Mercurial > repos > galaxyp > peptideshaker

annotate fasta_cli.xml @ 54:f5236b38562c draft default tip

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit fc2810c412d9954fa584ae74497562b986c52764"
author galaxyp
date Thu, 12 Aug 2021 14:06:16 +0000
parents c506a7ccb856
children
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f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
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1 <tool id="fasta_cli"
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
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2 name="FastaCLI"
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c807a13df45f "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 0f6ab8b5647a33b2b051d7aa808ef42546436b23"
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3 version="@SEARCHGUI_VERSION@+galaxy@SEARCHGUI_VERSION_SUFFIX@"
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f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
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4 profile="20.01"
f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
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5 >
48
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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6 <description>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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7 Appends decoy sequences to FASTA files
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8 </description>
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9 <macros>
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10 <import>macros_basic.xml</import>
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11 </macros>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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12 <requirements>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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13 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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14 </requirements>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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15 <expand macro="stdio" />
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16 <command>
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17 <![CDATA[
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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18 #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta"
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b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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20 mkdir output &&
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21 cwd=`pwd` &&
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b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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23 echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}' &&
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24 cp '${input_database}' '${input_database.display_name}' &&
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b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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26 ###########################################
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27 #### Creating decoy database ####
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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28 ###########################################
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b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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30 echo 'Creating decoy database.' &&
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31 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
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32 --exec_dir="./bin/"
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33 -use_log_folder 0
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
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34 -temp_folder `pwd`
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
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35 -in '${input_database.display_name}'
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36 -decoy
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
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37 -decoy_flag $database_processing_options.decoy_tag
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
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38 -suffix $database_processing_options.decoy_type
c506a7ccb856 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 1cb321cbce2a6528764abc9c9431687f56c57588"
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39 -decoy_suffix $database_processing_options.decoy_file_tag &&
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f2f4695ad996 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 44a20633e04b2396fad4b568904a257769b2bbc1"
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40 mv '${output_db_name}' output
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41 ]]>
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42 </command>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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43 <inputs>
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44 <param format="fasta" name="input_database" type="data" label="Protein Database"
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45 help="Select FASTA database from history"/>
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47 <section name="database_processing_options" expanded="true" title="Database Processing Options">
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48
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49 <param name="decoy_tag" type="text" value="_REVERSED" label="The decoy flag">
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50 </param>
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51 <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">
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52 <option value="1">Prefix</option>
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53 <option value="2" selected="True">Suffix</option>
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54 </param>
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b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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56 <param name="decoy_file_tag" type="text" value="_concatenated_target_decoy" label="Target decoy suffix">
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57 </param>
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58
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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59 </section>
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60 </inputs>
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61 <outputs>
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62 <data name="input_database_concatenated_target_decoy" format="fasta" label="${tool.name}: ${input_database.display_name} with decoys on ${on_string}">
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63 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" directory="output" visible="true" format="fasta" assign_primary_output="true" />
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64 </data>
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65 </outputs>
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66 <tests>
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67 <test>
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68 <param name="input_database" value="fastacli_searchgui_tinydb1.fasta" ftype="fasta"/>
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69 <output name="input_database_concatenated_target_decoy" file="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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70 </test>
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71 </tests>
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72 <help>
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73 **What it does**
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74
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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75 Appends decoy sequences to FASTA files. Default format is adequated to be used by SearchGUI and PeptideShaker tools, ie:
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76
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77 * Decoy flag: _REVERSED
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78
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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79 * Location: suffix
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80
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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81 * Target decoy suffix: _concatenated_target_decoy
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82
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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83 </help>
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
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84 <expand macro="citations" />
b72821cab1d7 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
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85 </tool>