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annotate pmd_fdr.xml @ 0:16a4d32ff901 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 5e132b0b06fdc870f13604c42d3583e1f9adf103
author galaxyp
date Tue, 01 Oct 2019 08:43:11 -0400
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16a4d32ff901 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/pmd_fdr commit 5e132b0b06fdc870f13604c42d3583e1f9adf103
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1 <tool id="pmd_fdr" name="PMD FDR" version="0.1.0">
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2 <description>recalculate FDR fom precursor mass discrepancy</description>
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3 <requirements>
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4 <requirement type="package" version="">R</requirement>
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5 <requirement type="package" version="">r-stringr</requirement>
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6 <requirement type="package" version="">r-argparser</requirement>
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7 <requirement type="package" version="">r-codetools</requirement>
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8 <requirement type="package" version="">r-runit</requirement>
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9 </requirements>
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10 <stdio>
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11 <exit_code range="1:" />
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12 </stdio>
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13 <command><![CDATA[
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14 Rscript '${__tool_directory__}/PMD_FDR_package_for_Galaxy.R'
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15 --psm_report '$psm_report'
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16 #if $psm_report_1_percent:
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17 --psm_report_1_percent '$psm_report_1_percent'
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18 #end if
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19 --input_file_type $input_file_type
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20 --score_field_name "$score_field_name"
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21 --output_g_fdr '$output_g_fdr'
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22 --output_i_fdr '$output_i_fdr'
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23 --output_densities '$output_densities'
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24 ]]></command>
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25 <inputs>
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26 <param argument="--psm_report" type="data" format="tabular" label="PSM report"/>
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27 <param argument="--psm_report_1_percent" type="data" format="tabular" label="PSM report at 1% FDR" optional="true"/>
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28 <param argument="--input_file_type" type="select" label="PSM report">
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29 <option value="PSM_Report" selected="true">PSM_Report</option>
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30 <option value="PMD_FDR_input_file">PMD_FDR_input_file</option>
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31 </param>
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32 <param argument="--score_field_name" type="text" value="" label="PSM report">
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33 <validator type="empty_field"/>
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34 <sanitizer>
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35 <valid initial="string.printable">
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36 </valid>
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37 </sanitizer>
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38 </param>
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39 </inputs>
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40 <outputs>
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41 <data name="output_g_fdr" format="tabular" label="${tool.name} on ${on_string} output_g_fdr"/>
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42 <data name="output_i_fdr" format="tabular" label="${tool.name} on ${on_string} output_i_fdr"/>
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43 <data name="output_densities" format="tabular" label="${tool.name} on ${on_string} output_densities"/>
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44 </outputs>
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45 <tests>
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46 <test>
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47 <param name="psm_report" ftype="tabular" value="test_PSM_Report.tabular"/>
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48 <param name="score_field_name" value="Confidence [%]"/>
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49 <output name="output_g_fdr" file="output_g_fdr.tabular" />
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50 <output name="output_i_fdr" file="output_i_fdr.tabular" />
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51 <output name="output_densities" file="output_densities.tabular" />
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 PMD_FDR_package_for_Galaxy.R
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56
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57 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]
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58
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59 Computes individual and global FDR using Precursor Mass Discrepancy (PMD-FDR)
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60
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61
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62 flags:
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63 -h, --help show this help message and exit
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64
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65 optional arguments:
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66 -x, --opts OPTS RDS file containing argument values
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67 -p, --psm_report PSM_REPORT full name and path to the PSM report
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68 --psm_report_1_percent PSM_REPORT_1_PERCENT full name and path to the PSM report for 1% FDR [default: ]
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69 -o, --output_i_fdr OUTPUT_I_FDR full name and path to the i-FDR output file [default: ]
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70 --output_g_fdr OUTPUT_G_FDR full name and path to the g-FDR output file [default: ]
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71 --output_densities OUTPUT_DENSITIES full name and path to the densities output file [default: ]
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72 -s, --score_field_name SCORE_FIELD_NAME name of score field (in R format) [default: ]
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73 -i, --input_file_type INPUT_FILE_TYPE type of input file (currently supports: PSM_Report) [default: PMD_FDR_input_file]
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74
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75 ]]></help>
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76 </tool>