annotate fasta_cli.xml @ 55:bb0130ff73ce draft

"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
author galaxyp
date Fri, 15 Jan 2021 14:06:27 +0000
parents
children da885ca16cb2
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
55
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
1 <tool id="fasta_cli" name="FastaCLI" version="1.0.1">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
2 <description>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
3 Appends decoy sequences to FASTA files
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
4 </description>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
5 <macros>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
6 <import>macros_basic.xml</import>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
7 </macros>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
8 <requirements>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
9 <requirement type="package" version="@SEARCHGUI_VERSION@">searchgui</requirement>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
10 </requirements>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
11 <expand macro="stdio" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
12 <command>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
13 <![CDATA[
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
14 #set $temp_stderr = "fasta_cli_stderr"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
15 #set $output_db_name = $input_database.display_name.replace(".fasta", "") + $database_processing_options.decoy_file_tag.value + ".fasta"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
16
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
17 mkdir output &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
18 cwd=`pwd` &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
19
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
20 echo 'DB: ${input_database.display_name} sequences: ${input_database.metadata.sequences}' &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
21 cp '${input_database}' '${input_database.display_name}' &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
22
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
23 ###########################################
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
24 #### Creating decoy database ####
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
25 ###########################################
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
26
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
27 echo 'Creating decoy database.' &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
28 searchgui -Djava.awt.headless=true eu.isas.searchgui.cmd.FastaCLI --exec_dir="./bin/" -temp_folder `pwd` -in '${input_database.display_name}' -decoy -decoy_flag $database_processing_options.decoy_tag -suffix $database_processing_options.decoy_type -decoy_suffix $database_processing_options.decoy_file_tag 2>> $temp_stderr &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
29 mv '${output_db_name}' output &&
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
30 cat $temp_stderr 2>&1;
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
31 ]]>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
32 </command>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
33 <inputs>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
34 <param format="fasta" name="input_database" type="data" label="Protein Database"
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
35 help="Select FASTA database from history"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
36
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
37 <section name="database_processing_options" expanded="true" title="Database Processing Options">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
38
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
39 <param name="decoy_tag" type="text" value="-REVERSED" label="The decoy flag">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
40 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
41 <param name="decoy_type" type="select" label="Location of the decoy flag: prefix or suffix">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
42 <option value="1">Prefix</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
43 <option value="2" selected="True">Suffix</option>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
44 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
45
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
46 <param name="decoy_file_tag" type="text" value="_concatenated_target_decoy" label="Target decoy suffix">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
47 </param>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
48
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
49 </section>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
50 </inputs>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
51 <outputs>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
52 <data name="input_database_concatenated_target_decoy" format="fasta" label="${tool.name}: ${input_database.display_name} with decoys on ${on_string}">
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
53 <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" directory="output" visible="true" format="fasta" assign_primary_output="true" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
54 </data>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
55 </outputs>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
56 <tests>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
57 <test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
58 <param name="input_database" value="fastacli_searchgui_tinydb1.fasta" ftype="fasta"/>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
59 <output name="input_database_concatenated_target_decoy" file="fastacli_searchgui_tinydb1_concatenated_target_decoy.fasta" ftype="fasta" compare="sim_size" delta="1000" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
60 </test>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
61 </tests>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
62 <help>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
63 **What it does**
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
64
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
65 Appends decoy sequences to FASTA files. Default format is adequated to be used by SearchGUI and PeptideShaker tools, ie:
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
66
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
67 * Decoy flag: -REVERSED
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
68
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
69 * Location: suffix
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
70
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
71 * Target decoy suffix: _concatenated_target_decoy
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
72
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
73 </help>
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
74 <expand macro="citations" />
bb0130ff73ce "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit f27e376ff604cd8faf57c63f25ddcfd61ca9db6a"
galaxyp
parents:
diff changeset
75 </tool>