" compare="sim_size" />
118 </test> 118 </test>
119 <test>
120 <param name="input" value="merged.osw" ftype="osw"/>
121 <param name="apply_weights" value="score.osw" ftype="osw"/>
122 <param name="level" value="ms2"/>
123 <param name="xeval_num_iter" value="2" />
124 <param name="ss_num_iter" value="2" />
125 <param name="pi0_lambda_start" value="0.1" />
126 <param name="pi0_lambda_end" value="0.3" />
127 <param name="pi0_lambda_steps" value="0.01" />
128 <param name="test_mode" value="True" />
129 <output name="output" file="score2.osw" compare="sim_size" />
130 <output name="score_report" file="score_report2.pdf" compare="sim_size" />
131 </test>
119 </tests> 132 </tests>
120 <help> 133 <help>
121 <![CDATA[ 134 <![CDATA[
122 **What it does** 135 **What it does**
123 136
131 144
132 ]]> 145 ]]>
133 </help> 146 </help>
134 <expand macro="citations"/> 147 <expand macro="citations"/>
135 </tool> 148 </tool>
149