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annotate 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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5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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1 <tool id="pmd_fdr" name="PMD FDR" version="0.1.0">
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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2 <description>recalculate FDR fom precursor mass discrepancy</description>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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3 <requirements>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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4 <requirement type="package" version="3.5.1">r-base</requirement>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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5 <requirement type="package" version="1.4.0">r-stringr</requirement>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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6 <requirement type="package" version="0.4">r-argparser</requirement>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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7 <requirement type="package" version="0.2-16">r-codetools</requirement>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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8 <requirement type="package" version="0.4.32">r-runit</requirement>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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9 </requirements>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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10 <command detect_errors="exit_code"><![CDATA[
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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11 Rscript '${__tool_directory__}/PMD_FDR_package_for_Galaxy.R'
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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12 --psm_report '$psm_report'
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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13 #if $psm_report_1_percent:
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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14 --psm_report_1_percent '$psm_report_1_percent'
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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15 #end if
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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16 --input_file_type $input_file_type
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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17 --output_g_fdr '$output_g_fdr'
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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18 --output_i_fdr '$output_i_fdr'
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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19 --output_densities '$output_densities'
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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20 ]]></command>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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21 <inputs>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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22 <param argument="--psm_report" type="data" format="tabular" label="PSM report (Peptide Spectrum Match)"/>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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23 <param argument="--psm_report_1_percent" type="data" format="tabular" label="PSM report at 1% FDR (Optional)" optional="true"/>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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24 <param argument="--input_file_type" type="select" label="Input file type">
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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25 <option value="PSM_Report" selected="true">PeptideShaker PSM_Report</option>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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26 <option value="PMD_FDR_input_file">PMD_FDR_input_file</option>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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27 </param>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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28 </inputs>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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29 <outputs>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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30 <data name="output_g_fdr" format="tabular" label="${tool.name} on ${on_string} output_g_fdr"/>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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31 <data name="output_i_fdr" format="tabular" label="${tool.name} on ${on_string} output_i_fdr"/>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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32 <data name="output_densities" format="tabular" label="${tool.name} on ${on_string} output_densities"/>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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33 </outputs>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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34 <tests>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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35 <test>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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36 <param name="psm_report" ftype="tabular" value="test_PSM_Report.tabular"/>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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37 <output name="output_g_fdr" file="output_g_fdr.tabular" />
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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38 <output name="output_i_fdr" file="output_i_fdr.tabular" />
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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39 <output name="output_densities" file="output_densities.tabular" />
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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40 </test>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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41 </tests>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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42 <help><![CDATA[
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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43 Computes individual and global False Discovery Rate (FDR) using Precursor Mass Discrepancy (PMD) from a Peptide Spectrum Match (PSM) report.
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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44
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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45 The PSM report must be from PeptideShaker (--input_file_type PSM_Report),
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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46 or otherwise (--input_file_type PMD_FDR_input_file) have columns with header names:
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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47
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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48 - PMD_FDR_input_score
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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49 - PMD_FDR_pmd
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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50 - PMD_FDR_spectrum_file
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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51 - PMD_FDR_proteins
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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52 - PMD_FDR_spectrum_title
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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53 - PMD_FDR_sequence
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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54 - PMD_FDR_decoy
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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55
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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56
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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57 PMD_FDR_package_for_Galaxy.R
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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58
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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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]
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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60
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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61 arguments:
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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62 -p, --psm_report PSM_REPORT full name and path to the PSM report
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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63 --psm_report_1_percent PSM_REPORT_1_PERCENT full name and path to the PSM report for 1% FDR [default: ]
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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64 -i, --input_file_type INPUT_FILE_TYPE type of input file (currently supports: PSM_Report) [default: PMD_FDR_input_file]
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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65 -o, --output_i_fdr OUTPUT_I_FDR full name and path to the i-FDR output file [default: ]
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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66 --output_g_fdr OUTPUT_G_FDR full name and path to the g-FDR output file [default: ]
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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67 --output_densities OUTPUT_DENSITIES full name and path to the densities output file [default: ]
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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68
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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69 ]]></help>
5cc0c32d05a2 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 00f85eca73cd8afedfefbeec94a4462455ac1a9a"
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70 </tool>