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comparison pdm_fdr.xml @ 0:6dfa920caa52 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pdm_fdr commit 53f3dc4ef4742606e24ab2b0e899b2dc56acac83
author galaxyp
date Fri, 27 Sep 2019 14:36:10 -0400
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children 5446df09e4ab
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-1:000000000000 0:6dfa920caa52
1 <tool id="pdm_fdr" name="PDM FDR" version="0.1.0">
2 <description>recalculate FDR fom precursor mass discrepancy</description>
3 <requirements>
4 <!--
5 <requirement type="package" version="3.2.1">R</requirement>
6 -->
7 <requirement type="package" version="1.4.0">r-stringr</requirement>
8 <requirement type="package" version="">r-runit</requirement>
9 </requirements>
10 <stdio>
11 <exit_code range="1:" />
12 </stdio>
13 <command><![CDATA[
14 Rscript '${__tool_directory__}/PMD_FDR_package_for_Galaxy.R'
15 --psm_report '$psm_report'
16 #if psm_report_1_percent:
17 --psm_report_1_percent '$psm_report_1_percent'
18 #end if
19 --input_file_type $input_file_type
20 --score_field_name "$score_field_name"
21 --output_g_fdr '$output_g_fdr'
22 --output_i_fdr '$output_i_fdr'
23 --output_densities '$output_densities'
24 ]]></command>
25 <inputs>
26 <param argument="--psm_report" type="data" format="tabular" label="PSM report"/>
27 <param argument="--psm_report_1_percent" type="data" format="tabular" label="PSM report at 1% FDR" optional="true"/>
28 <param argument="--input_file_type" type="select" label="PSM report">
29 <option value="PSM_Report" selected="true">PSM_Report</option>
30 <option value="PMD_FDR_input_file">PMD_FDR_input_file</option>
31 </param>
32 <param argument="--score_field_name" type="text" value="" label="PSM report">
33 <validator type="empty_field"/>
34 </param>
35 </inputs>
36 <outputs>
37 <data name="output_g_fdr" format="tabular" label="${tool.name} on ${on_string} output_g_fdr"/>
38 <data name="output_i_fdr" format="tabular" label="${tool.name} on ${on_string} output_i_fdr"/>
39 <data name="output_densities" format="tabular" label="${tool.name} on ${on_string} output_densities"/>
40 </outputs>
41 <tests>
42 <test>
43 <param name="psm_report" ftype="tabular" value="test_PSM_Report.tabular"/>
44 <param name="score_field_name" value="Confidence [%]"/>
45 <output name="output_g_fdr" file="output_g_fdr.tabular" />
46 <output name="output_i_fdr" file="output_i_fdr.tabular" />
47 <output name="output_densities" file="output_densities.tabular" />
48 </test>
49 </tests>
50 <help><![CDATA[
51 PMD_FDR_package_for_Galaxy.R
52
53 usage: PMD_FDR_package_for_Galaxy.R [--] [--help] [--opts OPTS] [--psm_report PSM_REPORT] [--psm_report_1_percent PSM_REPORT_1_PERCENT] [--output_i_fdr OUTPUT_I_FDR] [--output_g_fdr OUTPUT_G_FDR] [--output_densities OUTPUT_DENSITIES] [--score_field_name SCORE_FIELD_NAME] [--input_file_type INPUT_FILE_TYPE]
54
55 Computes individual and global FDR using Precursor Mass Discrepancy (PMD-FDR)
56
57
58 flags:
59 -h, --help show this help message and exit
60
61 optional arguments:
62 -x, --opts OPTS RDS file containing argument values
63 -p, --psm_report PSM_REPORT full name and path to the PSM report
64 --psm_report_1_percent PSM_REPORT_1_PERCENT full name and path to the PSM report for 1% FDR [default: ]
65 -o, --output_i_fdr OUTPUT_I_FDR full name and path to the i-FDR output file [default: ]
66 --output_g_fdr OUTPUT_G_FDR full name and path to the g-FDR output file [default: ]
67 --output_densities OUTPUT_DENSITIES full name and path to the densities output file [default: ]
68 -s, --score_field_name SCORE_FIELD_NAME name of score field (in R format) [default: ]
69 -i, --input_file_type INPUT_FILE_TYPE type of input file (currently supports: PSM_Report) [default: PMD_FDR_input_file]
70
71 ]]></help>
72 </tool>