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comparison pmd_fdr.xml @ 0:5cc0c32d05a2 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
author galaxyp
date Mon, 07 Oct 2019 11:59:37 -0400
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children 460edeedeb7d
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-1:000000000000 0:5cc0c32d05a2
1 <tool id="pmd_fdr" name="PMD FDR" version="0.1.0">
2 <description>recalculate FDR fom precursor mass discrepancy</description>
3 <requirements>
4 <requirement type="package" version="3.5.1">r-base</requirement>
5 <requirement type="package" version="1.4.0">r-stringr</requirement>
6 <requirement type="package" version="0.4">r-argparser</requirement>
7 <requirement type="package" version="0.2-16">r-codetools</requirement>
8 <requirement type="package" version="0.4.32">r-runit</requirement>
9 </requirements>
10 <command detect_errors="exit_code"><![CDATA[
11 Rscript '${__tool_directory__}/PMD_FDR_package_for_Galaxy.R'
12 --psm_report '$psm_report'
13 #if $psm_report_1_percent:
14 --psm_report_1_percent '$psm_report_1_percent'
15 #end if
16 --input_file_type $input_file_type
17 --output_g_fdr '$output_g_fdr'
18 --output_i_fdr '$output_i_fdr'
19 --output_densities '$output_densities'
20 ]]></command>
21 <inputs>
22 <param argument="--psm_report" type="data" format="tabular" label="PSM report (Peptide Spectrum Match)"/>
23 <param argument="--psm_report_1_percent" type="data" format="tabular" label="PSM report at 1% FDR (Optional)" optional="true"/>
24 <param argument="--input_file_type" type="select" label="Input file type">
25 <option value="PSM_Report" selected="true">PeptideShaker PSM_Report</option>
26 <option value="PMD_FDR_input_file">PMD_FDR_input_file</option>
27 </param>
28 </inputs>
29 <outputs>
30 <data name="output_g_fdr" format="tabular" label="${tool.name} on ${on_string} output_g_fdr"/>
31 <data name="output_i_fdr" format="tabular" label="${tool.name} on ${on_string} output_i_fdr"/>
32 <data name="output_densities" format="tabular" label="${tool.name} on ${on_string} output_densities"/>
33 </outputs>
34 <tests>
35 <test>
36 <param name="psm_report" ftype="tabular" value="test_PSM_Report.tabular"/>
37 <output name="output_g_fdr" file="output_g_fdr.tabular" />
38 <output name="output_i_fdr" file="output_i_fdr.tabular" />
39 <output name="output_densities" file="output_densities.tabular" />
40 </test>
41 </tests>
42 <help><![CDATA[
43 Computes individual and global False Discovery Rate (FDR) using Precursor Mass Discrepancy (PMD) from a Peptide Spectrum Match (PSM) report.
44
45 The PSM report must be from PeptideShaker (--input_file_type PSM_Report),
46 or otherwise (--input_file_type PMD_FDR_input_file) have columns with header names:
47
48 - PMD_FDR_input_score
49 - PMD_FDR_pmd
50 - PMD_FDR_spectrum_file
51 - PMD_FDR_proteins
52 - PMD_FDR_spectrum_title
53 - PMD_FDR_sequence
54 - PMD_FDR_decoy
55
56
57 PMD_FDR_package_for_Galaxy.R
58
59 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]
60
61 arguments:
62 -p, --psm_report PSM_REPORT full name and path to the PSM report
63 --psm_report_1_percent PSM_REPORT_1_PERCENT full name and path to the PSM report for 1% FDR [default: ]
64 -i, --input_file_type INPUT_FILE_TYPE type of input file (currently supports: PSM_Report) [default: PMD_FDR_input_file]
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
69 ]]></help>
70 </tool>