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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pdm_fdr commit e5fc2c55b297c797ae744f04b42dded24d8523e6
author | galaxyp |
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date | Fri, 27 Sep 2019 15:14:16 -0400 |
parents | 6dfa920caa52 |
children | 2e5889f6ca44 |
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<tool id="pdm_fdr" name="PDM FDR" version="0.1.0"> <description>recalculate FDR fom precursor mass discrepancy</description> <requirements> <!-- <requirement type="package" version="3.2.1">R</requirement> --> <requirement type="package" version="1.4.0">r-stringr</requirement> <requirement type="package" version="">r-runit</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> <command><![CDATA[ Rscript '${__tool_directory__}/PMD_FDR_package_for_Galaxy.R' --psm_report '$psm_report' #if $psm_report_1_percent: --psm_report_1_percent '$psm_report_1_percent' #end if --input_file_type $input_file_type --score_field_name "$score_field_name" --output_g_fdr '$output_g_fdr' --output_i_fdr '$output_i_fdr' --output_densities '$output_densities' ]]></command> <inputs> <param argument="--psm_report" type="data" format="tabular" label="PSM report"/> <param argument="--psm_report_1_percent" type="data" format="tabular" label="PSM report at 1% FDR" optional="true"/> <param argument="--input_file_type" type="select" label="PSM report"> <option value="PSM_Report" selected="true">PSM_Report</option> <option value="PMD_FDR_input_file">PMD_FDR_input_file</option> </param> <param argument="--score_field_name" type="text" value="" label="PSM report"> <validator type="empty_field"/> </param> </inputs> <outputs> <data name="output_g_fdr" format="tabular" label="${tool.name} on ${on_string} output_g_fdr"/> <data name="output_i_fdr" format="tabular" label="${tool.name} on ${on_string} output_i_fdr"/> <data name="output_densities" format="tabular" label="${tool.name} on ${on_string} output_densities"/> </outputs> <tests> <test> <param name="psm_report" ftype="tabular" value="test_PSM_Report.tabular"/> <param name="score_field_name" value="Confidence [%]"/> <output name="output_g_fdr" file="output_g_fdr.tabular" /> <output name="output_i_fdr" file="output_i_fdr.tabular" /> <output name="output_densities" file="output_densities.tabular" /> </test> </tests> <help><![CDATA[ PMD_FDR_package_for_Galaxy.R 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] Computes individual and global FDR using Precursor Mass Discrepancy (PMD-FDR) flags: -h, --help show this help message and exit optional arguments: -x, --opts OPTS RDS file containing argument values -p, --psm_report PSM_REPORT full name and path to the PSM report --psm_report_1_percent PSM_REPORT_1_PERCENT full name and path to the PSM report for 1% FDR [default: ] -o, --output_i_fdr OUTPUT_I_FDR full name and path to the i-FDR output file [default: ] --output_g_fdr OUTPUT_G_FDR full name and path to the g-FDR output file [default: ] --output_densities OUTPUT_DENSITIES full name and path to the densities output file [default: ] -s, --score_field_name SCORE_FIELD_NAME name of score field (in R format) [default: ] -i, --input_file_type INPUT_FILE_TYPE type of input file (currently supports: PSM_Report) [default: PMD_FDR_input_file] ]]></help> </tool>